The aim of this study was to explore the frequency and distribution of gene mutations that are related to isoniazid (INH) and rifampin (RIF)-resistance in the strains of the multidrug-resistant tuberculosis (MDR-TB) Mycobacterium tuberculosis (M.tb) in Beijing, China. In this retrospective study, the genotypes of 173 MDR-TB strains were analysed by spoligotyping. The katG, inhA genes and the promoter region of inhA, in which genetic mutations confer INH resistance; and the rpoB gene, in which genetic mutations confer RIF resistance, were sequenced. The percentage of resistance-associated nucleotide alterations among the strains of different genotypes was also analysed. In total, 90.8% (157/173) of the MDR strains belonged to the Beijing genotype. Population characteristics were not significantly different among the strains of different genotypes. In total, 50.3% (87/173) strains had mutations at codon S315T of katG; 16.8% (29/173) of strains had mutations in the inhA promoter region; of them, 5.5% (15/173) had point mutations at −15 base (C→T) of the inhA promoter region. In total, 86.7% (150/173) strains had mutations at rpoB gene; of them, 40% (69/173) strains had mutations at codon S531L of rpoB. The frequency of mutations was not significantly higher in Beijing genotypic MDR strains than in non-Beijing genotypes. Beijing genotypic MDR-TB strains were spreading in Beijing and present a major challenge to TB control in this region. A high prevalence of katG Ser315Thr, inhA promoter region (−15C→T) and rpoB (S531L) mutations was observed. Molecular diagnostics based on gene mutations was a useful method for rapid detection of MDR-TB in Beijing, China.

The prognostic factor for in-hospital mortality in tuberculosis (TB) patients requiring intensive care unit (ICU) care remains unclear. Therefore, a retrospective study was conducted aiming to estimate the in-hospital mortality rate and the risk factors for mortality in a high-burden setting. All patients with culture-confirmed TB that were admitted to the ICU of the hospital between March 2012 and April 2019 were identified retrospectively. Data, such as demographic characteristics, comorbidities, laboratory measures and mortality, were obtained from medical records. The Cox proportional hazards regression model was used to identify prognostic factors that influence in-hospital mortality. A total of 82 ICU patients with confirmed TB were included in the analysis, and 22 deaths were observed during the hospital stay, 21 patients died in the ICU. In the multivariable model adjusted for sex and age, the levels of serum albumin and white blood cell (WBC) count were significantly associated with mortality in TB patients requiring ICU care (all P < 0.01), the hazard ratios were 0.8 (95% confidence interval (CI): 0.7–0.9) per 1 g/l and 1.1 (95% CI: 1.0–1.2) per 1 × 109/l, respectively. In conclusion, in-hospital mortality remains high in TB patients requiring ICU care. Low serum albumin level and high WBC count significantly impact the risk of mortality in these TB patients in China.

This study applied causal criteria in directed acyclic graphs for handling covariates in associations for prognosis of severe coronavirus disease 2019 (COVID-19) cases. To identify non-specific blood tests and risk factors as predictors of hospitalisation due to COVID-19, one has to exclude noisy predictors by comparing the concordance statistics (area under the curve − AUC) for positive and negative cases of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Predictors with significant AUC at negative stratum should be either controlled for their confounders or eliminated (when confounders are unavailable). Models were classified according to the difference of AUC between strata. The framework was applied to an open database with 5644 patients from Hospital Israelita Albert Einstein in Brazil with SARS-CoV-2 reverse transcription – polymerase chain reaction (RT-PCR) exam. C-reactive protein (CRP) was a noisy predictor: hospitalisation could have happened due to causes other than COVID-19 even when SARS-CoV-2 RT-PCR is positive and CRP is reactive, as most cases are asymptomatic to mild. Candidates of characteristic response from moderate-to-severe inflammation of COVID-19 were: combinations of eosinophils, monocytes and neutrophils, with age as risk factor; and creatinine, as risk factor, sharpens the odds ratio of the model with monocytes, neutrophils and age.

The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is highly contagious, and the coronavirus disease 2019 (COVID-19) pandemic caused by it has forced many countries to adopt ‘lockdown’ measures to prevent the spread of the epidemic through social isolation of citizens. Some countries proposed universal mask wearing as a protection measure of public health to strengthen national prevention efforts and to limit the wider spread of the epidemic. In order to reveal the epidemic prevention efficacy of masks, this paper systematically evaluates the experimental studies of various masks and filter materials, summarises the general characteristics of the filtration efficiency of isolation masks with particle size, and reveals the actual efficacy of masks by combining the volume distribution characteristics of human exhaled droplets with different particle sizes and the SARS-CoV-2 virus load of nasopharynx and throat swabs from patients. The existing measured data show that the filtration efficiency of all kinds of masks for large particles and extra-large droplets is close to 100%. From the perspective of filtering the total number of pathogens discharged in the environment and protecting vulnerable individuals from breathing live viruses, the mask has a higher protective effect. If considering the weighted average filtration efficiency with different particle sizes, the filtration efficiencies of the N95 mask and the ordinary mask are 99.4% and 98.5%, respectively. The mask can avoid releasing active viruses to the environment from the source of infection, thus maximising the protection of vulnerable individuals by reducing the probability of inhaling a virus. Therefore, if the whole society strictly implements the policy of publicly wearing masks, the risk of large-scale spread of the epidemic can be greatly reduced. Compared with the overall cost of social isolation, limited personal freedoms and forced suspension of economic activities, the inconvenience for citizens caused by wearing masks is perfectly acceptable.

Hispanic/Latino populations are disproportionately impacted by coronavirus disease 2019 (COVID-19) in the United States. The impact of state reopening on COVID-19 in this population after stay-at-home orders is unknown. We evaluated the incidence, prevalence and trends during reopening of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) at a major federally qualified health centre in Providence, Rhode Island. A total of 14 505 patients were tested for SARS-CoV-2 from 19 March to 18 August 2020, of which, data on 13 318 (91.8%) patients were available; 70.0% were Hispanic/Latino, and 2905 were positive for SARS-CoV-2 infection. The urban Hispanic/Latino population was almost five times more likely to test positive for SARS-CoV-2 (risk ratio 4.97, 95% CI 2.59–9.53, P < 0.001) compared to non-Hispanic White. The positivity rates among the urban Hispanic/Latino population remained >10% during all phases of reopening. The trends of the incidence rates showed similar associations to those we observed for positivity rates. Public health interventions to address SARS-CoV-2 in Hispanic/Latino communities are urgently needed, even in latter phases of state reopening.

The prediction of prognosis is an important part of management in hepatitis B virus (HBV)-related decompensated cirrhosis patients with high long-term mortality. Lactate is a known predictor of outcome in critically ill patients. The aim of this study was to assess the prognostic value of lactate in HBV-related decompensated cirrhosis patients. We performed a single-centre, observational, retrospective study of 405 HBV-related decompensated cirrhosis patients. Individuals were evaluated within 24 h after admission and the primary outcome was evaluated at 6-months. Multivariable analyses were used to determine whether lactate was independently associated with the prognosis of HBV-related decompensated cirrhosis patients. The area under the ROC (AUROC) was calculated to assess the predictive accuracy compared with existing scores. Serum lactate level was significantly higher in non-surviving patients than in surviving patients. Multivariable analyses demonstrated that lactate was an independent risk factor of 6-months mortality (odds ratio: 2.076, P < 0.001). Receiver operating characteristic (ROC) curves were drawn to evaluate the discriminative ability of lactate for 6-months mortality (AUROC: 0.716, P < 0.001). Based on our patient cohort, the new scores (Model For End-Stage Liver Disease (MELD) + lactate score, Child–Pugh + lactate score) had good accuracy for predicting 6-months mortality (AUROC = 0.769, P < 0.001; AUROC = 0.766, P < 0.001). Additionally, the performance of the new scores was superior to those of existing scores (all P < 0.001). Serum lactate at admission may be useful for predicting 6-months mortality in HBV-related decompensated cirrhosis patients, and the predictive value of the MELD score and Child–Pugh score was improved by adjusting lactate. Serum lactate should be part of the rapid diagnosis and initiation of therapy to improve clinical outcome.

As the on-going severe acute respiratory syndrome coronavirus 2 pandemic, we aimed to understand whether economic reopening (EROP) significantly influenced coronavirus disease 2019 (COVID-19) incidence. COVID-19 data from Texas Health and Human Services between March and August 2020 were analysed. COVID-19 incidence rate (cases per 100 000 population) was compared to statewide for selected urban and rural counties. We used joinpoint regression analysis to identify changes in trends of COVID-19 incidence and interrupted time-series analyses for potential impact of state EROP orders on COVID-19 incidence. We found that the incidence rate increased to 145.1% (95% CI 8.4–454.5%) through 4th April, decreased by 15.5% (95% CI −24.4 −5.9%) between 5th April and 30th May, increased by 93.1% (95% CI 60.9–131.8%) between 31st May and 11th July and decreased by 13.2% (95% CI −22.2 −3.2%) after 12 July 2020. The study demonstrates the EROP policies significantly impacted trends in COVID-19 incidence rates and accounted for increases of 129.9 and 164.6 cases per 100 000 populations for the 24- or 17-week model, respectively, along with other county and state reopening ordinances. The incidence rate decreased sharply after 12th July considering the emphasis on a facemask or covering requirement in business and social settings.

The aim of this study was to explore the impact of polymorphism of PD-1 gene and its interaction with tea drinking on susceptibility to tuberculosis (TB). A total of 503 patients with TB and 494 controls were enrolled in this case–control study. Three single-nucleotide polymorphisms of PD-1 (rs7568402, rs2227982 and rs36084323) were genotyped and unconditional logistic regression analysis was used to identify the association between PD-1 polymorphism and TB, while marginal structural linear odds models were used to estimate the interactions. Genotypes GA (OR 1.434), AA (OR 1.891) and GA + AA (OR 1.493) at rs7568402 were more prevalent in the TB patients than in the controls (P < 0.05). The relative excess risk of interaction (RERI) between rs7568402 of PD-1 genes and tea drinking was −0.3856 (95% confidence interval −0.7920 to −0.0209, P < 0.05), which showed a negative interaction. However, the RERIs between tea drinking and both rs2227982 and rs36084323 of PD-1 genes were not statistically significant. Our data demonstrate that rs7568402 of PD-1 genes was associated with susceptibility to TB, and there was a significant negative interaction between rs7568402 and tea drinking. Therefore, preventive measures through promoting the consumption of tea should be emphasised in the high-risk populations.

New Zealand has a long-running campylobacter infection (campylobacteriosis) epidemic with contaminated fresh chicken meat as the major source. This is both the highest impact zoonosis and the largest food safety problem in the country. Adding to this burden is the recent rapid emergence of antibiotic resistance in these campylobacter infections acquired from locally-produced chicken. Campylobacteriosis rates halved in 2008, as compared with the previous 5 years, following the introduction of regulatory limits on allowable contamination levels in fresh chicken meat, with large health and economic benefits resulting. In the following decade, disease rates do not appear to have declined further. The cumulative impact would equate to an estimated 539 000 cases, 5480 hospitalisations, 284 deaths and economic costs of approximately US$380 million during the last 10 years (2009–2018). Additional regulatory interventions, that build on previously successful regulations in this country, are urgently needed to control the source of this epidemic.

This study was a retrospective multicentre cohort study of patients with coronavirus disease 2019 (COVID-19) diagnosed at 24 hospitals in Jiangsu province, China as of 15 March 2020. The primary outcome was the occurrence of acute respiratory failure during hospital stay. Of 625 patients, 56 (9%) had respiratory failure. Some selected demographic, epidemiologic, clinical and laboratory features as well as radiologic features at admission and treatment during hospitalisation were significantly different in patients with and without respiratory failure. The multivariate logistic analysis indicated that age (in years) (odds ratio [OR], 1.07; 95% confidence interval [CI]: 1.03–1.10; P = 0.0002), respiratory rate (breaths/minute) (OR, 1.23; 95% CI: 1.08–1.40; P = 0.0020), lymphocyte count (109/l) (OR, 0.18; 95% CI: 0.05–0.69; P = 0.0157) and pulmonary opacity score (per 5%) (OR, 1.38; 95% CI: 1.19–1.61; P < 0.0001) at admission were associated with the occurrence of respiratory failure. Older age, increased respiratory rate, decreased lymphocyte count and greater pulmonary opacity score at admission were independent risk factors of respiratory failure in patients with COVID-19. Patients having these risk factors need to be intensively managed during hospitalisation.

Bergamo province was badly hit by the coronavirus disease 2019 (COVID-19) epidemic. We organised a public-funded, multidisciplinary follow-up programme for COVID-19 patients discharged from the emergency department or from the inpatient wards of ‘Papa Giovanni XXIII’ Hospital, the largest public hospital in the area. As of 31 July, the first 767 patients had completed the first post-discharge multidisciplinary assessment. Patients entered our programme at a median time of 81 days after discharge. Among them, 51.4% still complained of symptoms, most commonly fatigue and exertional dyspnoea, and 30.5% were still experiencing post-traumatic psychological consequences. Impaired lung diffusion was found in 19%. Seventeen per cent had D-dimer values two times above the threshold for diagnosis of pulmonary embolism (two unexpected and clinically silent pulmonary thrombosis were discovered by investigating striking D-dimer elevation). Survivors of COVID-19 exhibit a complex array of symptoms, whose common underlying pathology, if any, has still to be elucidated: a multidisciplinary approach is fundamental, to address the different problems and to look for effective solutions.

This study proposed a novel ensemble analysis strategy to improve hand, foot and mouth disease (HFMD) prediction by integrating environmental data. The approach began by establishing a vector autoregressive model (VAR). Then, a dynamic Bayesian networks (DBN) model was used for variable selection of environmental factors. Finally, a VAR model with constraints (CVAR) was established for predicting the incidence of HFMD in Chengdu city from 2011 to 2017. DBN showed that temperature was related to HFMD at lags 1 and 2. Humidity, wind speed, sunshine, PM10, SO2 and NO2 were related to HFMD at lag 2. Compared with the autoregressive integrated moving average model with external variables (ARIMAX), the CVAR model had a higher coefficient of determination (R2, average difference: + 2.11%; t = 6.2051, P = 0.0003 < 0.05), a lower root mean-squared error (−24.88%; t = −5.2898, P = 0.0007 < 0.05) and a lower mean absolute percentage error (−16.69%; t = −4.3647, P = 0.0024 < 0.05). The accuracy of predicting the time-series shape was 88.16% for the CVAR model and 86.41% for ARIMAX. The CVAR model performed better in terms of variable selection, model interpretation and prediction. Therefore, it could be used by health authorities to identify potential HFMD outbreaks and develop disease control measures.

This paper describes the epidemiology of coronavirus disease 2019 (COVID-19) in Northern Ireland (NI) between 26 February 2020 and 26 April 2020, and analyses enhanced surveillance and contact tracing data collected between 26 February 2020 and 13 March 2020 to estimate secondary attack rates (SAR) and relative risk of infection among different categories of contacts of individuals with laboratory confirmed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection. Our results show that during the study period COVID-19 cumulative incidence and mortality was lower in NI than the rest of the UK. Incidence and mortality were also lower than in the Republic of Ireland (ROI), although these observed differences are difficult to interpret given considerable differences in testing and surveillance between the two nations. SAR among household contacts was 15.9% (95% CI 6.6%–30.1%), over 6 times higher than the SAR among ‘high-risk’ contacts at 2.5% (95% CI 0.9%–5.4%). The results from logistic regression analysis of testing data on contacts of laboratory-confirmed cases show that household contacts had 11.0 times higher odds (aOR: 11.0, 95% CI 1.7–70.03, P-value: 0.011) of testing positive for SARS-CoV-2 compared to other categories of contacts. These results demonstrate the importance of the household as a locus of SARS-CoV-2 transmission, and the urgency of identifying effective interventions to reduce household transmission.

Since December 2019, the clinical symptoms of coronavirus disease 2019 (COVID-19) and its complications are evolving. As the number of COVID patients requiring positive pressure ventilation is increasing, so is the incidence of subcutaneous emphysema (SE). We report 10 patients of COVID-19, with SE and pneumomediastinum. The mean age of the patients was 59 ± 8 years (range, 23–75). Majority of them were men (80%), and common symptoms were dyspnoea (100%), fever (80%) and cough (80%). None of them had any underlying lung disorder. All patients had acute respiratory distress syndrome on admission, with a median PaO2/FiO2 ratio of 122.5. Eight out of ten patients had spontaneous pneumomediastinum on their initial chest x-ray in the emergency department. The median duration of assisted ventilation before the development of SE was 5.5 days (interquartile range, 5–10 days). The highest positive end-expiratory pressure (PEEP) was 10 cmH2O for patients recieving invasive mechanical ventilation, while 8 cmH2O was the average PEEP in patients who had developed subcutaneous emphysema on non-invasive ventilation. All patients received corticosteroids while six also received tocilizumab, and seven received convalescent plasma therapy, respectively. Seven patients died during their hospital stay. All patients either survivor or non-survivor had prolonged hospital stay with an average of 14 days (range 8−25 days). Our findings suggest that it is lung damage secondary to inflammatory response due to COVID-19 triggered by the use of positive pressure ventilation which resulted in this complication. We conclude that the development of spontaneous pneumomediastinum and SE whenever present, is associated with poor outcome in critically ill COVID-19 ARDS patients.

One of the main concerns about the fast spreading coronavirus disease 2019 (Covid-19) pandemic is how to intervene. We analysed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) isolates data using the multifractal approach and found a rich in viral genome diversity, which could be one of the root causes of the fast Covid-19 pandemic and is strongly affected by pressure and health index of the hosts inhabited regions. The calculated mutation rate (mr) is observed to be maximum at a particular pressure, beyond which mr maintains diversity. Hurst exponent and fractal dimension are found to be optimal at a critical pressure (Pm), whereas, for P > Pm and P < Pm, we found rich genome diversity relating to complicated genome organisation and virulence of the virus. The values of these complexity measurement parameters are found to be increased linearly with health index values.

People living in urban slums or informal settlements are among the most vulnerable communities, highly susceptible to coronavirus disease 2019 (COVID-19) infection and vulnerable to the consequences of the measures taken to control the spread of the virus. Fear and stigma related to infection, mistrust between officials and the population, the often-asymptomatic nature of the disease is likely to lead to under-reporting. We conducted a cross-sectional study to determine the seroprevalence of COVID-19 infection in a large slum in South India 3 months after the index case and recruited 499 adults (age >18 years). The majority (74.3%) were females and about one-third of the population reported comorbidities. The overall seroprevalence of IgG antibody for COVID-19 was 57.9% (95% CI 53.4–62.3). Age, education, occupation and the presence of reported comorbidities were not associated with seroprevalence (P-value >0.05). Case-to-undetected-infections ratio was 1:195 and infection fatality rate was calculated as 2.94 per 10 000 infections. We estimated seroprevalence of COVID-19 was very high in our study population. The focus in this slum should shift from infection prevention to managing the indirect consequences of the pandemic. We recommend seroprevalence studies in such settings before vaccination to identify the vulnerability of COVID-19 infection to optimise the use of insufficient resources. It is a wake-up call to societies and nations, to dedicate paramount attention to slums into recovery and beyond – to build, restore and maintain health equity for the ‘Health and wellbeing of all’.

This systematic review and meta-analysis aimed to evaluate thrombocytopenia as a prognostic biomarker in patients with coronavirus disease 2019 (COVID-19). We performed a systematic literature search using PubMed, Embase and EuropePMC. The main outcome was composite poor outcome, a composite of mortality, severity, need for intensive care unit care and invasive mechanical ventilation. There were 8963 patients from 23 studies. Thrombocytopenia occurred in 18% of the patients. Male gender (P = 0.037) significantly reduce the incidence. Thrombocytopenia was associated with composite poor outcome (RR 1.90 (1.43–2.52), P < 0.001; I2: 92.3%). Subgroup analysis showed that thrombocytopenia was associated with mortality (RR 2.34 (1.23–4.45), P < 0.001; I2: 96.8%) and severity (RR 1.61 (1.33–1.96), P < 0.001; I2: 62.4%). Subgroup analysis for cut-off <100 × 109/l showed RR of 1.93 (1.37–2.72), P < 0.001; I2: 83.2%). Thrombocytopenia had a sensitivity of 0.26 (0.18–0.36), specificity of 0.89 (0.84–0.92), positive likelihood ratio of 2.3 (1.6–3.2), negative likelihood ratio of 0.83 (0.75–0.93), diagnostic odds ratio of 3 (2, 4) and area under curve of 0.70 (0.66–0.74) for composite poor outcome. Meta-regression analysis showed that the association between thrombocytopenia and poor outcome did not vary significantly with age, male, lymphocyte, d-dimer, hypertension, diabetes and CKD. Fagan's nomogram showed that the posterior probability of poor outcome was 50% in patients with thrombocytopenia, and 26% in those without thrombocytopenia. The Deek's funnel plot was relatively symmetrical and the quantitative asymmetry test was non-significant (P = 0.14). This study indicates that thrombocytopenia was associated with poor outcome in patients with COVID-19.

PROSPERO ID: CRD42020213974