The lung microbiome, which is believed to be stable or at least transient in healthy people, is now considered as a poly-microorganism component contributing to disease pathogenesis. Most research studies on the respiratory microbiome have focused on bacteria and their impact on lung health, but there is evidence that other non-bacterial organisms, comprising the viruses (virome) and fungi (mycobiome), are also likely to play an important role in healthy people as well as in patients. In the last few years, the lung mycobiome (previously named the fungal microbiota or microbiome) has drawn closer attention. There is growing evidence that the lung mycobiome has a significant impact on clinical outcome of chronic respiratory diseases (CRD) such as asthma, chronic obstructive pulmonary disease, cystic fibrosis, and bronchiectasis. Thanks to advances in culture independent methods, especially next generation sequencing, a number of fungi not detected by culture methods have been molecularly identified in human lungs. It has been shown that the structure and diversity of the lung mycobiome vary in different populations (healthy and different diseased individuals) which could play a role in CRD. Moreover, the link between lung mycobiome and different biomes of other body sites, especially the gut, has also been unraveled. By interacting with the bacteriome and/or virome, the respiratory mycobiome appears to be a cofactor in inflammation and in the host immune response, and therefore may contribute to the decline of the lung function and the disease progression. In this review, we report the recent limited explorations of the human respiratory mycobiome, and discuss the mycobiome’s connections with other local microbial communities, as well as the relationships with the different biomes of other body sites. These studies suggest several outlooks for this understudied emerging field, which will certainly call for a renewal of our understanding of pulmonary diseases.

Introduction and PurposePropidium monoazide (PMA)-pretreatment has increasingly been applied to remove the bias from dead or damaged cell artefacts, which could impact the microbiota analysis by high-throughput sequencing. Our study aimed to determine whether a PMA-pretreatment coupled with high-throughput sequencing analysis provides a different picture of the airway mycobiome and bacteriome.Results and DiscussionWe compared deep-sequencing data of mycobiota and microbiota of 15 sputum samples from 5 cystic fibrosis (CF) patients with and without prior PMA-treatment of the DNA-extracts. PMA-pretreatment had no significant effect on the entire and abundant bacterial community (genera expressed as operational taxonomic units (OTUs) with a relative abundance greater than or equal to 1%), but caused a significant difference in the intermediate community (less than 1%) when analyzing the alpha biodiversity Simpson index (p = 0.03). Regarding PMA impact on the airway mycobiota evaluated for the first time here; no significant differences in alpha diversity indexes between PMA-treated and untreated samples were observed. Regarding beta diversity analysis, the intermediate communities also differed more dramatically than the total and abundant ones when studying both mycobiome and bacteriome. Our results showed that only the intermediate (or low abundance) population diversity is impacted by PMA-treatment, and therefore that abundant taxa are mostly viable during acute exacerbation in CF. Given such a cumbersome protocol (PMA-pretreatment coupled with high-throughput sequencing), we discuss its potential interest within the follow-up of CF patients. Further studies using PMA-pretreatment are warranted to improve our “omic” knowledge of the CF airways.

The first cases of human melioidosis were described in Vietnam in the 1920s, almost a century ago. It was in Vietnam in the thirties that the saprophytic nature of B. pseudomallei was first recognized. Although a significant number of French and U.S. soldiers acquired the disease during the Vietnam wars, indigenous cases in the Vietnamese population were only sporadically reported over many decades. After reunification in 1975, only two retrospective studies reported relatively small numbers of indigenous cases from single tertiary care hospitals located in the biggest cities in the South and the North, respectively. Studies from provincial hospitals throughout the country were missing until the Research Network on Melioidosis and Burkholderia pseudomallei (RENOMAB) project started in 2014. From then on seminars, workshops, and national scientific conferences on melioidosis have been conducted to raise awareness among physicians and clinical laboratory staff. This led to the recognition of a significant number of cases in at least 36 hospitals in 26 provinces and cities throughout Vietnam. Although a widespread distribution of melioidosis has now been documented, there are still challenges to understand the true epidemiology of the disease. Establishment of national guidelines for diagnosis, management, and reporting of the disease together with more investigations on animal melioidosis, genomic diversity of B. pseudomallei and its environmental distribution are required.

Objectives: Quang Nam province in the Centre of Vietnam has faced an outbreak of dengue hemorrhagic fever (DHF) in 2018. Although DHF is a recurrent disease in this area, no epidemiological and microbiological reports on dengue virus serotypes have been conducted mainly due to lack of facilities for such a kind of advanced surveillance. The aim of this study was to detect different dengue virus serotypes in patients’ blood samples. Design and Methods: Suspected cases living in Quang Nam province (Vietnam) and presenting clinical and hematological signs of dengue hemorrhagic fever were included in the study. The screening was performed, and the results were compared by using two methodologies: RT real-time PCR (RT-rPCR) and the Dengue NS1 rapid test. Results: From December 2018 to February 2019, looking both at RT-rPCR [+] and NS1 [+] methodologies, a total of 488 patients were screened and 336 were positive for dengue virus detection (74 children and 262 adults); 273 of these patients (81.3%) underwent viral serotype identification as follows: 12.82% (35/273) D1 serotype, 17.95% (49/273) D2, 0.37% (1/273) D3, 68.50 (187/283) D4, and 0.37% (1/273) D2+D4 serotypes. The RT-rPCR outcomes showed higher sensitivity during the first three days of infection compared to NS1 (92.3% vs. 89.7%). The NS1 increased sensitivity after the first 3 days whilst the RT-rPCR decreased. Conclusions: Advanced surveillance with dengue virus serotypes identification, if performed routinely, may help to predict and prevent further DHF epidemics based on the exposure of the different serotypes during different periods that lead to the intensification of disease severity as a consequence of antibody-dependent enhancement (ADE).

Background Human papillomavirus vaccine (HPV) impact on cervical precancer (cervical intraepithelial neoplasia grades 2+ [CIN2+]) is observable sooner than impact on cancer. Biopsy-confirmed CIN2+ is not included in most US cancer registries. Billing codes could provide surrogate metrics; however, the International Classification of Diseases, ninth (ICD-9) to tenth (ICD-10) transition disrupts trends. We built, validated, and compared claims-based models to identify CIN2+ events in both ICD eras. Methods A database of Davidson County (Nashville), Tennessee, pathology-confirmed CIN2+ from the HPV Vaccine Impact Monitoring Project (HPV-IMPACT) provided gold standard events. Using Tennessee Medicaid 2008-2017, cervical diagnostic procedures (N = 8549) among Davidson County women aged 18-39 years were randomly split into 60% training and 40% testing sets. Relevant diagnosis, procedure, and screening codes were used to build models from CIN2+ tissue diagnosis codes alone, least absolute shrinkage and selection operator (LASSO), and random forest. Model-classified index events were counted to estimate incident events. Results HPV-IMPACT identified 983 incident CIN2+ events. Models identified 1007 (LASSO), 1245 (CIN2+ tissue diagnosis codes alone), and 957 (random forest) incident events. LASSO performed well in ICD-9 and ICD-10 eras: 77.3% (95% confidence interval [CI] = 72.5% to 81.5%) vs 81.1% (95% CI = 71.5% to 88.6%) sensitivity, 93.0% (95% CI = 91.9% to 94.0%) vs 90.2% (95% CI = 87.2% to 92.7%) specificity, 61.3% (95% CI = 56.6% to 65.8%) vs 60.3% (95% CI = 51.0% to 69.1%) positive predictive value, 96.6% (95% CI = 95.8% to 97.3%) vs 96.3% (95% CI = 94.1% to 97.8%) negative predictive value, 91.0% (95% CI = 89.9% to 92.1%) vs 88.8% (95% CI = 85.9% to 91.2%) accuracy, and 85.1% (95% CI = 82.9% to 87.4%) vs 85.6% (95% CI = 81.4% to 89.9%) C-indices, respectively; performance did not statistically significantly differ between eras (95% confidence intervals all overlapped). Conclusions Results confirmed model utility with good performance across both ICD eras for CIN2+ surveillance. Validated claims-based models may be used in future CIN2+ trend analyses to estimate HPV vaccine impact where population-based biopsies are unavailable.

Although Blastocystis sp. is the most common enteric protozoan in human stools worldwide, various geographical areas remain to be investigated regarding the frequency and circulation of this parasite. Such is the case of some developing countries in Southeast Asia that exhibit a higher risk for parasitic infections due to unsanitary conditions. While several epidemiological surveys have been conducted, for instance, in Thailand, little or no data are available from neighboring countries, such as Vietnam. Therefore, in order to determine the prevalence and subtype (ST) distribution of Blastocystis sp. and to clarify the transmission of the parasite, the first molecular epidemiological survey ever conducted in this country was performed. For this purpose, a total of 310 stool specimens were collected from patients enrolled at the Family Hospital of Da Nang and then tested for the presence of Blastocystis sp. by real-time Polymerase Chain Reaction (qPCR), followed by subtyping of the isolates. The overall prevalence of the parasite reached 34.5% in this Vietnamese cohort. No significant association was found between parasite infection and gender, age, symptomatic status, contact with animals or source of drinking water. Out of the 107 positive patients, nearly half presented mixed infections. Therefore, some of the corresponding samples were reanalyzed by end-point PCR, followed by PCR products cloning and sequencing. Of the 88 total subtyped isolates, ST3 was predominant, followed by ST10, ST14, ST7, ST1, ST4, ST6 and ST8. Our study was, thus, the first to report ST8, ST10 and ST14 in the Southeast Asian population. The predominance of ST3 within this Vietnamese cohort, coupled with its low intra-ST genetic variability, reflected a large inter-human transmission, while ST1 transmission was suggested to be not only anthroponotic, but also likely correlated to animal or environmental sources. Strikingly, isolates considered of animal origin (ST6-ST8, ST10 and ST14) accounted for more than 50% of the subtyped isolates. These findings improved our knowledge of the epidemiology and circulation of Blastocystis sp. in Southeast Asia, and in particular, in Vietnam, and highlighted both a major burden of the parasite in this country and a high risk of zoonotic transmission, mainly from poultry and livestock.

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