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The ring-infected erythrocyte surface antigen (RESA), is one of the falciparum malaria vaccine candidates rarely studied in Brazil. Fieldwork logistics to conduct serology studies is simplified when eluates from whole blood dried on filter paper can be used. Therefore, this study aimed to assess the inter-test reliability for the anti-RESA ELISA-based indices using eluates from filter paper and from serum samples. The study population consisted of 210 individuals (Brazil) from whom matched samples were collected. Anti-RESA ELISA-based index means (±S.D.) were 15.29% (±28.13%) for filter paper and 11.79% (±23.67%) for serum samples. The intra-class correlation coefficient was estimated to be 82.38%, indicating high test reliability. However, there was a significant tendency for filter paper test results to have higher values than serum sample test results (P

SummaryLarge-scale surveys of immunity to vaccine-preventable diseases may be limited by the inconvenience and expense involved in collection of blood by venepuncture. An alternative method of collecting blood on filter paper for measurement of immunity to diphtheria and tetanus is described. The precut filter disks (Elisadiscs), originally developed for serological diagnosis of disease in pigs, have advantages over previously described methods in that they allow safe handling of minimal volumes of blood (5 μl) which can be conveniently quantified.To compare values obtained by venepuncture and fingerprick, paired samples were collected from 60 subjects and diphtheria and tetanus antitoxin concentrations were measured by ELISA. There was no significant difference detected between samples collected by the two methods.The results suggest that Elisadiscs are a reliable alternative to venepuncture for monitoring immunity to diphtheria and tetanus and would be useful for sample collection in remote areas and from children.

Predicting the need for hospitalisation of patients with coronavirus disease 2019 (COVID-19) is important for preventing healthcare disruptions. This observational study aimed to use the COVID-19 Registry Japan (COVIREGI-JP) to develop a simple scoring system to predict respiratory failure due to COVID-19 using only underlying diseases and symptoms. A total of 6873 patients with COVID-19 admitted to Japanese medical institutions between 1 June 2020 and 2 December 2020 were included and divided into derivation and validation cohorts according to the date of admission. We used multivariable logistic regression analysis to create a simple risk score model, with respiratory failure as the outcome for young (18–39 years), middle-aged (40–64 years) and older (≥65 years) groups, using sex, age, body mass index, medical history and symptoms. The models selected for each age group were quite different. Areas under the receiver operating characteristic curves for the simple risk score model were 0.87, 0.79 and 0.80 for young, middle-aged and elderly derivation cohorts, and 0.81, 0.80 and 0.67 in the validation cohorts. Calibration of the model was good. The simple scoring system may be useful in the appropriate allocation of medical resources during the COVID-19 pandemic.

Serosurveillance is an important epidemiologic tool for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), used to estimate infection rates and the degree of population immunity. There is no general agreement on which antibody biomarker(s) should be used, especially with the rollout of vaccines globally. Here, we used random forest models to demonstrate that a single spike or receptor-binding domain (RBD) antibody was adequate for classifying prior infection, while a combination of two antibody biomarkers performed better than any single marker for estimating time-since-infection. Nucleocapsid antibodies performed worse than spike or RBD antibodies for classification, but can be useful for estimating time-since-infection, and in distinguishing infection-induced from vaccine-induced responses. Our analysis has the potential to inform the design of serosurveys for SARS-CoV-2, including decisions regarding a number of antibody biomarkers measured.

This study investigated the characteristics of transmission routes of COVID-19 cluster infections (⩾10 linked cases within a short period) in Gangwon Province between 22 February 2020 and 31 May 2021. Transmission routes were divided into five major categories and 35 sub-categories according to the relationship between the infector and the infectee and the location of transmission. A total of 61 clusters occurred during the study period, including 1741 confirmed cases (55.7% of all confirmed cases (n = 3125)). The the five major routes of transmission were as follows: ‘using (staying in) the same facility (50.7%), ‘cohabiting family members’ (23.3%), ‘social gatherings with acquaintances’ (10.8%), ‘other transmission routes’ (7.0%), and ‘social gatherings with non-cohabiting family members/relatives’ (5.5%). For transmission caused by using (staying in) the same facility, the highest number of confirmed cases was associated with churches, followed by medical institutions (inpatient), sports facilities, military bases, offices, nightlife businesses, schools, restaurants, day-care centres and kindergarten, and service businesses. Our analysis highlights specific locations with frequent transmission of infections, and transmission routes that should be targeted in situations where adherence to disease control rules is difficult.

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.

This study aimed to evaluate the performance of Cobas human papillomavirus (HPV) test in cervical cancer screening. A total of 3442 women aged ⩾20 years used Cobas HPV and hybrid capture 2 (HC2) tests were included in this study. Women with any positive result were examined by liquid-based cytology (LBC) test. Then subjects with abnormal LBC or positive Cobas HPV16/18 were further checked by colposcopy to observe the visible lesions to perform the pathological examination. Of these 3442 women, 328 cases were Cobas HPV positive, and the positive rate was 9.53% (95% confidence interval (CI) 8.50–10.53). The positive rate of HPV16, HPV18, and other 12 types of high-risk HPV were 1.54% (95% CI 1.12–1.95), 0.55% (95% CI 0.30–0.80), and 7.44% (95% CI 6.56–8.32), respectively. The coincidence rate of Cobas HPV test and HC2 test was 90% (95% CI 89.00–91.00; Kappa = 0.526) in the primary screening. Age had a non-linear relationship with Cobas HPV positive rate (χ2 = 4.240, P = 0.040) and HPV16/18 typing positive rate (χ2 = 6.610, P = 0.010). Compared with the LBC test, the Cobas HPV test had higher sensitivity when detecting patients with high cervical intraepithelial neoplasia (CIN2+ and CIN3+).

The prevalence of human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) is increasing day by day in the region, including Turkey. The study aimed to examine AIDS-related deaths in Turkey between 2009 and 2018 according to the national death registration system records. In this descriptive study, data on AIDS-related deaths were obtained from the Turkish Statistical Institute. The data consist of the cause of death codes, year of death, age and gender. Findings were presented using numbers and percentages. Seven hundred twenty-one AIDS-related deaths were reported in Turkey between 2009 and 2018. AIDS-related deaths in Turkey increased more than twice at the end of 10 years. The male/female death ratio is 4.5. Deaths under the age of 15 were 4.2% in total; however, they were increased to 10.2% in 2018. AIDS-related deaths are decreasing in the world but increasing in Turkey. The data from the Ministry of Health do not match the data of the national death registration system. Establishing a strong and accurate HIV/AIDS reporting system and identifying the causes and risk groups of this increase in AIDS-related deaths are critical.

In August 2019, public health surveillance systems in Scotland and England identified seven, geographically dispersed cases infected with the same strain (defined as isolates that fell within the same five single nucleotide polymorphism single linage cluster) of Shiga toxin-producing Escherichia coli O157:H7. Epidemiological analysis of enhanced surveillance questionnaire data identified handling raw beef and shopping from the same national retailer (retailer A) as the common exposure. Concurrently, a microbiological survey of minced beef at retail identified the same strain in a sample of minced beef sold by retailer A, providing microbiological evidence of the link. Between September and November 2019, a further four primary and two secondary cases infected with the same strain were identified; two cases developed haemolytic uraemic syndrome. None of the four primary cases reported consumption of beef from retailer A and the transmission route of these subsequent cases was not identified, although all four primary cases visited the same petting farm. Generally, outbreaks of STEC O157:H7 in the UK appear to be distinct, short-lived events; however, on-going transmission linked to contaminated food, animals or environmental exposures and person-to-person contact do occur. Although outbreaks of STEC caused by contaminated fresh produce are increasingly common, undercooked meat products remain a risk of infection.

Human papillomavirus (HPV) has been confirmed as the causative agent for cervical cancer. In this study, a total of 301 880 women were recruited from four different regions of Western China, with 301 880 exfoliated cervical cell samples collected from women for DNA isolation and purification. The HPV genotype was tested by polymerase chain reaction. The overall HPV prevalence rate, high-risk (HR) HPV infection rate, low-risk (LR) HPV infection rate and mixed HPV infection rate was 18.24%, 79.14%, 12.56% and 8.30%, respectively. The four most common HR HPV subtypes were HPV-52, 16, 58 and 53, which accounted for 20.49%, 19.93%, 14.54% and 10.01%, respectively. In LR HPV genotype, HPV-6 ranked the highest (28.17%), followed by HPV-81 (9.09%) and HPV-11 (3.78%). HPV genotype subgroup analysis also showed that single-type infection was the most common (77.26%) among HPV-positive individuals. Among multi-infection genotypes, double infection was the most common with frequencies of 76.04%. The overall prevalence of HPV is high in Western China, whose distribution demonstrates different patterns across different ages and regions. Viral genotypes HPV 53, 6 were frequently detected in this population, which is worth of significant clinical attention.

Brucellosis remains one of the main zoonoses worldwide. Epidemiological data on human brucellosis in Spain are scarce. The objective of this study was to assess the epidemiological characteristics of inpatient brucellosis in Spain between 1997 and 2015. A retrospective longitudinal descriptive study was performed. Data were requested from the Health Information Institute of the Ministry of Health and Equality, which provided us with the Minimum Basic Data Set of patients admitted to the National Health System. We also obtained data published in the System of Obligatory Notifiable Diseases. A total of 5598 cases were registered. The period incidence rate was 0.67 (95% CI 0.65–0.68) cases per 100 000 person-years. We observed a progressive decrease in the number of cases and annual incidence rates. A total of 3187 cases (56.9%) came from urban areas. The group most at risk comprised men around the fifth decade of life. The average (±s.d.) hospital stay was 12.6 days (±13.1). The overall lethality rate of the cohort was 1.5%. The number of inpatients diagnosed with brucellosis decreased exponentially. The group of patients with the highest risk of brucellosis in our study was males under 45 years of age and of urban origin. The lethality rate has reduced to minimum values. It is probable that hospital discharge records could be a good database for the epidemiological analysis of the hospital management of brucellosis and offer a better information collection system than the notifiable diseases system (EDO in Spanish).

The study aims to estimate and compare the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence, the fraction of asymptomatic or subclinical infections in the population, determine the demographic risk factors and analyse the antibody development at different time points among adults in Bhubaneswar city, India. This was a serial three-round cross-sectional, community-based study where participants were selected from the residents of Bhubaneswar city using multi-stage random sampling. Blood samples were collected during household visits along with demographic and clinical data from every participant. Total anti-SARS-CoV-2 antibody present in serum was assessed using the electro-chemiluminescence immunoassay platform. Temporal comparisons of the community seroprevalence were performed against the detected number of cumulative cases, active cases, recoveries and deaths. A total of 3693 participants were enrolled in this study with a cumulative non-response rate of 18.33% in all the three rounds. The gender-weighted seroprevalence for the city in the first round was 1.55% (95% confidence interval (CI) 0.84–2.58), second round was 5.27% (95% CI 4.13–6.59) and in the third round was 49.04% (95% CI 46.39–51.68). In the first round, the seroprevalence was found to be highest in the elderly population, whereas the seroprevalence for the second and third phases was highest in the age group of 30–39 years. Seroprevalence showed an increasing trend over the three time periods, with the highest seropositivity rates among individuals sampled between 16 and 18 September 2020. By the third round, 93.93% of those who had previously been tested positive by real-time reverse transcription polymerase chain reaction had seroconversion and 46.57% of those who had been tested negative also showed seroconversion. Infection to case ratio during first round was 27.05, for second round and third round it was 5.62 and 17.91, respectively.

Brazil ranks second in the number of confirmed cases of COVID-19 worldwide. In spite of this, coping measures differ throughout the national territory, as does the disease's impact on the population. This cross-sectional observational study, with 59 695 cases of COVID-19 registered in the state of Alagoas between March and August 2020, analysed clinical-epidemiological variables, incidence rate, mortality rate, case fatality rate (CFR) and the social indicators municipal human development index (MHDI) and social vulnerability index (SVI). Moran statistics and regression models were applied. Logistic regression analysis was applied to determine the predictors of death. The incidence rate was 1788.7/100 000 inhabitants; mortality rate was 48.0/100 000 and CFR was 2.7%. The highest incidence rates were observed in municipalities with better human development (overall MHDI (I = 0.1668; p = 0.002), education MHDI (I = 0.1649; p = 0.002) and income MHDI (I = 0.1880; p = 0.005)) and higher social vulnerability (overall SVI (I = 0.0599; p = 0.033)). CFR was associated with higher social vulnerability (SVI human capital (I = 0.0858; p = 0.004) and SVI urban infrastructure (I = 0.0985; p = 0.040)). Of the analysed cases, 55.4% were female; 2/3 were Black or Brown and the median age was 41 years. Among deaths, most were male (919; 57.4%) and elderly (1171; 73.1%). The predictors of death were male sex, advanced age and the presence of comorbidities. In Alagoas, Brazil, the disease has undergone a process of interiorisation and caused more deaths in poorer municipalities. The presence of comorbidities and advanced age were predictors of death.

Although many people became infected and recovered during the COVID-19 epidemic, the immunity duration and re-infection in recovered patients have recently attracted many researchers. The aim of this study was to evaluate the recurrence of the infection in recovered individuals over a 9-month period after the onset of the COVID-19 epidemic. In this study, data related to COVID-19 patients in Shahroud city were collected using the electronic system for registering suspicious patients and also by checking patients' hospital records. In this study, from 20 March 2020 to 20 November 2020 (9 months), a total of 8734 suspected patients with respiratory symptoms were observed and followed up. RT-PCR was positive for 4039 patients. During this period, out of the total number of positive cases of COVID-19, 10 cases became re-infected after complete recovery. The risk of re-infection was 2.5 per thousand (0.95 CI 1.2–4.5). The mean time interval between the first infection and re-infection was 134.4 ± 64.5 days (range 41–234 days). The risk of re-infection between male and females was not statistically different (1.98 per 1000 women and 2.96 per 1000 men). Exposure to COVID-19 may not establish long-term protective immunity to all patients and may predispose them to re-infection. This fact can be reminded that the use of masks, social distancing and other preventive measures are very important in recovered patients and should be emphasised especially in health care personnel who are more exposed to the virus.

Recurrent outbreaks of haemolytic uraemic syndrome (HUS) caused by Shiga toxin-producing Escherichia coli (STEC) serotype O55:H7 occurred in England between 2014 and 2018. We reviewed the epidemiological evidence to identify potential source(s) and transmission routes of the pathogen, and to assess the on-going risk to public health. Over the 5-year period, there were 43 confirmed and three probable cases of STEC O55:H7. The median age of cases was 4 years old (range 6 months to 69 years old) and over half of all cases were female (28/46, 61%). There were 36/46 (78.3%) symptomatic cases, and over half of all cases developed HUS (25/46, 54%), including two fatal cases. No common food or environmental exposures were identified, although the majority of cases lived in rural or semi-rural environments and reported contact with both wild and domestic animals. This investigation informed policy on the clinical and public health management of HUS caused by STEC other than serotype O157:H7 (non-O157 STEC) in England, including comprehensive testing of all household contacts and household pets and more widespread use of polymerase chain reaction assays for the rapid diagnosis of STEC-HUS.

Background The median duration of hospital stays due to COVID-19 has been reported in several studies on China as 10−13 days. Global studies have indicated that the length of hospitalisation depends on different factors, such as the time elapsed from exposure to symptom onset, and from symptom onset to hospital admission, as well as specificities of the country under study. The goal of this paper is to identify factors associated with the median duration of hospital stays of COVID-19 patients during the second COVID-19 wave that hit Vietnam from 5 March to 8 April 2020. Method We used retrospective data on 133 hospitalised patients with COVID-19 recorded over at least two weeks during the study period. The Cox proportional-hazards regression model was applied to determine the potential risk factors associated with length of hospital stay. Results There were 65 (48.9%) females, 98 (73.7%) patients 48 years old or younger, 15 (11.3%) persons with comorbidities, 21 (16.0%) severely ill patients and 5 (3.8%) individuals with life-threatening conditions. Eighty-two (61.7%) patients were discharged after testing negative for the SARS-CoV-2 virus, 51 were still in the hospital at the end of the study period and none died. The median duration of stay in a hospital was 21 (IQR: 16–34) days. The multivariable Cox regression model showed that age, residence and sources of contamination were significantly associated with longer duration of hospitalisation. Conclusion A close look at how long COVID-19 patients stayed in the hospital could provide an overview of their treatment process in Vietnam, and support the country's National Steering Committee on COVID-19 Prevention and Control in the efficient allocation of resources over the next stages of the COVID-19 prevention period.

For outbreaks of gastrointestinal disease, rapid identification of the source is crucial to enable public health intervention and prevent further cases. Outbreak investigation comprises analyses of exposure information from cases and, if required, undertaking analytical epidemiological studies. Hypothesis generation has been reliant on empirical knowledge of exposures historically associated with a given pathogen. Epidemiology studies are resource-intensive and prone to bias, one of the reasons being the difficulties in recruiting appropriate controls. For this paper, the information from cases was compared against pre-defined background exposure information. As exemplars, three past outbreaks were used, one of common and two of rare exposures. Information from historical case trawling questionnaires was used to define background exposure having removed any exposures implicated with the outbreak. The case-background approach showed good sensitivity and specificity, identifying correctly all outbreak-related exposures. One additional exposure related to a retailer was identified and four food items where all cases had been exposed. In conclusion, the case-background method, a development of the case-case design, can be used to assist with hypothesis generation or when a case-control study may not be possible to carry out.

Although handwashing is an effective way to prevent infections, there is scarce evidence on predictors of handwashing during a pandemic. This paper aims to identify behavioural and demographic predictors of handwashing. The study surveyed 674 adults in Malaysia in May 2020 regarding whether the time spent on social media predicted handwashing contingent on gender and number of children. More time spent on social media was positively associated with handwashing for males with three or more children. However, for males without children, social media use was negatively associated with handwashing. The association was not significant for males with one or two children. For females, more time spent on social media was significantly linked to more handwashing only for females with one child. Gender, a traditional predictor of handwashing, was a useful predictor only for those who spent more than three hours per day on social media and had at most one child. Number of children was a novel negative predictor for males who did not use social media and who averaged one hour per day on social media, a positive predictor for males who spent lots of time on social media, but not a predictor for females. In sum, social media use predicts handwashing, and is thus a helpful variable for use in targeted health communication during a pandemic – particularly through social media. Further, more conventional predictors like gender and number of children exhibit contingency effects with social media use.

To assess the relationship between the neutrophil-to-lymphocyte ratio (NLR) and related parameters to the severity of coronavirus disease 2019 (COVID-19) symptoms. Clinical data from 38 COVID-19 patients who were diagnosed, treated and discharged from the Qishan Hospital in Yantai over the period from January to February 2020 were analysed. NLR and procalcitonin (PCT) were determined in the first and fourth weeks after their admission, along with the clinical characteristics and laboratory test results of these patients. Based on results as obtained on the first and fourth weeks after admission, five indices consisting of NLR, white blood cells, neutrophils, lymphocytes (LY) and monocytes (MON) were selected to generate receiver operating characteristic curves, while optimal cutoff values, sensitivities and specificities were obtained according to the Yuden index. Statistically significant differences in neutrophils, LY and the NLR were present in the severe vs. moderate COVID-19 group from the first to the fourth week of their hospitalisation. The cut-off value of NLR for predicting the severity of COVID-19 was 4.425, with a sensitivity of 0.855 and a specificity of 0.979. A statistically significant positive correlation was present between PCT and NLR in the severe group as determined within the first week of admission. NLR can serve as a predictor of COVID-19 disease severity as patients' progress from the first to the fourth week of their hospitalisation. The statistically significant positive correlation between levels of NLR and PCT in severe patients indicated that increases in NLR were accompanied with gradual increases in PCT.

COVID-19, although a respiratory illness, has been clinically associated with non-respiratory symptoms. We conducted a negative case–control study to identify the symptoms associated with SARS-CoV-2-positive results in Portugal. Twelve symptoms and signs included in the clinical notification of COVID-19 were selected as predictors, and the dependent variable was the RT-PCR test result. The χ2 tests were used to compare notified cases on sex, age group, health region and presence of comorbidities. The best-fit prediction model was selected using a backward stepwise method with an unconditional logistic regression. General and gastrointestinal symptoms were strongly associated with a positive test (P < 0.001). In this sense, the inclusion of general symptoms such as myalgia, headache and fatigue, as well as diarrhoea, together with actual clinical criteria for suspected cases, already updated and included in COVID-19 case definition, can lead to increased identification of cases and represent an effective strength for transmission control.

We report the development of a regression model to predict the prevalence of severe acute respiratory syndrome coronavirus (SARS-CoV-2) antibodies on a population level based on self-reported symptoms. We assessed participant-reported symptoms in the past 12 weeks, as well as the presence of SARS-CoV-2 antibodies during a study conducted in April 2020 in Ischgl, Austria. We conducted multivariate binary logistic regression to predict seroprevalence in the sample. Participants (n = 451) were on average 47.4 years old (s.d. 16.8) and 52.5% female. SARS-CoV-2 antibodies were found in n = 197 (43.7%) participants. In the multivariate analysis, three significant predictors were included and the odds ratios (OR) for the most predictive categories were cough (OR 3.34, CI 1.70–6.58), gustatory/olfactory alterations (OR 13.78, CI 5.90–32.17) and limb pain (OR 2.55, CI 1.20–6.50). The area under the receiver operating characteristic curve was 0.773 (95% CI 0.727–0.820). Our regression model may be used to estimate the seroprevalence on a population level and a web application is being developed to facilitate the use of the model.

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.

Tuberculosis (TB) remains a global public health threat. Misdiagnosis and delayed therapy of sputum smear-negative TB can affect the treatment outcomes and promote pathogen transmission. The application of Xpert MTB/RIF assay in bronchoalveolar lavage fluid (BALF) has been recommended but needs clinical evidence. We carried out a prospective study in the Nanjing Public Health Medical Center from September 2018 to August 2019. Pulmonary tuberculosis (PTB) patients were enrolled in the study if they had negative results of sputum smear. We compared the performance of Xpert MTB/RIF assay in sputum and BALF using sputum culture as the reference. In addition to this, we applied parallel tests using sputum culture, sputum-based Xpert MTB/RIF assay and BALF-based Xpert MTB/RIF assay to jointly detect smear-negative PTB using clinical diagnosis as the reference. With mycobacterial culture as the reference standard, Xpert MTB/RIF of BALF showed a higher sensitivity (14/16, 87.5%), but a relatively lower specificity (57/92, 62.0%). Xpert MTB/RIF of sputum showed relatively lower sensitivity (6/10, 60.0%) and higher specificity (63/88, 71.6%). Compared with sputum culture, Xpert MTB /RIF assay reduced the median detection time of MTB from 30 to 0 days, which significantly shortened the diagnosis time of the smear-negative TB patients. Among the combined detections, the positive detection proportion was improved with significant differences comparing with sputum culture only, from 11.1% (10/90) to 46.7% (42/90) (P < 0.05). Our study showed Xpert MTB/RIF in BALF had a better performance in detecting MTB of smear-negative patients.

Pre-existing health conditions may exacerbate the severity of coronavirus disease 2019 (COVID-19). We aimed to estimate the case-fatality rate (CFR) and rate ratios (RR) for patients with hypertension (HBP) and diabetes mellitus (DM) in the New York state. We obtained the age-specific number of COVID-19 confirmed cases and deaths from public reports provided by the New York State Department of Health, and age-specific prevalence of HBP and DM from the Behavioral Risk Factor Surveillance System 2017. We calculated CFR and RR for COVID-19 patients with HBP and DM based on the reported number of deaths with the comorbidity divided by the expected number of COVID-19 cases with the comorbidity. We performed subgroup analysis by age and calculated the CFR and RR for ages of 18–44, 45–64 and 65+ years, respectively. We found that the older population had a higher CFR, but the elevated RRs associated with comorbidities are more pronounced among the younger population. Our findings suggest that besides the elderly, the young population with comorbidity should also be considered as a vulnerable group.

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.

Much of our current understanding about novel coronavirus disease 2019 (COVID-19) comes from hospitalised patients. However, the spectrum of mild and subclinical disease has implications for population-level screening and control. Forty-nine participants were recruited from a group of 99 adults repatriated from a cruise ship with a high incidence of COVID-19. Respiratory and rectal swabs were tested by polymerase chain reaction (PCR) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sera were tested for anti-SARS-CoV-2 antibodies by enzyme-linked immunosorbent assay (ELISA) and microneutralisation assay. Symptoms, viral shedding and antibody response were examined. Forty-five participants (92%) were considered cases based on either positive PCR or positive ELISA for immunoglobulin G. Forty-two percent of cases were asymptomatic. Only 15% of symptomatic cases reported fever. Serial respiratory and rectal swabs were positive for 10% and 5% of participants respectively about 3 weeks after median symptom onset. Cycle threshold values were high (range 31–45). Attempts to isolate live virus were unsuccessful. The presence of symptoms was not associated with demographics, comorbidities or antibody response. In closed settings, incidence of COVID-19 could be almost double that suggested by symptom-based screening. Serology may be useful in diagnosis of mild disease and in aiding public health investigations.

Tuberculosis (TB) is a common infectious disease, and the present study aims to explore the associations of single nucleotide polymorphisms (SNPs) at rs1135216 and rs1057141 of transporter-associated antigen processing (TAP1) and rs2228396 of TAP2 with pulmonary tuberculosis (PTB) risk. A case–control study including 168 smear-positive PTB cases and 251 controls was conducted. Genotyping of the SNPs at rs1135216, rs1057141 and rs2228396 was performed, and their associations with PTB risk were analysed with SPSS software version 19.0. After conducting stratification for age, a significant association was detected for rs1057141 with increased PTB risk (OR = 0.17, 95% CI 0.04–0.79) among those aged ≥60 years. For those aged

SUMMARYThis study aimed to analyze the geographical distribution of COVID-19 and to identify highrisk areas for the occurrence of cases and deaths from the disease in the indigenous population of Brazil. This is an ecological study whose units of analysis were the Special Indigenous Sanitary Districts. Cases and deaths by COVID-19 notified by the Special Secretariat for Indigenous Health between March and October 2020 were included. To verify the spatial association, the Getis-Ord General G and Getis-Ord Gi * techniques were used. High spatial risk clusters have been identified by the scan statistics technique. 32,041 cases of COVID-19 and 471 deaths were reported. The incidence and mortality rates were between 758.14 and 18530.56 cases and 5.96 and 265.37 deaths per 100 thousand inhabitants, respectively. The non-randomness of cases (z-score = 5.40; p

This study analysed the reported incidence of COVID-19 and associated epidemiological and socio-economic factors in the WHO African region. Data from COVID-19 confirmed cases and SARS-CoV-2 tests reported to the WHO by Member States between 25 February and 31 December 2020 and publicly available health and socio-economic data were analysed using univariate and multivariate binomial regression models. The overall cumulative incidence was 1846 cases per million population. Cape Verde (21 350 per million), South Africa (18 060 per million), Namibia (9840 per million), Eswatini (8151 per million) and Botswana (6044 per million) recorded the highest cumulative incidence, while Benin (260 per million), Democratic Republic of Congo (203 per million), Niger (141 cases per million), Chad (133 per million) and Burundi (62 per million) recorded the lowest. Increasing percentage of urban population (β= −0.011,P= 0.04) was associated with low cumulative incidence, while increasing number of cumulative SARS-CoV-2 tests performed per 10 000 population (β= 0.0006,P= 0.006) and the proportion of population aged 15–64 years (adjustedβ= 0.174,P< 0.0001) were associated with high COVID-19 cumulative incidence. With limited testing capacities and overwhelmed health systems, these findings highlight the need for countries to increase and decentralise testing capacities and adjust testing strategies to target most at-risk populations.

Little is known about the impact of COVID-19 on the outcomes of patients undergoing surgery and intervention. This study was conducted between 20 March and 20 May 2020 in six hospitals in Istanbul, and aimed to investigate the effects of surgery and intervention on COVID-19 disease progression, intensive care (ICU) need, mortality and virus transmission to patients and healthcare workers. Patients were examined in three groups: group I underwent emergency surgery, group II had an emergency non-operating room intervention, and group III received inpatient COVID-19 treatment but did not have surgery or undergo intervention. Mortality rates, mechanical ventilation needs and rates of admission to the ICU were compared between the three groups. During this period, patient and healthcare worker transmissions were recorded. In total, 1273 surgical, 476 non-operating room intervention patients and 1884 COVID-19 inpatients were examined. The rate of ICU requirement among patients who had surgery was nearly twice that for inpatients and intervention patients, but there was no difference in mortality between the groups. The overall mortality rates were 2.3% in surgical patients, 3.3% in intervention patients and 3% in inpatients. COVID-19 polymerase chain reaction positivity among hospital workers was 2.4%. Only 3.3% of infected frontline healthcare workers were anaesthesiologists. No deaths occurred among infected healthcare workers. We conclude that emergency surgery and non-operating room interventions during the pandemic period do not increase postoperative mortality and can be performed with low transmission rates.

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 (allP< 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.

Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) pandemic is still ongoing along with the global vaccination efforts against it. Here, we aimed to understand the longevity and strength of anti-SARS-CoV-2 IgG responses in a small community (n = 283) six months following local SARS-COV-2 outbreak in March 2020. Three serological assays were compared and neutralisation capability was also determined. Overall 16.6% (47/283) of the participants were seropositive and 89.4% (42/47) of the IgG positives had neutralising antibodies. Most of the symptomatic individuals confirmed as polymerase chain reaction (PCR) positive during the outbreak were seropositive (30/32, 93.8%) and 33.3% of the individuals who quarantined with a PCR confirmed patient had antibodies. Serological assays comparison revealed that Architect (Abbott) targeting the N protein LIASON® (DiaSorin) targeting the S protein and enzyme-linked immunosorbent assay (ELISA) targeting receptor binding domain detected 9.5% (27/283), 17.3% (49/283) and 17% (48/283), respectively, as IgG positives. The latter two assays highly agreed (kappa = 0.89) between each other. In addition, 95%, (19/20, by ELISA) and 90.9% (20/22, with LIASON) and only 71.4% (15/21, by Architect) of individuals that were seropositive in May 2020 were found positive also in September. The unexpected low rate of overall immunity indicates the absence of un-noticed, asymptomatic infections. Lack of overall high correlation between the assays is attributed mainly to target-mediated antibody responses and suggests that using a single serological assay may be misleading.

Rabies post-exposure prophylaxis (R-PEP) including wound treatment, vaccination and application of rabies immunoglobulin (RIG) is essential in preventing rabies mortality. Today, Germany is officially declared free from terrestrial rabies and rabies is only found in bats. However, physicians in A&E Departments are frequently consulted on the need for R-PEP. We retrospectively analysed patients who received R-PEP at the A&E Department of the University Hospital Bonn between 01.01.2013 and 30.06.2019. Demographic data, travel history, clinical and laboratory findings, previous rabies vaccinations and R-PEP vaccination regimen were recorded. During the study period, 90 patients received R-PEP at the University Hospital Bonn, in 10 cases without indication for R-PEP. Altogether, we found deviations from R-PEP guidelines in 51% (n = 41/80). Infiltration of RIG was missed in 12 patients and incorrectly administrated in 24 patients. Furthermore, vaccination scheme was incorrect in 11 patients. Correct wound washing and documentation of tetanus status was missing in 14% and 63% of patients, respectively. Despite rabies elimination in Germany patients frequently seek advice for R-PEP, the majority returning from foreign travel. Our data show that there is a high need for education on indication for R-PEP before and after travel and for implementation of precise R-PEP guidelines in daily clinical practice.

Hebei Province was affected by two coronavirus disease 2019 (COVID-19) outbreak waves during the period 22 January 2020 through 27 February 2020 (wave 1) and 2 January 2021 through 14 February 2021 (wave 2). To evaluate and compare the epidemiological characteristics, containment delay, cluster events and social activity, as well as non-pharmaceutical interventions of the two COVID-19 outbreak waves, we examined real-time update information on all COVID-19-confirmed cases from a publicly available database. Wave 1 was closely linked with the COVID-19 pandemic in Wuhan, whereas wave 2 was triggered, to a certain extent, by the increasing social activities such as weddings, multi-household gatherings and church events during the slack agricultural period. In wave 2, the epidemic spread undetected in the rural areas, and people living in the rural areas had a higher incidence rate than those living in the urban areas (5.3 vs. 22.0 per 1 000 000). Furthermore, Rt was greater than 1 in the early stage of the two outbreak waves, and decreased substantially after massive non-pharmaceutical interventions were implemented. In China's ‘new-normal’ situation, development of targeted and effective intervention remains key for COVID-19 control in consideration of the potential threat of new coronavirus strains.

The novel coronavirus identified as severe acute respiratory syndrome-coronavirus-2 causes acute respiratory distress syndrome (ARDS). Our aim in this study is to assess the incidence of life-threatening complications like pneumothorax, haemothorax, pneumomediastinum and subcutaneous emphysema, probable risk factors and effect on mortality in coronavirus disease-2019 (COVID-19) ARDS patients treated with mechanical ventilation (MV). Data from 96 adult patients admitted to the intensive care unit with COVID-19 ARDS diagnosis from 11 March to 31 July 2020 were retrospectively assessed. A total of 75 patients abiding by the study criteria were divided into two groups as the group developing ventilator-related barotrauma (BG) (N = 10) and the group not developing ventilator-related barotrauma (NBG) (N = 65). In 10 patients (13%), barotrauma findings occurred 22 ± 3.6 days after the onset of symptoms. The mortality rate was 40% in the BG-group, while it was 29% in the NBG-group with no statistical difference identified. The BG-group had longer intensive care admission duration, duration of time in prone position and total MV duration, with higher max positive end-expiratory pressure (PEEP) levels and lower min pO2/FiO2 levels. The peak lactate dehydrogenase levels in blood were higher by statistically significant level in the BG-group (P < 0.05). The contribution of MV to alveolar injury caused by infection in COVID-19 ARDS patients may cause more frequent barotrauma compared to classic ARDS and this situation significantly increases the MV and intensive care admission durations of patients. In terms of reducing mortality and morbidity in these patients, MV treatment should be carefully maintained within the framework of lung-protective strategies and the studies researching barotrauma pathophysiology should be increased.

With the rapid rise in the prevalence of non-tuberculous mycobacteria (NTM) diseases across the world, the microbiological diagnosis of NTM isolates is becoming increasingly important for the diagnosis and treatment of NTM disease. In this study, the clinical presentation, species distribution and drug susceptibility of patients with NTM disease visiting the Chongqing Public Health Medical Centre during March 2016–April 2019 were retrospectively analysed. Among the 146 patients with NTM disease, eight NTM species (complex) were identified. The predominant NTM species in these patients were identified to be Mycobacterium abscessus complex (53, 36.3%), M. intracellulare (38, 26%) and M. fortuitum (17, 11.7%). In addition, two or more species were isolated from 7.5% of the patients. Pulmonary NTM disease (142, 97.3%) showed the highest prevalence among the patients. It was observed that 40.1% of the patients with pulmonary NTM disease had chronic pulmonary obstructive disease and bronchiectasis, while 22.5% had prior tuberculosis. Male patients showed more association with the conditions of cough and haemoptysis than the female patients. In an in vitro antimicrobial susceptibility testing, most of the species showed susceptibility to linezolid, amikacin and clarithromycin, while M. fortuitum exhibited low susceptibility to tobramycin. In conclusion, the prevalence of NTM disease, especially that of the pulmonary NTM disease, is common in Southwest China. Species identification and drug susceptibility testing are thus extremely important to ensure appropriate treatment regimens for patient care and management.

An acute gastroenteritis (AGE) outbreak caused by a norovirus occurred at a hospital in Shanghai, China, was studied for molecular epidemiology, host susceptibility and serological roles. Rectal and environmental swabs, paired serum samples and saliva specimens were collected. Pathogens were detected by real-time polymerase chain reaction and DNA sequencing. Histo-blood group antigens (HBGA) phenotypes of saliva samples and their binding to norovirus protruding proteins were determined by enzyme-linked immunosorbent assay. The HBGA-binding interfaces and the surrounding region were analysed by the MegAlign program of DNAstar 7.1. Twenty-seven individuals in two care units were attacked with AGE at attack rates of 9.02 and 11.68%. Eighteen (78.2%) symptomatic and five (38.4%) asymptomatic individuals were GII.6/b norovirus positive. Saliva-based HBGA phenotyping showed that all symptomatic and asymptomatic cases belonged to A, B, AB or O secretors. Only four (16.7%) out of the 24 tested serum samples showed low blockade activity against HBGA-norovirus binding at the acute phase, whereas 11 (45.8%) samples at the convalescence stage showed seroconversion of such blockade. Specific blockade antibody in the population played an essential role in this norovirus epidemic. A wide HBGA-binding spectrum of GII.6 supports a need for continuous health attention and surveillance in different settings.

The outbreak of coronavirus disease-2019 (COVID-19) impacts public health dramatically around the world. The demographic characteristics, exposure history, dates of illness onset and dates of confirmed diagnosis were collected from the data of 24 family clusters from Beijing. The characteristics of the cases and the estimated key epidemiologic time-to-event distributions were described. The basic reproductive number (R0) was calculated. Among 89 confirmed COVID-19 patients from 24 family clusters, the median age was 38.0 years and 43.8% were male. The median of incubation period was 5.08 days (95% confidence interval (CI) 4.17–6.21). The median of serial interval was 6.00 days (95% CI 5.00–7.00). The basic reproductive number (R0) was 2.06 (95% CI 2.02–2.08). The median of onset-to-care-seeking days and the median of onset-to-hospital admission days were significantly reduced after 23 January 2020, which implied the enhanced public health awareness among families. With epidemic containment measures in place, the results can inform health authorities about possible extent of epidemic transmission within families. Furthermore, following initiation of interventions, public health measures are not only important for curbing the epidemic spread at the community level but also improve health seeking behaviour at the individual level.

Data on the prevalence of extrapulmonary tuberculosis (EPTB) patients are limited in many African countries including Malawi. We conducted a retrospective review of all histology reports for cancer suspected patients at Mzuzu Central Hospital (MZCH) between 2013 and 2018 to determine the proportion of EPTB cases among cancer suspected patients and characterised them epidemiologically. All reports with inconclusive findings were excluded. In total, 2214 reports were included in the review, 47 of which reported EPTB, representing 2.1% (95% CI 1.6−2.8). The incidence of EPTB was significantly associated with sex, age and HIV status. Men were more than twice (OR 2.1; 95% CI 1.2–3.9) as likely to have EPTB as women while those with HIV were more than six times (OR 6.4; 95% CI 1.7–24.8) as likely to have EPTB compared to those who were HIV-negative. EPTB demonstrated an inverse relationship with age. The highest proportion of EPTB was found from neck lymph nodes (10.3% (5.4–17.2)). A reasonable number of EPTB cases are diagnosed late or missed in Malawi's hospitals. There is a need for concerted efforts to increase EPTB awareness and likely come up with a policy to consider EPTB as a differential diagnosis in cancer suspected patients.

The magnitude and consistency of the sex differences in meningococcal disease incidence rates (IR) have not been systematically examined in different age groups, countries and time periods. We obtained national data on meningococcal disease IR by sex, age group and time period, from 10 countries. We used meta-analytic methods to combine the male to female incidence rate ratios (IRRs) by country and year for each age group. Meta-regression analysis was used to assess the contribution of age, country and time period to the variation in the IRRs. The pooled male to female IRRs (with 95% CI) for ages 0–1, 1–4, 5–9, 10–14 and 15–44, were 1.25 (1.19–1.32), 1.24 (1.20–1.29), 1.13 (1.07–1.20), 1.21 (1.13–1.29) and 1.15 (1.10–1.21), respectively. In the age groups 45−64 and over 65, the IR were lower in males with IRRs of 0.83 (0.78–0.88) and 0.64 (0.60–0.69), respectively. Sensitivity analysis and meta-regression confirmed that the results were robust. The excess meningococcal IR in young males and the higher rates in females at older ages were consistent in all countries, except the Czech Republic. While behavioural factors could explain some of the sex differences in the older age groups, the excess rates in very young males suggest that genetic and hormonal differences could be important.

The mortality of coronavirus disease 2019 (COVID-19) differs between countries and regions. This study aimed to clarify the clinical characteristics of imported and second-generation cases in Shaanxi. This study included 134 COVID-19 cases in Shaanxi outside Wuhan. Clinical data were compared between severe and non-severe cases. We further profiled the dynamic laboratory findings of some patients. In total, 34.3% of the 134 patients were severe cases, 11.2% had complications. As of 7 March 2020, 91.8% patients were discharged and one patient (0.7%) died. Age, lymphocyte count, C-reactive protein, erythrocyte sedimentation rate, direct bilirubin, lactate dehydrogenase and hydroxybutyrate dehydrogenase showed difference between severe and no-severe cases (allP< 0.05). Baseline lymphocyte count was higher in survived patients than in non-survivor case, and it increased as the condition improved, but declined sharply when death occurred. The interleukin-6 (IL-6) level displayed a downtrend in survivors, but rose very high in the death case. Pulmonary fibrosis was found on later chest computed tomography images in 51.5% of the pneumonia cases. Imported and second-generation cases outside Wuhan had a better prognosis than initial cases in Wuhan. Lymphocyte count and IL-6 level could be used for evaluating prognosis. Pulmonary fibrosis as the sequelae of COVID-19 should be taken into account.

Tuberculosis (TB) is one of the top 10 leading causes of morbidity and mortality worldwide [1]. In 2017, approximately 10 million people were infected with TB and 1.3 million patients faced mortality [1]. Patients with active TB can infect up to 10–15 people over a year. There is a greater risk of transmission in overcrowded areas with limited air ventilation including large family units, prisons and slums [1, 2]. Without proper diagnosis and treatment, roughly 45% of non-HIV positive TB patients face mortality [1]. With the help of global organizations and national TB treatment and control programmes, the global incidence of TB is declining by approximately 2% each year [1]. The World Health Organization (WHO) TB-strategy aims to end the TB epidemic and encourages partners to fund national TB programmes to improve diagnosis and treatment of TB. The goal is to ultimately decrease death rates by 90% and decrease incidence rates by 80% [1]. To achieve these goals, the decline in TB incidence needs to reach approximately 4–5% per year [1]. The WHO 2018 TB report identified multidrug resistant TB (MDR-TB) as the leading factor hindering that goal [1]. The incidence and spread of MDR-TB has drastically increased, where approximately 558 000 new cases of MDR-TB were diagnosed in 2017 causing more than 230 000 deaths globally [1]. MDR-TB is identified by resistance to the two most powerful anti-TB treatment drugs including isoniazid and rifampicin [3]. Patients with MDR-TB are required to start second-line anti-TB drugs (SLDs), which are limited, expensive, less effective and more toxic [1,2]. Therapy duration is one of the major limitations of second-line treatments, which may require up to two years of consistent use. Since TB affects mostly developing countries, long treatment durations and associated costs become a major challenge. In 2015, 15% of new TB cases were reported as MDR-TB, which drastically increased to 24% by 2017 [1]. Even with significant improvements in molecular tests and diagnostic methods, MDR-TB is still on the rise where the success rate of treatments is between 50 and 60% [1]. Additional characteristics including socioeconomic and sociocultural factors need to be considered when targeting and treating patients with MDR-TB.

Antibiotic-resistant Gram-negative bacteraemias (GNB) are increasing in incidence. We aimed to investigate the impact of empirical antibiotic therapy on clinical outcomes by carrying out an observational 6-year cohort study of patients at a teaching hospital with community-onset Escherichia coli bacteraemia (ECB), Klebsiella pneumoniae bacteraemia (KPB) and Pseudomonas aeruginosa bacteraemia (PsAB). Antibiotic therapy was considered concordant if the organism was sensitive in vitro and discordant if resistant. We estimated the association between concordant vs. discordant empirical antibiotic therapy on odds of in-hospital death and ICU admission for KPB and ECB. Of 1380 patients, 1103 (79.9%) had ECB, 189 (13.7%) KPB and 88 (6.4%) PsAB. Discordant therapy was not associated with increased odds of either outcome. For ECB, severe illness and non-urinary source were associated with increased odds of both outcomes (OR of in-hospital death for non-urinary source 3.21, 95% CI 1.73–5.97). For KPB, discordant therapy was associated with in-hospital death on univariable but not multivariable analysis. Illness severity was associated with increased odds of both outcomes. These findings suggest broadening of therapy for low-risk patients with community-onset GNB is not warranted. Future research should focus on the relationship between patient outcomes, clinical factors, infection focus and causative organism and resistance profile.

The Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a public health emergency of international concern. The current study aims to explore whether the neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) are associated with the development of death in patients with COVID-19. A total of 131 patients diagnosed with COVID-19 from 13 February 2020 to 14 March 2020 in a hospital in Wuhan designated for treating COVID-19 were enrolled in the current study. These 131 patients had a median age of 64 years old (interquartile range: 56–71 years old). Furthermore, among these patients, 111 (91.8%) patients were discharged and 12 (9.2%) patients died in the hospital. The pooled analysis revealed that the NLR at admission was significantly elevated for non-survivors, when compared to survivors (P< 0.001). The NLR of 3.338 was associated with all-cause mortality, with a sensitivity of 100.0% and a specificity of 84.0% (area under the curve (AUC): 0.963, 95% confidence interval (CI) 0.911–1.000;P< 0.001). In view of the small number of deaths (n= 12) in the current study, NLR of 2.306 might have potential value for helping clinicians to identify patients with severe COVID-19, with a sensitivity of 100.0% and a specificity of 56.7% (AUC: 0.729, 95% CI 0.563–0.892;P= 0.063). The NLR was significantly associated with the development of death in patients with COVID-19. Hence, NLR is a useful biomarker to predict the all-cause mortality of COVID-19.

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.

Another large outbreak of mumps occurred in Lothian from October 2017, which coincided with the commencement of the higher education term. During this period 324 cases were notified, most of whom were aged 18–22 years old. Although previous outbreaks had a focus in student populations, 43% of current cases reported that they were not a student. There has been increases in private student housing where students from all universities live, which may have contributed to the wide spread of the outbreak and complicated outbreak control. Information on vaccination status was available for 244 cases (75%), of whom the majority (75.8%) reported having two MMR doses. To investigate potential waning vaccine immunity the mean length of time since last mumps containing vaccine was calculated as 14.3 years. The outbreak was declared over in May 2018 after case numbers returned to background levels. This outbreak highlighted that mumps outbreaks occur cyclically coinciding with new cohorts of susceptible students entering the Lothian population. The lessons from this outbreak are to encourage students to have two MMR doses and also be prepared for mumps outbreaks in the near future. In future outbreaks the utility of a third MMR for outbreak control could be examined.

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.

Although patients with end-stage renal disease (ESRD) are known to be at high risk for developing bloodstream infections (BSI), the risk associated with lesser degrees of renal dysfunction is not well defined. We sought to determine the risk for acquiring and dying from community-onset BSIs among patients with renal dysfunction. A retrospective, population-based cohort study was conducted among adult residents without ESRD in the western interior of British Columbia. Estimated glomerular filtration rates (eGFR) were determined for cases and incidence rate ratios (IRR) were calculated using prevalence estimates. Overall, 1553 episodes of community-onset BSI were included of which 39%, 32%, 17%, 9%, 2% and 1% had preceding eGFRs of ≥90, 60–89, 45–59, 30–44, 15–29 and 2, respectively. As compared to those with eGFR ≥60 ml/min/m2, patients with eGFR 30–59 ml/min/m2(IRR 4.4; 95% confidence interval (CI) 3.9–4.9) and eGFR 2(IRR 7.0; 95% CI 5.0–9.5) were at significantly increased risk for the development of community-onset BSI. An eGFR 2was an independent risk factor for death (odds ratio 2.3; 95% CI 1.01–5.15). Patients with renal dysfunction are at increased risk for developing and dying from community-onset BSI that is related to the degree of dysfunction.

This study presents enhanced surveillance data from 2004 to 2018 for all community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) specimens collected in Western Australia (WA), and describes the changing epidemiology over this period. A total of 57 557 cases were reviewed. Annual incidence rates increased from 86.2 cases per 100 000 population to 245.6 per 100 000 population (IRR = 2.9, CI95 2.7–3.0). The proportion of isolates carrying Panton–Valentine leucocidin (PVL)-associated genes increased from 3.4% to 59.8% (χ2 test for trend 7021.9, P < 0.001). The emergence of PVL-positive, ‘Queensland CA-MRSA’ (ST93-IV) and ‘WA 121’ (ST5-IV) accounted for the majority of increases in CA-MRSA across the study period. It is unclear why some clones are more prolific in certain regions. In WA, CA-MRSA rates increase as indices of temperature and humidity increase after controlling for socioeconomic disadvantage. We suggest climatic conditions may contribute to transmission, along with other socio-behavioural factors. A better understanding of the ability for certain clones to form ecological niches and cause outbreaks is required.