In daycare centres, the close contact of children with other children and employees favours the transmission of infections. The majority of children <6 years attend daycare programmes in Germany, but the role of daycare centres in the SARS-CoV-2 pandemic is unclear. We investigated the transmission risk in daycare centres and the spread of SARS-CoV-2 to associated households. 30 daycare groups with at least one recent laboratory-confirmed SARS-CoV-2 case were enrolled in the study (10/2020–06/2021). Close contact persons within daycare and households were examined over a 12-day period (repeated SARS-CoV-2 PCR tests, genetic sequencing of viruses, symptom diary). Households were interviewed to gain comprehensive information on each outbreak. We determined primary cases for all daycare groups. The number of secondary cases varied considerably between daycare groups. The pooled secondary attack rate (SAR) across all 30 daycare centres was 9.6%. The SAR tended to be higher when the Alpha variant was detected (15.9% vs. 5.1% with evidence of wild type). The household SAR was 53.3%. Exposed daycare children were less likely to get infected with SARS-CoV-2 than employees (7.7% vs. 15.5%). Containment measures in daycare programmes are critical to reduce SARS-CoV-2 transmission, especially to avoid spread to associated households.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, first notified in China, has spread around the world causing high morbidity and mortality, which is due to factors such as the subversion of the immune response. The aims of the study are to summarise and present the immunopathological relationship of COVID-19 with innate immunity. This is a systematic review conducted by the National Library of Medicine – National Institutes of Health, USA (PUBMED), Latin American and Caribbean Literature on Health Sciences (LILACS), Medical Literature Analysis and Retrieval System Online (MEDLINE) and Scientific Electronic Library Online (SCIELO) databases with clinical trials, in vitro assays, case-controls, cohort studies, systematic reviews and meta-analyses between February 2020 and July 2021. The version 2 of the Cochrane risk-of-bias tool for RCTs (RoB 2), Joana Briggs Institute (JBI) Critical Appraisal (for the review articles) and the Risk of Bias in Non-randomised Studies of Interventions (ROBINS-I) tools were used to evaluate the quality and the risk of bias of the studies included in this review. The innate immune response through the generation of interferons, alternative pathways and complement system lectins and the joint action of innate immune cells and cytokines and chemokines lead to different clinical outcomes, taking into account the exacerbated inflammatory response and pathogenesis. Then, in addition to interacting as a bridge for adaptive immunity, the innate immune response plays an essential role in primary defense and is one of the starting points for immune evasion by SARS-CoV-2.

In October 2021, the WHO published an ambitious strategy to ensure that all countries had vaccinated 40% of their population by the end of 2021 and 70% by mid-2022. The end of June 2022 marks 18 months of implementation of coronavirus disease 2019 (COVID-19) vaccination in the African region and provides an opportunity to look back and think ahead about COVID-19 vaccine set targets, demand and delivery strategies. As of 26 June 2022 two countries in the WHO African region have achieved this target (Mauritius and Seychelles) and seven are on track, having vaccinated between 40% and 69% of their population. By the 26 June 2022, seven among the 20 countries that had less than 10% of people fully vaccinated at the end of January 2022, have surpassed 15% of people fully vaccinated at the end of June 2022. This includes five targeted countries, which are being supported by the WHO Regional Office for Africa through the Multi-Partners' Country Support Team Initiative. As we enter the second semester of 2022, a window of opportunity has opened to provide new impetus to COVID-19 vaccination rollout in the African region guided by the four principles: Scale-up, Transition, Consolidation and Communication. Member States need to build on progress made to ensure that this impetus is not lost and that the African region does not remain the least vaccinated global region, as economies open up and world priorities change.

Natural infection with the influenza virus is believed to generate cross-protective immunity across both types and subtypes. However, less is known about the persistence of this immunity and thus the susceptibility of individuals to repeat infection. We used 13 years (2005–2017) of surveillance data from Queensland, Australia, to describe the incidence and distribution of repeat influenza infections. Consecutive infections that occurred within 14 days of prior infection were considered a mixed infection; those that occurred more than 14 days later were considered separate (repeat) infections. Kaplan-Meier plots were used to investigate the probability of reinfection over time and the Prentice, Williams and Peterson extension of the Cox proportional hazards model was used to assess the association of age and gender with reinfection. Among the 188 392 notifications received during 2005–2017, 6165 were consecutively notified for the same individual (3.3% of notifications), and 2958 were mixed infections (1.6%). Overall, the probability of reinfection was low: the cumulative incidence was <1% after one year, 4.6% after five years, and 9.6% after ten years. The majority of consecutive infections were the result of two type A infections (43%) and were most common among females (adjusted hazard ratio (aHR): 1.15, 95% confidence interval (CI) 1.09–1.21), children aged less than 5 years (relative to adults aged 18–64 years aHR: 1.58, 95% CI 1.47–1.70) and older adults aged at least 65 years (aHR: 1.35; 95% CI 1.24–1.47). Our study suggests consecutive infections are possible but rare. These findings have implications for our understanding of population immunity to influenza.

This paper uses a robust method of spatial epidemiological analysis to assess the spatial growth rate of multiple lineages of SARS-CoV-2 in the local authority areas of England, September 2020–December 2021. Using the genomic surveillance records of the COVID-19 Genomics UK (COG-UK) Consortium, the analysis identifies a substantial (7.6-fold) difference in the average rate of spatial growth of 37 sample lineages, from the slowest (Delta AY.4.3) to the fastest (Omicron BA.1). Spatial growth of the Omicron (B.1.1.529 and BA) variant was found to be 2.81× faster than the Delta (B.1.617.2 and AY) variant and 3.76× faster than the Alpha (B.1.1.7 and Q) variant. In addition to AY.4.2 (a designated variant under investigation, VUI-21OCT-01), three Delta sublineages (AY.43, AY.98 and AY.120) were found to display a statistically faster rate of spatial growth than the parent lineage and would seem to merit further investigation. We suggest that the monitoring of spatial growth rates is a potentially valuable adjunct to outbreak response procedures for emerging SARS-CoV-2 variants in a defined population.

Tuberculosis is a major public health issue in Yemen, a country located at the southwestern tip of the Arabian Peninsula, while the situation of tuberculosis had been further exacerbated since the war started in 2015. The objective of this study is to investigate the incidence of tuberculosis in Yemen before the outbreak of COVID-19, from 2006 to 2018. During the 13-year period, 92 482 patients were enrolled in the TB programme records from the 22 governorates. Almost equal number of cases were diagnosed between males and females (a male to female ratio, 1.03:1). A notable rising incidence was observed in all age groups starting from 2011. The sharpest increase occurred in children under age 15, rising by 8.0-fold from 0.5 in the period 2006–2010 to 4.1 in the period 2011–2018. Paediatric TB accounted for 9.6% of all reported cases. In terms of the patient residence, incidence has more than doubled in Sana'a city, Sana'a Gov., Hajjah and Saadah. Concomitant diseases with tuberculosis included diabetes mellitus (14.0%), brucellosis (6.1%), hepatitis (6.0%), rheumatoid arthritis (4.3%), renal disorders (2.5%) and HIV infection (2.5%). Development of interventions to reduce tuberculosis incidence in children and concomitant communicable diseases is urgently needed.

Hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) is a severe and life-threatening complication, characterised by multi-organ failure and high short-term mortality. However, there is limited information on the impact of various comorbidities on HBV-ACLF in a large population. This study aimed to investigate the relationship between comorbidities, complications and mortality. In this retrospective observational study, we identified 2166 cases of HBV-ACLF hospitalised from January 2010 to March 2018. Demographic data from the patients, medical history, treatment, laboratory indices, comorbidities and complications were collected. The mortality rate in our study group was 47.37%. Type 2 diabetes mellitus was the most common comorbidity, followed by alcoholic liver disease. Spontaneous bacterial peritonitis, pneumonia and hepatic encephalopathy (HE) were common in these patients. Diabetes mellitus and hyperthyroidism are risk factors for death within 90 days, together with gastrointestinal bleeding and HE at admission, HE and hepatorenal syndrome during hospitalisation. Knowledge of risk factors can help identify HBV-ACLF patients with a poor prognosis for HBV-ACLF with comorbidities and complications.

Resistance to carbapenems in human pathogens is a growing clinical and public health concern. The carbapenems are in an antimicrobial class considered last-resort, they are used to treat human infections caused by multidrug-resistant Enterobacterales, and they are classified by the World Health Organization as ‘High Priority Critically Important Antimicrobials’. The presence of carbapenem-resistant Enterobacterales (CREs) of animal-origin is of concern because targeted studies of Canadian retail seafood revealed the presence of carbapenem resistance in a small number of Enterobacterales isolates. To further investigate this issue, a risk profile was developed examining shrimp and salmon, the two most important seafood commodities consumed by Canadians and Escherichia coli, a member of the Enterobacterales order. Carbapenem-resistant E. coli (CREc) isolates have been identified in shrimp and other seafood products. Although carbapenem use in aquaculture has not been reported, several classes of antimicrobials are utilised globally and co-selection of antimicrobial-resistant microorganisms in an aquaculture setting is also of concern. CREs have been identified in retail seafood purchased in Canada and are currently thought to be uncommon. However, data concerning CRE or CREc occurrence and distribution in seafood are limited, and argue for implementation of ongoing or periodic surveillance.

Hepatitis E is an increasingly serious worldwide public health problem that has attracted extensive attention. It is necessary to accurately predict the incidence of hepatitis E to better plan ahead for future medical care. In this study, we developed a Bi-LSTM model that incorporated meteorological factors to predict the prevalence of hepatitis E. The hepatitis E data used in this study are collected from January 2005 to March 2017 by Jiangsu Provincial Center for Disease Control and Prevention. ARIMA, GBDT, SVM, LSTM and Bi-LSTM models are adopted in this study. The data from January 2009 to September 2014 are used as the training set to fit models, and data from October 2014 to March 2017 are used as the testing set to evaluate the predicting accuracy of different models. Selecting models and evaluating the effectiveness of the models are based on mean absolute per cent error (MAPE), root mean square error (RMSE) and mean absolute error (MAE). A total of 44 923 cases of hepatitis E are detected in Jiangsu Province from January 2005 to March 2017. The average monthly incidence rate is 0.35 per 100 000 persons in Jiangsu Province. Incorporating meteorological factors of temperature, water vapour pressure, and rainfall as a combination into the Bi-LSTM Model achieved the state-of-the-art performance in predicting the monthly incidence of hepatitis E, in which RMSE is 0.044, MAPE is 11.88%, and MAE is 0.0377. The Bi-LSTM model with the meteorological factors of temperature, water vapour pressure, and rainfall can fully extract the linear and non-linear information in the hepatitis E incidence data, and has significantly improved the interpretability, learning ability, generalisability and prediction accuracy.

While incidence studies based on hospitalisation counts are commonly used for public health decision-making, no standard methodology to define hospitals' catchment population exists. We conducted a review of all published community-acquired pneumonia studies in England indexed in PubMed and assessed methods for determining denominators when calculating incidence in hospital-based surveillance studies. Denominators primarily were derived from census-based population estimates of local geographic boundaries and none attempted to determine denominators based on actual hospital access patterns in the community. We describe a new approach to accurately define population denominators based on historical patient healthcare utilisation data. This offers benefits over the more established methodologies which are dependent on assumptions regarding healthcare-seeking behaviour. Our new approach may be applicable to a wide range of health conditions and provides a framework to more accurately determine hospital catchment. This should increase the accuracy of disease incidence estimates based on hospitalised events, improving information available for public health decision making and service delivery planning.

Soil-transmitted helminths, such as Ascaris lumbricoides, are the most prevalent parasites globally. Optimal anthelmintic treatment for A. lumbricoides in endemically infected communities is challenged by several host-related and environmental factors influencing infection acquisition. We assessed the risk of A. lumbricoides (re)infection after treatment in a Venezuelan rural community. Individual merthiolate-iodine-formaldehyde-fixed faecal samples were collected from 224 persons before a single-dose pyrantel treatment and at 1, 3, 6, 9 and 15 months after treatment. Effects of age, sex and socioeconomic status (SES) on A. lumbricoides prevalence, eggs/gram faeces (EPG) and infection (re)acquisition were assessed using both generalised linear mixed-effects models and survival analysis. Pre-treatment A. lumbricoides prevalence was 39.7%. Higher prevalence was associated with younger age and lower SES. Higher EPG values were observed among young children. Median time to A. lumbricoides infection was six months after treatment: at 1, 3, 6, 9 and 15 months post-treatment, cumulative incidence was 6.7%, 18.9%, 34.6%, 42.2%, and 52.6%, respectively. Younger age, lower SES, and pre-treatment A. lumbricoides infection status showed significantly elevated hazard ratios. Mass drug administration protocols would benefit from considering these factors in selective treatment strategies and possibly more than just annual or biannual treatments in the target population.

Approximately one-quarter of annual global cervical cancer deaths occur in India, possibly due to cultural norms promoting vaccine hesitancy. We sought to determine whether people of Indian ancestry (POIA) in the USA exhibit disproportionately lower human papilloma virus (HPV) vaccination rates than the rest of the US population. We utilised the 2018 National Health Interview Survey to compare HPV vaccine initiation and completion rates between POIA and the general US population and determined factors correlating with HPV vaccine uptake among POIA. Compared to other racial groups, POIA had a significantly lower rate of HPV vaccination (8.18% vs. 12.16%, 14.70%, 16.07% and 12.41%, in White, Black, Other Asian and those of other/mixed ancestry, respectively, P = 0.003), but no statistically significant difference in vaccine series completion among those who received at least one injection (3.17% vs. 4.27%, 3.51%, 4.31% and 5.04%, P = 0.465). Among POIA, younger individuals (vs. older), single individuals (vs. married), those with high English proficiency (vs. low English proficiency), those with health insurance and those born in the USA (vs. those born outside the USA) were more likely to obtain HPV vaccination (P = 0.018, P = 0.006, P = 0.029, P = 0.020 and P = 0.019, respectively). Public health measures promoting HPV vaccination among POIA immigrants may substantially improve vaccination rates among this population.

Antimicrobial resistance (AMR) is a complex problem that is a threat to global public health. Consumption of turkey meat may be an important source of foodborne exposure to resistant bacteria; recent outbreaks of multi-drug-resistant Salmonella Reading in Canada and the USA have implicated raw turkey products. To better understand the epidemiology of AMR in farmed turkey production, a scoping review was conducted. The objectives were to identify (1) modifiable factors potentially associated with antimicrobial-resistant Campylobacter, Enterococcus, Escherichia coli and Salmonella enterica along the farm-to-fork pathway in turkeys, and (2) data gaps with respect to factors potentially associated with AMR and Canadian commercial turkey production. A comprehensive search of the peer-reviewed literature was conducted in 2019 and updated in 2021. Thirteen references were included, reporting 36 factors. Antimicrobial use factors and their potential associations with AMR were most frequently reported (n = 15 factors; 42%), followed by biosecurity (n = 11; 31%) and management practices (n = 10; 28%). This review revealed important data gaps; no factors pertaining to S. enterica or to stages other than the farm (e.g. abattoir, retail) were identified, and only one Canadian reference was identified. These findings will inform priorities for future research and surveillance regarding turkeys and AMR.

In March 2018, the US Food and Drug Administration (FDA), US Centers for Disease Control and Prevention, California Department of Public Health, Los Angeles County Department of Public Health and Pennsylvania Department of Health initiated an investigation of an outbreak of Burkholderia cepacia complex (Bcc) infections. Sixty infections were identified in California, New Jersey, Pennsylvania, Maine, Nevada and Ohio. The infections were linked to a no-rinse cleansing foam product (NRCFP), produced by Manufacturer A, used for skin care of patients in healthcare settings. FDA inspected Manufacturer A's production facility (manufacturing site of over-the-counter drugs and cosmetics), reviewed production records and collected product and environmental samples for analysis. FDA's inspection found poor manufacturing practices. Analysis by pulsed-field gel electrophoresis confirmed a match between NRCFP samples and clinical isolates. Manufacturer A conducted extensive recalls, FDA issued a warning letter citing the manufacturer's inadequate manufacturing practices, and federal, state and local partners issued public communications to advise patients, pharmacies, other healthcare providers and healthcare facilities to stop using the recalled NRCFP. This investigation highlighted the importance of following appropriate manufacturing practices to minimize microbial contamination of cosmetic products, especially if intended for use in healthcare settings.

Healthcare-associated infection (HAI) is a major cause of morbidity, mortality and cost, which vary widely by region and hospital. In this case-control study, we calculated losses attributable to HAI in central China. A total of 2976 patients in 10 hospitals were enrolled, and the incidence rate of HAI (range, 0.88–4.15%) was significantly, but negatively associated with the cost per 1000 beds of its prevention (range, $24 929.76–$53 146.41; r = −0.76). The per capita economic loss attributable to HAIs was $2047.07 (interquartile range, $327.63–$6429.17), mainly from the pharmaceutical cost (median, $1044.39). The HAIs, which occurred in patients with commercial medical insurance, affected the haematologic system and caused by Acinetobacter baumannii, contributed most to the losses (median, $3881.55, $4734.20 and $9882.75, respectively). Furthermore, the economic losses attributable to device-associated infections and hospital-acquired multi-drug resistant bacteria were two to four times those of the controls. The burden attributable to HAI is heavy, and opportunities for easing this burden exist in several areas, including that strengthening antibiotic stewardship and practicing effective bundle of HAI prevention for patients carrying high-risk factors, for example, elders or those with catheterisations in healthcare institutions, and accelerating the medical insurance payment system reform based on diagnosis-related groups by policy-making departments.

Human immunodeficiency virus (HIV) has been widely prevalent among older men (aged ≥50 years old) in Sichuan Province. The study aimed to discover associated factors with the new HIV infection in older men, and provide a scientific basis for the prevention and control of acquired immunodeficiency syndrome (AIDS) in this group. A cross-sectional survey study of newly reported HIV/AIDS and general male residents aged 50 years and older was conducted between April and June 2019, with a resample of respondents to identify cases and controls, followed by a case–control study. Logistic regression was applied to analyse the association between the selected factors and new HIV infection among older men. At last, 242 cases and 968 controls were included. The results of multiple logistic regression suggested that many factors including living alone/concentrated (OR 1.56, 95% CI 1.20–2.04, P = 0.001), have a history of migrant worker (OR 2.10, 95% CI 1.61–2.73, P < 0.001), have commercial sexual behaviour (OR 1.71, 95% CI 1.32–2.22, P < 0.001), married (OR 0.48, 95% CI 0.37–0.64, P < 0.001), have a history of HIV antibody testing (OR 0.73, 95% CI 0.56–0.96, P = 0.026), HIV-related knowledge (OR 0.55, 95% CI 0.42–0.72, P < 0.001) were associated with new HIV infection among older men. The present study revealed some potential risky/protective factors altogether. The results highlighted the direction of HIV/AIDS prevention and control among older men, and it is a social issue that requires the joint participation of the whole society.

We examined the possible sex and age differences in the proportion of experienced Coronavirus Disease 2019 (COVID-19) symptoms in unaware (previously) infected adults, and their uninfected counterparts, estimated by serostatus prior to vaccination, at the end of 2020 (Wuhan strain). A cross-sectional community-based study using a convenience sample of 10 001 adult inhabitants of a southern Dutch province, heavily affected by COVID-19, was conducted. Participants donated a blood sample to indicate past infection by serostatus (positive/negative). Experienced symptoms were assessed by questionnaire, before the availability of the serological test result. Only participants without confirmed SARS-CoV-2 infection were included (n = 9715, age range 18–90 years). The seroprevalence was comparable between men (17.3%) and women (18.0%), and participants aged 18–60 years (17.3%) and aged 60 years and older (18.6%). We showed sex and age differences in the proportion experienced symptoms by serostatus in a large cohort of both unaware (untested) seropositive compared with seronegative reference participants. Irritability only differed by serostatus in men (independent of age), while stomach ache, nausea and dizziness only differed by serostatus in women aged 60 years and older. Besides, the proportion of experiencing pain when breathing and headache differed by serostatus in men aged 18–60 years only. Our study highlights the importance of taking possible sex and age differences into account with respect to acute and long-term COVID-19 outcomes. Identifying symptom profiles for sex and age subgroups can contribute to timely identification of infection, gaining importance once governments currently move away from mass testing again.

Our study aimed to investigate the epidemiology of extrapulmonary tuberculosis (EPTB) and analyse the epidemiological characteristics of EPTB patients with or without pulmonary tuberculosis (PTB). EPTB cases admitted in our hospital from January 2015 to December 2020 were included. Uni- and multi-variable logistic regression analysis was carried out to identify risk factors and prognostic factors of concomitant EPTB and PTB or exclusively EPTB. A total of 3488 EPTB patients were reviewed, including 2086 patients with concurrent PTB and EPTB, and 1402 patients with exclusively EPTB. Logistic regression analysis showed that age >60 years (OR = 1.674, 95% CI = 1.438–1.949, P < 0.001) and female (OR = 1.325, 95% CI = 1.155–1.520, P < 0.001) were risk factors of exclusively EPTB, while co-morbidities (OR = 0.676, 95% CI = 0.492–0.929, P = 0.016) and severe symptoms (OR = 0.613, 95% CI = 0.405–0.929, P = 0.021) were risk factors for concurrence of EPTB and PTB. Age >60 years was an independent prognostic factor in EPTB patients with or without PTB (HR = 11.059, 95%CI = 5.097–23.999, P < 0.001; HR = 23.994, 95%CI = 3.093–186.151, P = 0.0020). Female gender was an independent prognostic factor in patients with concurrent PTB and EPTB (HR = 23.994, 95%CI = 3.093–186.151, P = 0.002). Our study disclosed the differential epidemiological characteristics of EPTB patients with or without PTB in China.

We recently described a simple model through which we assessed what effect subjecting travellers to a single on-arrival test might have on reducing risk of importing disease cases during simulated outbreaks of coronavirus disease 2019 (COVID-19), influenza, severe acute respiratory syndrome (SARS) and Ebola. We build upon this work to allow for the additional requirement that inbound travellers also undergo a period of self-isolation upon arrival, where upon completion the traveller is again tested for signs of infection prior to admission across the border. Prior results indicated that a single on-arrival test has the potential to detect 9% of travellers infected with COVID-19, compared to 35%, 10% and 3% for travellers infected with influenza, SARS and Ebola, respectively. Our extended model shows that testing administered after a 2-day isolation period could detect up to 41%, 97%, 44% and 15% of COVID-19, influenza, SARS and Ebola infected travellers, respectively. Longer self-isolation periods increase detection rates further, with an 8-day self-isolation period suggesting detection rates of up to 94%, 100%, 98% and 62% for travellers infected with COVID-19, influenza, SARS and Ebola, respectively. These results therefore suggest that testing arrivals after an enforced period of self-isolation may present a reasonable method of protecting against case importation during international outbreaks.

Patient-important outcomes related to coronavirus disease 2019 (COVID-19) continue to drive the pandemic response across the globe. Various prognostic factors for COVID-19 severity have emerged and their replication across different clinical settings providing health services is ongoing. We aimed to describe the clinical characteristics and their association with outcomes in patients hospitalised with COVID-19 in the University Hospital of Ioannina. We assessed a cohort of 681 consecutively hospitalised patients with COVID-19 from January 2020 to December 2021. Demographic data, underlying comorbidities, clinical presentation, biochemical markers, radiologic findings, COVID-19 treatment and outcome data were collected at the first day of hospitalisation and up to 90 days. Multivariable Cox regression analyses were performed to investigate the associations between clinical characteristics (hazard ratios (HRs) per standard deviation (s.d.)) with intubation and/or mortality status. The participants' mean age was 62.8 (s.d., 16.9) years and 57% were males. The most common comorbidities were hypertension (45%), cardiovascular disease (19%) and diabetes mellitus (21%). Patients usually presented with fever (81%), cough (50%) and dyspnoea (27%), while lymphopenia and increased inflammatory markers were the most common laboratory abnormalities. Overall, 55 patients (8%) were intubated, and 86 patients (13%) died. There were statistically significant positive associations between intubation or death with age (HR: 2.59; 95% CI 1.52–4.40), lactate dehydrogenase (HR: 1.44; 95% CI 1.04–1.98), pO2/FiO2 ratio < 100 mmHg (HR: 3.52; 95% CI 1.14–10.84), and inverse association with absolute lymphocyte count (HR: 0.54; 95% CI 0.33–0.87). These data might help to identify points for improvement in the management of COVID-19 patients.