Metagenomic Sequencing Analysis for Acne Using Machine Learning Methods Adapted to Single or Multiple Data.

The human health status can be assessed by the means of research and analysis of the human microbiome. Acne is a common skin disease whose morbidity increases year by year. The lipids which influence acne to a large extent are studied by metagenomic methods in recent years. In this paper, machine learning methods are used to analyze metagenomic sequencing data of acne, i.e., all kinds of lipids in the face skin. Firstly, lipids data of the diseased skin (DS) samples and the healthy skin (HS) samples of acne patients and the normal control (NC) samples of healthy person are, respectively, analyzed by using principal component analysis (PCA) and kernel principal component analysis (KPCA). Then, the lipids which have main influence on each kind of sample are obtained. In addition, a multiset canonical correlation analysis (MCCA) is utilized to get lipids which can differentiate the face skins of the above three samples. The experimental results show the machine learning methods can effectively analyze metagenomic sequencing data of acne. According to the results, lipids which only influence one of the three samples or the lipids which simultaneously have different degree of influence on these three samples can be used as indicators to judge skin statuses.

Evaluation of facial cleanliness and environmental improvement activities: Lessons learned from Malawi, Tanzania, and Uganda.

The World Health Organization promotes the SAFE (Surgery, Antibiotics, Facial cleanliness, and Environmental improvements) strategy for trachoma control and prevention. The F&E components of the strategy focus on promotion of healthy hygiene and sanitation behaviors. In order to monitor F&E activities implemented across villages and schools in Malawi, Tanzania, and Uganda, an F&E Monitoring and Evaluation (FEME) framework was developed to track quarterly program outputs and to provide the basis for a pre and post evaluation of the activities. Results showed an increase in knowledge at the school and household levels, and in some cases, an increase in presence of hand/face washing stations. However, this did not always result in a change in trachoma prevention behaviors such as facial cleanliness or keeping compounds free of human feces. The results highlight that the F&E programs were effective in increasing awareness of trachoma prevention but not able to translate that knowledge into changes in behavior during the time between pre and post-surveys. This study also indicates the potential to improve the data collection and survey design and notes that the period of intervention was not long enough to measure significant changes.

Connectivity dynamics in Irish mudflats between microorganisms including Vibrio spp., common cockles Cerastoderma edule, and shorebirds.

Shellfish, including the key species the common cockle Cerastoderma edule, living and feeding in waters contaminated by infectious agents can accumulate them within their tissues. It is unknown if microbial pathogens and microparasites can subsequently be transmitted via concomitant predation to their consumers, including shorebirds. The objective of this study was to assess if pathogens associated with C. edule could be detected seasonally in the faeces of shorebirds that feed on C. edule and in the physical environment (sediment) in which C. edule reside, along the Irish and Celtic Seas. Two potentially pathogenic global groups, Vibrio and Haplosporidia, were detected in C. edule. Although Haplosporidia were not detected in the bird faeces nor in the sediment, identical strains of Vibrio splendidus were detected in C. edule and bird faecal samples at sites where the oystercatcher Haematopus ostralegus and other waders were observed to be feeding on cockles. Vibrio spp. prevalence was seasonal and increased in C. edule and bird faecal samples during the warmer months, possibly due to higher seawater temperatures that promote the replication of this bacteria. The sediment samples showed an overall higher prevalence of Vibrio spp. than the bird faecal and C. edule samples, and its detection remained consistently high through the sites and throughout the seasons, which further supports the role of the sediment as a Vibrio reservoir. Our findings shed light on the fact that not all pathogen groups are transmitted from prey to predator via feeding but bacteria such as V. splendidus can be. As most of the wading birds observed in this study are migratory, the results also indicate the potential for this bacterium to be dispersed over greater geographic distances, which will have consequences for areas where it may be introduced.

Comparative analysis of human facial skin microbiome between topical sites compared to entire face.

BACKGROUND: Skin is an essential outer barrier and supports the growth of commensal microorganisms that protects a host from the offense of foreign toxic organisms. With the rapid development of next-generation sequencing (NGS)-based applications, skin microbiome research for facial health care has reached industry growth, such as therapy and cosmetic product development. Despite the acceleration of skin microbiome research, experimental standardization protocol has not yet been established in the facial site and method of sampling. OBJECTIVE: Thus, we aimed to investigate the differences in microbial composition at each facial site (cheek, mouth, forehead, and entire face) using comprehensive microbiome analysis. METHODS: Twelve specimens from three men (four specimens per one person) were collected. The hypervariable regions (V3-V4) of the bacterial 16S rRNA gene were targeted for 16S amplicon library construction and classification of bacterial taxonomy. Skin microbial composition for all specimens was investigated, and the differences site-by-site in skin microbial composition were analyzed and evaluated by the various statistical tests. RESULTS: We were able to validate the independent correlation between the skin microbiome composition and the facial sites. The cheek site showed the highest alpha-diversity in richness and evenness scores compared to the forehead and mouth. The cheek and mouth sites showed a positive correlation (R2 value > 0.93) with the entire face, while the forehead sites were negatively correlated (R2 value < 0.2). Given the relative abundance based on statistical correlation analysis, we estimated that the cheek site could be considered an optimal topical site to replace the entire face. CONCLUSION: Our study suggests that skin microbiome profiling of four facial sites confirms that the cheek shows the most similar skin flora with the entire face. This study would be informative for preventing bias caused by sampling methods before researching and understanding skin cosmetics development or skin diseases.

Effect of the skincare product on facial skin microbial structure and biophysical parameters: A pilot study.

Daily use of cosmetics is known to affect the skin microbiome. This study aimed to determine the bacterial community structure and skin biophysical parameters following the daily application of a skincare product on the face. Twenty-five Korean women, who used the same skincare product for four weeks participated in the study. During this period, skin hydration, texture, sebum content, and pH were measured, and skin swab samples were collected on the cheeks. The microbiota was analyzed using the MiSeq system. Through these experiments, bacterial diversity in facial skin increased and the microbial community changed after four weeks of skincare product application. The relative abundance of Cutibacterium and Staphylococcus increased, significant changes in specific bacterial modules of the skin microbial network were observed, and skin hydration and texture improved. It was suggested that daily use of skincare products could affect the microbial structure of facial skin as well as the biophysical properties of the facial skin. These findings expand our understanding of the role of skincare products on the skin environment.

Environmental factors and hygiene behaviors associated with facial cleanliness and trachoma in Kongwa, Tanzania.

BACKGROUND: Having a clean face is protective against trachoma. In the past, long distances to water were associated with unclean faces and increased trachoma. Other environmental factors have not been extensively explored. We need improved clarity on the environmental factors associated with facial cleanliness and trachoma prevalence, especially when the disease burden is low. METHODOLOGY/PRINCIPLE FINDINGS: A cross-sectional survey focusing on household environments was conducted in all 92 villages in Kongwa, Tanzania, in a random selection of 1798 households. Children aged 0-5 years in these households were examined for facial cleanliness. In each of the 50 randomly-selected villages, 50 children aged 1-9 years were randomly selected and examined for trachoma. In a multivariate model adjusting for child age, we found that children were more likely to have clean faces if the house had a clean yard (OR 1.62, 95% CI 1.37-1.91), an improved latrine (OR 1.11, 95% CI 1.01-1.22), and greater water storage capacity (OR 1.02, 95% CI 1.00-1.04), and if there were clothes washed and drying around the house (OR 1.30, 95% CI 1.09-1.54). However, measures of crowding, wealth, time spent on obtaining water, or the availability of piped water was not associated with clean faces. Using a cleanliness index (clean yard, improved latrine, washing clothes, ≥1 child in the household having a clean face), the community prevalence of trachoma decreased with an increase in the average value of the index (OR 2.28, 95% CI 1.17-4.80). CONCLUSIONS/SIGNIFICANCE: Access to water is no longer a significant limiting factor in children's facial cleanliness in Kongwa. Instead, water storage capacity and the way that water is utilized are more important in facial cleanliness. A household cleanliness index with a holistic measure of household environment is associated with reduced community prevalence of trachoma.

Development and comparative evaluation of droplet digital PCR and quantitative PCR for the detection and quantification of Chlamydia psittaci.

Chlamydia psittaci is a zoonotic pathogen mainly transmitted by psittacine birds and poultry. The low shedding rate of the pathogen in the apparently healthy birds and human clinical cases may result in false-negative results. In the present study, a droplet digital PCR (ddPCR) assay was developed and compared with optimized quantitative PCR (qPCR) for the detection of C. psittaci from the clinical samples. The ddPCR assay was found to be comparatively more sensitive than the qPCR, wherein the limit of detection (LOD) of ddPCR was upto 2.4 copies of the DNA template, whereas, the qPCR could detect upto 38 copies of the DNA template in the reaction mixture. Overall, the developed ddPCR assay was found to be robust, specific, and could reliably quantify up to 17.8 copies of the DNA template. Finally, the applicability of the developed ddPCR assay was tested by screening the field samples (n = 124), comprising lung tissues from dead poultry and feral birds; pooled faecal samples from the free-living birds, commercial and backyard poultry farms; pharyngeal and cloacal swabs collected from the duck farms. Of these, a total of seven samples were found to be positive by the ddPCR, whereas, three samples could be detected as positive using the qPCR. The developed ddPCR could serve as a reliable screening tool, particularly in those clinical samples wherein the shedding of C. psittaci is substantially very low.

Taxonomic profiling of skin microbiome and correlation with clinical skin parameters in healthy Koreans.

The interest in skin microbiome differences by ethnicity, age, and gender is increasing. Compared to other ethnic groups, studies on the skin microbiome of Koreans remains insufficient; we investigated facial skin microbiome characteristics according to gender and age among Koreans. Fifty-one healthy participants were recruited, the facial skin characteristics of each donor were investigated, their skin bacterial DNA was isolated and metagenomic analysis was performed. The donors were divided into two groups for age and sex each to analyze their skin microbiomes. Moreover, we investigated the correlation between the skin microbiome and clinical characteristics. The alpha diversity of the skin microbiome was significantly higher in the elderly, and beta diversity was significantly different according to age. The comparative skin microbials showed that the genus Lawsonella was more abundant in the younger age group, and Enhydrobacter was predominant in the older age group. Staphylococcus and Corynebacterium were more abundant in males, while Lactobacillus was more abundant in females. Lawsonella had a negative correlation with skin moisture and brown spots. Staphylococcus and Corynebacterium both had negative correlations with the number of UV spots and positive correlations with transepidermal water loss (TEWL). Furthermore, Staphylococcus aureus had a negative correlation with skin moisture parameters.

Rhinofacial conidiobolomycosis: Clinical and microbiological characterisation and shift in the management of a rare disease.

BACKGROUND: Conidiobolomycosis is a rare tropical rhinofacial fungal infection which has not been well characterised. The available evidence in its management is sparse due to lack of clinical studies and the limited data on antifungal susceptibility patterns. OBJECTIVE: To analyse the clinical manifestations, antifungal treatment and outcomes of patients with conidiobolomycosis and to determine antifungal susceptibility profiles of the isolates. PATIENTS/METHODS: Retrospective analysis of data of all patients with a diagnosis of conidiobolomycosis confirmed by histopathology and culture at a tertiary care hospital from 2012 to 2019 was done. RESULTS: There were 22 patients, 21 males and one female, with a mean age of 37.1 years. Most common presenting symptom was nasal obstruction, found in 20 (90.90%) patients. Patients who presented within 12 months had a better cure rate (85%) compared to those who presented late (67%). Among the 19 patients who had a follow-up, good outcome was seen in 15 of the 17 (88.24%) patients who were on itraconazole or potassium iodide containing regimen. Of the six patients who received additional trimethoprim-sulphamethoxazole (co-trimoxazole), 67% showed good outcome with two patients showing complete cure and two patients still on treatment with significant improvement. High minimum inhibitory concentration (MIC) values were noted for azoles and amphotericin B, whereas co-trimoxazole showed lowest MIC ranges. CONCLUSION: Itraconazole and potassium iodide are reasonable first-line options for the treatment of conidiobolomycosis. Good clinical response to KI and comparatively lower MIC of co-trimoxazole are promising. Further studies are required for developing clinical breakpoints that can predict therapeutic outcomes.

Temporal Variation of the Facial Skin Microbiome: A 2-Year Longitudinal Study in Healthy Adults.

BACKGROUND: The human skin microbiome is highly personalized, depending on, for example, body site, age, gender, and lifestyle factors. The temporal stability of an individual's skin microbiome-its resiliency and robustness over months and years-is also a personalized feature of the microbiome. The authors measured the temporal stability of the facial skin microbiome in a large cohort of subjects. In addition to measuring microbiome dynamics, they tracked facial skin condition using noninvasive, objective imaging and biophysical measures to identify significant facial features associated with temporal changes in microbiome diversity and composition. METHODS: The authors used 16S ribosomal RNA amplicon sequencing to track cheek and forehead skin microbiome diversity and composition annually over a 2-year period (2017-2019) in 115 healthy adult men and women. Skin metadata included facial features, such as wrinkles, hyperpigmentation, porphyrins, and skin color tone, as well as biophysical parameters for stratum corneum barrier function, pH, hydration, and elasticity. RESULTS: Across the subject population, the facial skin microbiome composition and diversity were relatively stable, showing minor variation over the 2-year period. However, for some subjects, composition, diversity, and relative abundance of specific organisms showed substantial changes from one year to the next, and these changes were associated with changes in stratum corneum barrier function and follicular porphyrins. CONCLUSIONS: For healthy people, facial skin microbiome diversity and composition are relatively stable from year to year. Tracking the temporal changes in the microbiome along with skin phenotypic changes allows for a deeper understanding of the skin microbiome's role in health and disease. These results should be helpful in the design of longer-term intervention trials with microbiome-based skin care treatments.

Diagnosis of Hyper IgM syndrome in a Previously Healthy Adolescent Boy Presented with Cutaneous and Cerebral Cryptococcosis.

X-linked hyper IgM (X-HIGM) syndrome is a combined immunodeficiency disease caused by mutations in the CD40LG gene, leading to a defect in immunoglobulin (Ig) class switching recombination and effector T-cell responses. X-HIGM patients usually present in early life with pyogenic bacterial and opportunistic infections. Herein, we report a previously healthy 13-year-old Thai boy who first presented with cutaneous and meningoencephalitis cryptococcosis. Whole-exome sequencing revealed that he was hemizygous for a missense c.514T>C (p.Tyr172His) in CD40LG, confirming a diagnosis of X-HIGM. This report demonstrates that X-HIGM could have an age of onset in teens and systemic cryptococcosis could be its presenting symptoms.

Facial cleanliness indicators by time of day: results of a cross-sectional trachoma prevalence survey in Senegal.

BACKGROUND: The World Health Organization-recommended strategy for trachoma elimination as a public health problem is known by the acronym "SAFE", where "F" stands for facial cleanliness to reduce transmission of ocular Chlamydia trachomatis infection. Accurately and reliably measuring facial cleanliness is problematic. Various indicators for measuring an unclean face exist, however, the accuracy and reliability of these indicators is questionable and their relationship to face washing practices is poorly described. METHODS: Clean face indicator (ocular or nasal discharge, flies on the face, and dirt on the face), trachoma clinical sign, and ocular C. trachomatis infection data were collected for 1613 children aged 0-9 years in 12 Senegalese villages as part of a cross-sectional trachoma prevalence study. Time of examination was recorded to the nearest half hour. A risk factor questionnaire containing Water, Sanitation and Hygiene (WASH) questions was administered to heads of compounds (households that shared a common doorway) and households (those who shared a common cooking pot). RESULTS: WASH access and use were high, with 1457/1613 (90.3%) children living in households with access to a primary water source within 30 min. Despite it being reported that 1610/1613 (99.8%) children had their face washed at awakening, > 75% (37/47) of children had at least one unclean face indicator at the first examination time-slot of the day. The proportion of children with facial cleanliness indicators differed depending on the time the child was examined. Dirt on the face was more common, and ocular discharge less common, in children examined after 11:00 h than in children examined at 10:30 h and 11:00 h. CONCLUSIONS: Given the high reported WASH access and use, the proportion of children with an unclean face indicator should have been low at the beginning of the day. This was not observed, explained either by: the facial indicators not being reliable measures of face washing; eye discharge, nose discharge or dirt rapidly re-accumulated after face washing in children in this population at the time of fieldwork; and/or responder bias to the risk factor questionnaire. A high proportion of children had unclean face indicators throughout the day, with certain indicators varying by time of day. A reliable, standardised, practical measure of face washing is needed, that reflects hygiene behaviour rather than environmental or cultural factors.

Relationship between the composition of the intestinal microbiota and the tracheal and intestinal colonization by opportunistic pathogens in intensive care patients.

OBJECTIVE: Infections caused by multidrug-resistant Gram-negative bacilli (MDR-GNB) are a major issue in intensive care. The intestinal and oropharyngeal microbiota being the reservoir of MDR-GNB. Our main objective was to assess the link between the composition of the intestinal microbiota and the tracheal and intestinal colonization by MDR-GNB, and also by Enterococcus spp. and yeasts. METHODS: We performed a 2-month prospective, monocentric cohort study in the medical intensive care unit of our hospital. Patients ventilated >3 days and spontaneously passing feces were included. A fecal sample and an endotracheal aspiration (EA) were collected twice a week. MDR-GNB but also Enterococcus faecium and yeasts (as potential dysbiosis surrogate markers) were detected by culture methods. The composition of the intestinal microbiota was assessed by 16S profiling. RESULTS: We collected 62 couples of feces and EA from 31 patients, including 18 feces and 9 EA positive for MDR-GNB. Forty-eight fecal samples were considered for 16S profiling. We did not observe a link between the diversity and the richness of the intestinal microbiota and the MDR-GNB intestinal relative abundance (RA). Conversely, we observed a negative link between the intestinal diversity and richness and the RA of Enterococcus spp. (p<0.001). CONCLUSION: The fecal MDR-GNB RA was not associated to the diversity nor the richness of the intestinal microbiota, but that of Enterococcus spp. was.

Frequency of face touching with and without a mask in pediatric hematology/oncology health care professionals.

The impact of wearing a mask on face-touching behavior is unknown. We conducted a survey of pediatric hematology/oncology staff to assess the perception of how masks would affect face-touching behavior and a brief observational study of providers during conferences in a children's hospital to quantify how masks affect face-touching behavior. Most felt that the mask would either increase (37.4%) or decrease (36.6%) their face-touching behavior. During a total of 330 person-minutes of observation, median face-touching rate was 5.4 face touches/hour (FT/h) while wearing a mask and 20 FT/h without a mask. Masks may reduce face-touching behavior amongst health care professionals.

Odontogenic cutaneous sinus tracts due to infection with nontuberculous mycobacteria: a report of three cases.

BACKGROUND: Soft tissue or skin infections due to nontuberculous mycobacteria (NTM) have been reported frequently and are mostly associated with trauma or cosmetic interventions like plastic surgery. However, infection with NTM as a result of a dental procedure have rarely been described and the lack of clinical suspicion and a clear clinical manifestation makes diagnosis challenging. CASE PRESENTATION: We report on three patients with a facial cutaneous sinus tract of dental origin, due to an infection with respectively Mycobacterium fortuitum, M. abscessus and M. peregrinum. The infection source was the dental unit waterlines (DUWLs), which were colonized with NTM. CONCLUSIONS: Water of the DUWL can pose a health risk. This report emphasizes the need for quality control and certification of water flowing through DUWLs, including the absence of NTM. Our report also shows the need for a rapid recognition of NTM infections and accurate laboratory diagnosis in order to avoid long-term ineffective antibiotic treatment.

Validation and uncertainty analysis of a stormwater biofilter treatment model for faecal microorganisms.

Stormwater biofilters, also known as rain gardens or bioretention systems, are effective stormwater treatment systems. This paper presents the validation, sensitivity and uncertainty analyses of a model for microbial removal in stormwater biofilters. The model, previously developed based on a rather limited laboratory study, was fully validated using the data collected in extensive laboratory experiments and field tests. The lab-scale and field-scale systems used for validation were of various designs (e.g., system size, plant type, media type), and have been operated under a wide range of operational conditions (e.g., length of antecedent dry period, and the inflow volume and concentration). For each tested biofilter design, the predicted E. coli concentrations in biofilters' outflow showed relatively good agreement with the measured ones: e.g., Nash-Sutcliffe Efficiency (Ec) ranged from 0.50 to 0.60 for the laboratory tests, and Ec = 0.55 for the field system. The results from sensitivity analysis confirmed the significance of adsorption and desorption processes, and also revealed the impact of temperature on microbial die-off (which was not fully represented in the model development stage). Finally, parameter transferability from one system to another with similar design was examined, achieving generally promising Ec values (0.04-0.56 with the best-fit parameter set for the other system; maximum value: 0.46-0.63) and acceptable uncertainties (intersection between prediction uncertainty band and observation: 50%-97%). Most importantly, the prediction of E. coli outflow concentrations from the field system was reasonably good when laboratory-determined parameter values were adopted: with the best-fit parameter set for the lab-scale system, Ec = 0.39; maximum Ec = 0.55; intersection between prediction and observation = 83%. These results suggested that the very rare biofilter model for microbial removal could provide reliable prediction for large scale field systems, by simply calibrating parameters with limited laboratory-scale experiments.