After the 2003 SARS epidemic, China started constructing a primary-level emergency response system and focused on strengthening and implementation of policies, resource allocation. After 17 years of restructuring, China's primary-level response capabilities towards public health emergencies have greatly improved. During the coronavirus disease 2019 epidemic, primary-level administrative and medical personnel, social organisations, volunteers, etc. have played a significant role in providing professional services utilising the primary-level emergency response system of 17 years. However, China's organisations did not learn their lesson from the SARS epidemic, and certain problems are exposed in the system. By analysing the experience and shortcomings of China's disease prevention and control system at the primary level, we can focus on the development of disease control systems for major epidemics in the future.

Despite consistent public health efforts, the burden of viral disease in India remains high. The present study was undertaken to understand the aetiology, frequency and distribution of viral disease outbreaks in the state of Odisha between 2010 and 2019. This was a prospective study conducted at the Virology Research and Diagnostic Laboratory located at ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, wherein all the outbreaks of viral aetiologies were investigated and analysed to provide a comprehensive picture of the state of viral disease outbreaks in the region. A total of 191 suspected viral outbreaks were investigated by the team from VRDL during September 2010 and September 2019 reported from all the 30 districts of Odisha. Annual number of suspected cases ranged from 185 to 1002. The most commonly suspected outbreaks were of viral hepatitis (55 outbreaks; 1223 cases) followed by dengue (45 outbreaks; 1185 cases), chickenpox (30 outbreaks; 421 cases), viral encephalitis (27 outbreaks; 930 cases), measles (23 outbreaks; 464 cases), chikungunya (10 outbreaks; 593 cases) and rubella (1 outbreak; 60). The outbreaks peaked in frequency and intensity during the months of July and September. The epidemiology of viral disease outbreaks in the region is presented in the study. Health system preparedness based on evidence is essential for early detection and adequate response to such viral outbreaks.

Case fatality rate (CFR) and doubling time are important characteristics of any epidemic. For coronavirus disease 2019 (COVID-19), wide variations in the CFR and doubling time have been noted among various countries. Early in the epidemic, CFR calculations involving all patients as denominator do not account for the hospitalised patients who are ill and will die in the future. Hence, we calculated cumulative CFR (cCFR) using only patients whose final clinical outcomes were known at a certain time point. We also estimated the daily average doubling time. Calculating CFR using this method leads to temporal stability in the fatality rates, the cCFR stabilises at different values for different countries. The possible reasons for this are an improved outcome rate by the end of the epidemic and a wider testing strategy. The United States, France, Turkey and China had high cCFR at the start due to low outcome rate. By 22 April, Germany, China and South Korea had a low cCFR. China and South Korea controlled the epidemic and achieved high doubling times. The doubling time in Russia did not cross 10 days during the study period.

The emergence of 2019 novel coronavirus disease (COVID-19) is currently a global concern. In this study, our goal was to explore the changing expression levels of acute-phase reaction proteins (APRPs) in the serum of COVID-19 patients and to elucidate the immunological characteristics of COVID-19. In the study design, we recruited 72 COVID-19 patients, including 22 cases of mild degree, 38 cases of moderate degree and 12 cases of severe degree. We also recruited 20 patients with community-acquired pneumonia (CAP) and 20 normal control subjects as a comparison. Fasting venous blood was taken to detect the content of complement 3 (C3), complement 4 (C4), C-reactive protein (CRP), serum amyloid A (SAA) and prealbumin (PA). When compared the COVID-19 group with the CAP and normal control groups, respectively, the mean value of CRP and SAA in the COVID-19 group (including mild, moderate and severe patients) had increased significantly (P < 0.01), whereas the mean values of C3, C4 and PA decreased (P < 0.01). For the asymptomatic or mild symptomatic patients with COVID-19, the actual aggravation of disease may be more advanced than the clinical appearances. Meanwhile, the statistical analyses indicated that the development of COVID-19 brought about a significant increase in the content of CRP and SAA (P < 0.01), and a decline in the content of C3, C4 and PA (P < 0.01). These findings suggested that the changes in the level of APRPs could be used as indicators to identify the degree and progression of COVID-19, and the significant changes might demonstrate the aggravation of disease. This study provided a new approach to improve the clinical management plan and prognosis of COVID-19.

Pulsed-xenon-ultraviolet light (PX-UVL) is increasingly used as a supplemental disinfection method in healthcare settings. We undertook a systematic search of the literature through several databases and conducted a meta-analysis to evaluate the efficacy of PX-UVL in reducing healthcare-associated infections. Eleven studies were included in the systematic review and nine in the meta-analysis. Pooled analysis of seven studies with before-after data indicated a statistically significant reduction of Clostridium difficile infection (CDI) rates with the use of the PX-UVL (incidence rate ratio (IRR): 0.73, 95% CI 0.57–0.94, I2 = 72%, P = 0.01), and four studies reported a reduction of risk of methicillin-resistant Staphylococcus aureus (MRSA) infections (IRR: 0.79, 95% CI 0.64–0.98, I2 = 35%, P = 0.03). However, a further four trials found no significant reduction in vancomycin-resistant enterococci (VRE) infection rates (IRR: 0.80, 95% CI 0.63–1.01, I2 = 60%, P = 0.06). The results for CDI and MRSA proved unstable on sensitivity analysis. Meta-regression analysis did not demonstrate any influence of study duration or intervention duration on CDI rates. We conclude that the use of PX-UVL, in addition to standard disinfection protocols, may help to reduce the incidence of CDI and MRSA but not VRE infection rates. However, the quality of evidence is not high, with unstable results and wide confidence intervals, and further high-quality studies are required to supplement the current evidence.

Following the importation of coronavirus disease (COVID-19) into Nigeria on 27 February 2020 and then the outbreak, the question is: How do we anticipate the progression of the ongoing epidemic following all the intervention measures put in place? This kind of question is appropriate for public health responses and it will depend on the early estimates of the key epidemiological parameters of the virus in a defined population.

In this study, we combined a likelihood-based method using a Bayesian framework and compartmental model of the epidemic of COVID-19 in Nigeria to estimate the effective reproduction number (R(t)) and basic reproduction number (R0) – this also enables us to estimate the initial daily transmission rate (β0). We further estimate the reported fraction of symptomatic cases. The models are applied to the NCDC data on COVID-19 symptomatic and death cases from 27 February 2020 and 7 May 2020.

In this period, the effective reproduction number is estimated with a minimum value of 0.18 and a maximum value of 2.29. Most importantly, the R(t) is strictly greater than one from 13 April till 7 May 2020. The R0 is estimated to be 2.42 with credible interval: (2.37–2.47). Comparing this with the R(t) shows that control measures are working but not effective enough to keep R(t) below 1. Also, the estimated fraction of reported symptomatic cases is between 10 and 50%.

Our analysis has shown evidence that the existing control measures are not enough to end the epidemic and more stringent measures are needed.

The outbreak of novel coronavirus pneumonia (coronavirus disease 2019 (COVID-19)), declared as a ‘global pandemic’ by the World Health Organization (WHO), is a public health emergency of international concern (PHEIC). The outbreak in multiple locations shows a trend of accelerating spread around the world. China has taken a series of powerful measures to contain the spread of the novel coronavirus. In response to the COVID-19 pandemic, in addition to actively finding effective treatment drugs and developing vaccines, it is more important to identify the source of infection at the community level as soon as possible to block the transmission path of the virus to prevent the spread of the pandemic. The implementation of grid management in the community and the adoption of precise management and control measures to reduce unnecessary personnel movement can effectively reduce the risk of pandemic spread. This paper mainly describes that the grid management mode can promote the refinement and comprehensiveness of community management. As a management system with potential to improve the governance ability of community affairs, it may be helpful to strengthen the prevention and control of the epidemic in the community.

This study aimed to identify clinical features for prognosing mortality risk using machine-learning methods in patients with coronavirus disease 2019 (COVID-19). A retrospective study of the inpatients with COVID-19 admitted from 15 January to 15 March 2020 in Wuhan is reported. The data of symptoms, comorbidity, demographic, vital sign, CT scans results and laboratory test results on admission were collected. Machine-learning methods (Random Forest and XGboost) were used to rank clinical features for mortality risk. Multivariate logistic regression models were applied to identify clinical features with statistical significance. The predictors of mortality were lactate dehydrogenase (LDH), C-reactive protein (CRP) and age based on 500 bootstrapped samples. A multivariate logistic regression model was formed to predict mortality 292 in-sample patients with area under the receiver operating characteristics (AUROC) of 0.9521, which was better than CURB-65 (AUROC of 0.8501) and the machine-learning-based model (AUROC of 0.4530). An out-sample data set of 13 patients was further tested to show our model (AUROC of 0.6061) was also better than CURB-65 (AUROC of 0.4608) and the machine-learning-based model (AUROC of 0.2292). LDH, CRP and age can be used to identify severe patients with COVID-19 on hospital admission.

Trichosporon is a yeast-like basidiomycete, a conditional pathogenic fungus that is rare in the clinic but often causes fatal infections in immunocompromised individuals. Trichosporon asahii is the most common pathogenic fungus in this genus and the occurrence of infections has dramatically increased in recent years. Here, we report a systematic literature review detailing 140 cases of T. asahii infection reported during the past 23 years. Statistical analysis shows that T. asahii infections were most frequently reported within immunodeficient or immunocompromised patients commonly with blood diseases. Antibiotic use, invasive medical equipment and chemotherapy were the leading risk factors for acquiring infection. In vitro susceptibility, clinical information and prognosis analysis showed that voriconazole is the primary drug of choice in the treatment of T. asahii infection. Combination treatment with voriconazole and amphotericin B did not show superiority over either drug alone. Finally, we found that the types of infections prevalent in China are significantly different from those in other countries. These results provide detailed information and relevant clinical treatment strategies for the diagnosis and treatment of T. asahii infection.

To provide comprehensive information on the epidemiology and burden of respiratory syncytial virus hospitalisation (RSVH) in preterm infants, a pooled analysis was undertaken of seven multicentre, prospective, observational studies from across the Northern Hemisphere (2000–2014). Data from all 320–356 weeks' gestational age (wGA) infants without comorbidity were analysed. RSVH occurred in 534/14 504 (3.7%) infants; equating to a rate of 5.65 per 100 patient-seasons, with the rate in individual wGA groups dependent upon exposure time (P = 0.032). Most RSVHs (60.1%) occurred in December–January. Median age at RSVH was 88 days (interquartile range (IQR): 54–159). Respiratory support was required by 82.0% of infants: oxygen in 70.4% (median 4 (IQR: 2–6) days); non-invasive ventilation in 19.3% (median 3 (IQR: 2–5) days); and mechanical ventilation in 10.2% (median 5 (IQR: 3–7) days). Intensive care unit admission was required by 17.9% of infants (median 6 days (IQR: 2–8) days). Median overall hospital length of stay (LOS) was 5 (IQR: 3–8) days. Hospital resource use was similar across wGA groups except for overall LOS, which was shortest in those born 35 wGA (median 3 vs. 4–6 days for 32–34 wGA; P < 0.001). Strategies to reduce the burden of RSVH in otherwise healthy 32–35 wGA infants are indicated.

Catheter-related blood-stream infections (CRBSIs) are the most common healthcare-associated blood-stream infections. They can be diagnosed by either semi-quantitative or quantitative methods, which may differ in diagnostic accuracy. A meta-analysis was undertaken to compare the diagnostic accuracy of semi-quantitative and quantitative methods for CRBSI. A systematic search of Medline, Scopus, Cochrane and Embase databases up to January 2020 was performed and subjected to a QUADAS (quality assessment of diagnostic accuracy studies 2) tool to evaluate the risk of bias among studies. The pooled sensitivity and specificity of the methods were determined and heterogeneity was evaluated using the χ2 test and I2. Publication bias was assessed using a Funnel plot and the Egger's test. In total, 45 studies were analysed with data from 11 232 patients. The pooled sensitivity and specificity of semi-quantitative methods were 85% (95% CI 79–90%) and 84% (95% CI 79–88%), respectively; and for quantitative methods were 85% (95% CI 79–90%) and 95% (95% CI 91–97%). Considerable heterogeneity was statistically evident (P < 0.001) by both methods with a correspondingly symmetrical Funnel plot that was confirmed by a non-significant Deek's test. We conclude that both semi-quantitative and quantitative methods are highly useful for screening for CRBSI in patients and display high sensitivity and specificity. Quantitative methods, particularly paired quantitative cultures, had the highest sensitivity and specificity and can be used to identify CRBSI cases with a high degree of certainty.

Outbreaks of cyclosporiasis, a food-borne illness caused by the coccidian parasite Cyclospora cayetanensis have increased in the USA in recent years, with approximately 2300 laboratory-confirmed cases reported in 2018. Genotyping tools are needed to inform epidemiological investigations, yet genotyping Cyclospora has proven challenging due to its sexual reproductive cycle which produces complex infections characterized by high genetic heterogeneity. We used targeted amplicon deep sequencing and a recently described ensemble-based distance statistic that accommodates heterogeneous (mixed) genotypes and specimens with partial genotyping data, to genotype and cluster 648 C. cayetanensis samples submitted to CDC in 2018. The performance of the ensemble was assessed by comparing ensemble-identified genetic clusters to analogous clusters identified independently based on common food exposures. Using these epidemiologic clusters as a gold standard, the ensemble facilitated genetic clustering with 93.8% sensitivity and 99.7% specificity. Hence, we anticipate that this procedure will greatly complement epidemiologic investigations of cyclosporiasis.

The Biofire® Film Array Meningitis Encephalitis (FAME) panel can rapidly diagnose common aetiologies but its impact in Colombia is unknown. A retrospective study of adults with CNS infections in one tertiary hospital in Colombia. The cohort was divided into two time periods: before and after the implementation of the Biofire® FAME panel in May 2016. A total of 98 patients were enrolled, 52 and 46 were enrolled in the Standard of Care (SOC) group and in the FAME group, respectively. The most common comorbidity was human immunodeficiency virus infection (47.4%). The median time to a change in therapy was significantly shorter in the FAME group than in the SOC group (3 vs. 137.3 h, P < 0.001). This difference was driven by the timing to appropriate therapy (2.1 vs. 195 h, P < 0.001) by identifying viral aetiologies. Overall outcomes and length of stay were no different between both groups (P > 0.2). The FAME panel detected six aetiologies that had negative cultures but missed identifying one patient with Cryptococcus neoformans. The introduction of the Biofire FAME panel in Colombia has facilitated the identification of viral pathogens and has significantly reduced the time to the adjustment of empirical antimicrobial therapy.

Coronavirus disease 2019 (COVID-19) is a global health threat. A hospital in Zhuhai adopted several measures in Fever Clinic Management (FCM) to respond to the outbreak of COVID-19. FCM has been proved to be effective in preventing nosocomial cross infection. Faced with the emergency, the hospital undertook creative operational steps in relation to the control and spread of COVID-19, with special focuses on physical and administrative layout of buildings, staff training and preventative procedures. The first operational step was to set up triaging stations at all entrances and then complete a standard and qualified fever clinic, which was isolated from the other buildings within our hospital complex. Secondly, the hospital established its human resource reservation for emergency response and the allocation of human resources to ensure strict and standardised training methods through the hospital for all medical staff and ancillary employees. Thirdly, the hospital divided the fever clinic into partitioned areas and adapted a three-level triaging system. The experiences shared in this paper would be of practical help for the facilities that are encountering or will encounter the challenges of COVID-19, i.e. to prevent nosocomial cross infection among patients and physicians.

Our study aimed to systematically analyse the risk factors of coronavirus disease 2019 (COVID-19) patients with severe disease. An electronic search in eight databases to identify studies describing severe or critically ill COVID-19 patients from 1 January 2020 to 3 April 2020. In the end, we meta-analysed 40 studies involving 5872 COVID-19 patients. The average age was higher in severe COVID-19 patients (weighted mean difference; WMD = 10.69, 95%CI 7.83–13.54). Patients with severe disease showed significantly lower platelet count (WMD = −18.63, 95%CI −30.86 to −6.40) and lymphocyte count (WMD = −0.35, 95%CI −0.41 to −0.30) but higher C-reactive protein (CRP; WMD = 42.7, 95%CI 31.12–54.28), lactate dehydrogenase (LDH; WMD = 137.4, 95%CI 105.5–169.3), white blood cell count（WBC), procalcitonin（PCT）, D-dimer, alanine aminotransferase (ALT), aspartate aminotransferase (AST) and creatinine（Cr）. Similarly, patients who died showed significantly higher WBC, D-dimer, ALT, AST and Cr but similar platelet count and LDH as patients who survived. These results indicate that older age, low platelet count, lymphopenia, elevated levels of LDH, ALT, AST, PCT, Cr and D-dimer are associated with severity of COVID-19 and thus could be used as early identification or even prediction of disease progression.

The aim of this study was to determine the most cost-effective strategy for the prevention and control of multidrug-resistant organisms (MDROs) in intensive care units (ICUs) in areas with limited health resources. The study was conducted in 12 ICUs of four hospitals. The total cost for the prevention of MDROs and the secondary attack rate (SAR) of MDROs for each strategy were collected retrospectively from 2046 subjects from January to December 2017. The average cost-effectiveness ratio (CER), incremental cost-effectiveness ratio (ICER) and cost-effectiveness acceptability curve were calculated. Hand hygiene (HH) had the lowest total cost (2149.6 RMB) and SAR of MDROs (8.8%) while single-room isolation showed the highest cost (33 700.2 RMB) and contact isolation had the highest SAR of MDROs (31.8%). The average cost per unit infection prevention was 24 427.8 RMB, with the HH strategy followed by the environment disinfection strategy (CER = 21 314.67). HH had the highest iterative cost effect under willingness to pay less than 2000 RMB. Due to the low cost for repeatability and obvious effectiveness, we conclude that HH is the optimal strategy for MDROs infections in ICUs in developing countries. The cost-effectiveness of the four prevention strategies provides some reference for developing countries but multiple strategies remain to be examined.

Increased population movements and increased mobility made it possible for severe acute respiratory syndrome coronavirus 2, which is mainly spread by respiratory droplets, to spread faster and more easily. This study tracked and analysed the development of the coronavirus 2019 (COVID-19) outbreak in the top 100 cities that were destinations for people who left Wuhan before the city entered lockdown. Data were collected from the top 100 destination cities for people who travelled from Wuhan before the lockdown, the proportion of people travelling into each city, the intensity of intracity travel and the daily reports of COVID-19. The proportion of the population that travelled from Wuhan to each city from 10 January 2020 to 24 January 2020, was positively correlated with and had a significant linear relationship with the cumulative number of confirmed cases of COVID-19 in each city after 24 January (all P < 0.01). After the State Council launched a multidepartment joint prevention and control effort on 22 January 2020 and compared with data collected on 18 February, the average intracity travel intensity of the aforementioned 100 cities decreased by 60−70% (all P < 0.001). The average intensity of intracity travel on the nth day in these cities during the development of the outbreak was positively related to the growth rate of the number of confirmed COVID-19 cases on the n + 5th day in these cities and had a significant linear relationship (P < 0.01). Higher intensities of population movement were associated with a higher incidence of COVID-19 during the pandemic. Restrictions on population movement can effectively curb the development of an outbreak.

Different countries have adopted strategies for the early detection of SARS-CoV-2 since the declaration of community transmission by the World Health Organization (WHO) and timely diagnosis has been considered one of the major obstacles for surveillance and healthcare. Here, we report the increase of the number of laboratories to COVID-19 diagnosis in Brazil. Our results demonstrate an increase and decentralisation of certified laboratories, which does not match the much higher increase in the number of COVID-19 cases. Also, it becomes clear that laboratories are irregularly distributed over the country, with a concentration in the most developed state, São Paulo.

Raw milk cheeses are commonly consumed in France and are also a common source of foodborne outbreaks (FBOs). Both an FBO surveillance system and a laboratory-based surveillance system aim to detect Salmonella outbreaks. In early August 2018, five familial FBOs due to Salmonella spp. were reported to a regional health authority. Investigation identified common exposure to a raw goats' milk cheese, from which Salmonella spp. were also isolated, leading to an international product recall. Three weeks later, on 22 August, a national increase in Salmonella Newport ST118 was detected through laboratory surveillance. Concomitantly isolates from the earlier familial clusters were confirmed as S. Newport ST118. Interviews with a selection of the laboratory-identified cases revealed exposure to the same cheese, including exposure to batches not included in the previous recall, leading to an expansion of the recall. The outbreak affected 153 cases, including six cases in Scotland. S. Newport was detected in the cheese and in the milk of one of the producer's goats. The difference in the two alerts generated by this outbreak highlight the timeliness of the FBO system and the precision of the laboratory-based surveillance system. It is also a reminder of the risks associated with raw milk cheeses.