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Klebsiella pneumoniae is rapidly becoming untreatable using last-line antibiotics. It is especially problematic in hospitals, where it causes a range of acute infections. To approach controlling such a bacterium, we first must define what it is and how it varies genetically. Here we have determined the DNA sequence of K . pneumoniae isolates from around the world and present a detailed analysis of these data. We show that there is a wide spectrum of diversity, including variation within shared sequences and gain and loss of whole genes. Using this detailed blueprint, we show that there is an unrecognized association between the possession of specific gene profiles associated with virulence and antibiotic resistance and the differing disease outcomes seen for K . pneumoniae . Klebsiella pneumoniae is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. K . pneumoniae is ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure of K . pneumoniae , so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework for K . pneumoniae based on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting of K . pneumoniae into three distinct species, KpI ( K . pneumoniae ), KpII ( K . quasipneumoniae ), and KpIII ( K . variicola ). Further, for K . pneumoniae (KpI), the entity most frequently associated with human infection, we show the existence of >150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We show K . pneumoniae has a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasive K . pneumoniae infections; our data provide the whole-genome framework against which to track the emergence of such threats.

It is unclear why the severity of influenza varies in healthy adults or why the burden of severe influenza shifts to young adults when pandemic strains emerge. One possibility is that cross-protective T cell responses wane in this age group in the absence of recent infection. We therefore compared the acute cellular immune response in previously healthy adults with severe versus mild pandemic H1N1 infection. 49 previously healthy adults admitted to the National Hospital of Tropical Diseases, Viet Nam with RT-PCR-confirmed 2009 H1N1 infection were prospectively enrolled. 39 recovered quickly whereas 10 developed severe symptoms requiring supplemental oxygen and prolonged hospitalization. Peripheral blood lymphocyte subset counts and activation (HLADR, CD38) and differentiation (CD27, CD28) marker expression were determined on days 0, 2, 5, 10, 14 and 28 by flow cytometry. NK, CD4 and CD8 lymphopenia developed in 100%, 90% and 60% of severe cases versus 13% (p<0.001), 28%, (p = 0.001) and 18% (p = 0.014) of mild cases. CD4 and NK counts normalized following recovery. B cell counts were not significantly associated with severity. CD8 activation peaked 6-8 days after mild influenza onset, when 13% (6-22%) were HLADR+CD38+, and was accompanied by a significant loss of resting/CD27+CD28+ cells without accumulation of CD27+CD28- or CD27-CD28- cells. In severe influenza CD8 activation peaked more than 9 days post-onset, and/or was excessive (30-90% HLADR+CD38+) in association with accumulation of CD27+CD28- cells and maintenance of CD8 counts. Severe influenza is associated with transient T and NK cell deficiency. CD8 phenotype changes during mild influenza are consistent with a rapidly resolving memory response whereas in severe influenza activation is either delayed or excessive, and partially differentiated cells accumulate within blood indicating that recruitment of effector cells to the lung could be impaired.

Background Debuting sexual intercourse marks exposure to pregnancy or fatherhood and sexually transmitted infections (STIs), including HIV. In sub-Saharan Africa (SSA), sexual debut varies according to cultural, religious, and economic factors, and encouraging delay has been a longstanding component of behavioural HIV prevention strategies. Age at first sex (AFS) is routinely collected in national household surveys, but data are affected by reporting biases, limiting utility to monitor trends and guide sexual health interventions. Methods We collated individual-level data from nationally-representative household surveys to analyse timing and national trends in AFS in 42 SSA countries. We used a log-skew-logistic distribution to characterize the time to AFS in a Bayesian spatio-temporal model, providing estimates of the sexual debut rate by sex, age, time, and country. We statistically adjusted for reporting biases by comparing AFS reported by the same birth cohorts in multiple survey rounds, allowing different reporting biases by sex and country. Results Median AFS in 2015 ranged from 15.8 among Angolan women to 25.3 among men in Niger. AFS was younger for women than men in 37/40 countries. The gap was largest for Sahel region countries and minimal in southern African countries. The distribution of female AFS was asymmetric with half debuting sex in an age range of 3.9 years [IQR 3.4–5.0 across countries]. Median AFS increased slightly between 1985 and 2020, ranging 0.84 years [IQR 0.11–1.55] and 0.79 [IQR -0.23–1.98] for females and males, respectively. The gender gap changed little over time in most countries. Female teens often reported higher AFS compared to when asked in their late twenties while male teens reported lower AFS; both sexes recalled a higher AFS in older ages compared to their thirties. Conclusions AFS increased slightly in most SSA countries, but changes were modest relative to large and persistent variation between countries and sexes, indicating relatively entrenched socio-cultural practices around sexual debut. Sexual health, family planning, and HIV/STI prevention services should adapt to local practices rather than focusing interventions to change AFS. These estimates for rates of sexual debut provide data to guide programmatic prioritization and implementation of sexual health services.

Vietnam is an important producer of aquaculture products, and aquatic products are essential to the Vietnamese diet. However, Vietnam also has very little enforced regulation pertaining to antibiotic usage in domestic aquaculture, which raises concerns for antibiotic resistance in pathogenic bacteria. In this study, analysis was conducted on the presence of antibiotic residues in domestically sold fish and shrimp raised in freshwater farms in Vietnam, and an assessment of farmers’ knowledge of proper antibiotics usage was performed. The results indicated that a quarter of tested aquaculture products were antibiotic screening test positive, and there is a general lack of knowledge about the purpose and proper usage of antibiotics by aquaculture producers. Farmers’ decision-making processes about antimicrobial use are influenced by biased sources of information, such as drug manufacturers and sellers, and by financial incentives.

Tenofovir disoproxil fumarate (TDF) is still widely prescribed for human immunodeficiency virus (HIV)-infected pregnant women, despite its renal and bone toxicity. Although TDF-exposed infants often show transient growth impairment, it is not clear whether maternal TDF causes infantile rickets via maternal/fetal renal dysfunction in Asian populations. This prospective observational study was conducted in Vietnam and involved pregnant HIV-infected women treated with TDF-based regimen (TDF group) or zidovudine-based regimen (AZT-group). At birth, 3, 12, and 18 months of age, and included body length, weight, head circumference, serum alkaline phosphatase (ALP), creatinine, calcium, phosphorus, urine-β2-microglobulin (U-BMG), percentage of tubular reabsorption of phosphate (%TRP), and radiographic wrist score for rickets. Age-adjusted multivariate linear regression analysis evaluated the association of TDF/AZT use during pregnancy with fetal renal function and bone health. The study included 63 mother-infant pairs (TDF group = 53, AZT group = 10). In the mothers, detectable U-BMG (>252 μg/L) was observed more frequently in the TDF- than AZT group (89 vs 50%, p<0.001), but other renal/bone parameters were similar. In infants, maternal TDF use was not associated with growth impairment, renal dysfunction, or abnormal bone findings, but with a slightly higher ALP levels (p = 0.019). However, shorter length was associated with maternal AZT (p = 0.021), and worse radiographic scores were associated with LPV/r (p = 0.024). In Vietnamese population, TDF usage during pregnancy was not associated with infant transient rickets, growth impairment, or renal dysfunction, despite mild maternal tubular impairment. Maternal AZT and LPV/r influenced infant growth and bone health, though further studies are needed to confirm this finding.

Background. The hallmark of severe dengue is increased microvascular permeability, but alterations in the microcirculation and their evolution over the course of dengue are unknown. Methods. We conducted a prospective observational study to evaluate the sublingual microcirculation using side-stream darkfield imaging in patients presenting early (<72 hours after fever onset) and patients hospitalized with warning signs or severe dengue in Vietnam. Clinical findings, microvascular function, global hemodynamics assessed with echocardiography, and serological markers of endothelial activation were determined at 4 time points. Results. A total of 165 patients were enrolled. No difference was found between the microcirculatory parameters comparing dengue with other febrile illnesses. The proportion of perfused vessels (PPV) and the mean flow index (MFI) were lower in patients with dengue with plasma than those without leakage (PPV, 88.1% vs 90.6% [P= .01]; MFI, 2.1 vs 2.4 [P = .007]), most markedly during the critical phase. PPV and MFI were correlated with the endothelial activation markers vascular cell adhesion molecule 1 (P <.001 for both) and angiopoietin 2 (P < .001 for both), negatively correlated. Conclusions. Modest microcirculatory alterations occur in dengue, are associated with plasma leakage, and are correlate with molecules of endothelial activation, angiopoietin 2 and vascular cell adhesion molecule 1.

Background. Influenza A(H7N9) viruses isolated from humans show features suggesting partial adaptation to mammals. To provide insights into the pathogenesis of H7N9 virus infection, we compared risk factors, clinical presentation, and progression of patients hospitalized with H7N9, H5N1, and 2009 pandemic H1N1 (pH1N1) virus infections. Methods. We compared individual-level data from patients hospitalized with infection by H7N9 (n = 123), H5N1 (n = 119; 43 China, 76 Vietnam), and pH1N1 (n = 3486) viruses. We assessed risk factors for hospitalization after adjustment for age- and sex-specific prevalence of risk factors in the general Chinese population. Results. The median age of patients with H7N9 virus infection was older than other patient groups (63 years; P < .001) and a higher proportion was male (71%; P < .02). After adjustment for age and sex, chronic heart disease was associated with an increased risk of hospitalization with H7N9 (relative risk, 9.68; 95% confidence interval, 5.24–17.9). H7N9 patients had similar patterns of leukopenia, thrombocytopenia, and elevated alanine aminotransferase, creatinine kinase, C-reactive protein, and lactate dehydrogenase to those seen in H5N1 patients, which were all significantly different from pH1N1 patients (P < .005). H7N9 patients had a longer duration of hospitalization than either H5N1 or pH1N1 patients (P < .001), and the median time from onset to death was 18 days for H7N9 (P = .002) vs 11 days for H5N1 and 15 days for pH1N1 (P = .154). Conclusions. The identification of known risk factors for severe seasonal influenza and the more protracted clinical course compared with that of H5N1 suggests that host factors are an important contributor to H7N9 severity.

Background The pandemic and its preventive measures disrupted daily routines and posed unforeseen obstacles for families. Users of public online forums chronicled these challenges by freely expressing their sentiments in unrestricted text-length formats. We explored a German COVID-19 forum to understand family perspectives and experiences of pandemic measures, particularly in terms of testing and vaccinating children. Our findings aim to inform future epidemic health policies. Methods We retrieved all 11,207 entries from a COVID-19 forum during its lifespan (June 2020 - December 2021), posted during the height of the pandemic. We classified the entries into topic clusters including general pandemic situation, testing, or vaccination using state-of-the-art text embeddings and clustering algorithms. The clusters were selected based on the research’s aims and analysed qualitatively using a health policy triangle framework. Results Users generally appreciated pandemic public health safety measures for everyone’s protection, yet voiced concerns about inconsistent policies and disproportional disadvantages for children compared to other societal groups, like the elderly. Non-compliers were overwhelmingly regarded with skepticism and critiqued. Users found COVID-19 (exit) strategies and information about the benefits of vaccination unclear. This created hurdles for parents and caregivers in navigating their children’s school and social life. Users endorsed vaccinating children mainly for “normalising” children’s lives rather than for their physical health benefits. Some users suggested prioritising teachers and early childhood educators on the vaccination eligibility list to speed up a return to “normality”. Conclusions During pandemics, governments should prioritize addressing the societal and mental health needs of children by implementing participatory and family-oriented public health measures for schools and kindergartens. Clear communication coupled with consistent design and implementation of safety measures and regulations, would be crucial for building trust in the general population and for ensuring compliance regarding testing and vaccination. Communicating the benefits and risks of vaccinating children is of paramount importance  for informed decision-making among parents. In future epidemics, computer-aided analysis of large online qualitative data would offer valuable insights into public sentiments and concerns, enabling proactive and adaptive epidemic responses.

has many mechanisms of resistance to fluoroquinolones. The main mechanism is to change the effect of two enzymes that open the DNA helix - the enzyme DNA gyrase ( ) and the topoisomerase IV ( ). In addition, mutations that render the MexAB-oprM pump ( ) dysfunctional, leading to its overexpression, also enhance resistance to fluoroquinolones. In this study, we aim to detect point mutations of , , and genes that are predicted to be associated with fluoroquinolone resistance in 141 fluoroquinolone-resistant clinical isolates of isolated in Vietnam during 2013-2016. We tested minimum inhibitory concentrations (MICs) of fluoroquinolone antibiotics in 141 clinical isolates of using the VITEK 2 Compact System, followed by PCR assay, to detect and clone the fluoroquinolone resistance-determining region (FRDR) of , , and . Point mutations were analyzed through Sanger sequencing, and the correlation between genetic mutations and phenotypic resistance of 141 clinical isolates was undertaken. Fluoroquinolone-resistant substitution mutations such as Ile for Thr83 and Met for Thr133 in , Leu for Ser87 in , and Val for Glu126 in the repressor of were mainly detected. Comparative analytical data indicated that amino acid alterations within the and genes are highly associated with resistance to ciprofloxacin (CIP) and levofloxacin (LEV) in the isolates, whereas alterations in the efflux regulatory gene are not highly consistent with resistance in these isolates. Moreover, fluoroquinolone-resistant clinical isolates of were mainly isolated from pus and sputum specimens. In clinical isolates of , a high correlation was observed between MICs of CIP and LEV and alterations in and genes. However, mutations occurring in did not highly correlate with the antibiotic resistance of the bacterium.

Community acquired K. pneumoniae pneumonia is still common in Asia and is reportedly associated with alcohol use. Oropharyngeal carriage of K. pneumoniae could potentially play a role in the pathogenesis of K. pneumoniae pneumonia. However, little is known regarding K. pneumoniae oropharyngeal carriage rates and risk factors. This population-based cross-sectional study explores the association of a variety of demographic and socioeconomic factors, as well as alcohol consumption with oropharyngeal carriage of K. pneumoniae in Vietnam. 1029 subjects were selected randomly from age, sex, and urban and rural strata. An additional 613 adult men from a rural environment were recruited and analyzed separately to determine the effects of alcohol consumption. Demographic, socioeconomic, and oropharyngeal carriage data was acquired for each subject. The overall carriage rate of K. pneumoniae was 14.1% (145/1029, 95% CI 12.0%-16.2%). By stepwise logistic regression, K. pneumoniae carriage was found to be independently associated with age (OR 1.03, 95% CI 1.02-1.04), smoking (OR 1.9, 95% CI 1.3-2.9), rural living location (OR 1.6, 95% CI 1.1-2.4), and level of weekly alcohol consumption (OR 1.7, 95% CI 1.04-2.8). Moderate to heavy weekly alcohol consumption, old age, smoking, and living in a rural location are all found to be associated with an increased risk of K. pneumoniae carriage in Vietnamese communities. Whether K. pneumoniae carriage is a risk factor for pneumonia needs to be elucidated.