SARS-CoV-2 rapidly spreads among humans via social networks, with social mixing and network characteristics potentially facilitating transmission. However, limited data on topological structural features has hindered in-depth studies. Existing research is based on snapshot analyses, preventing temporal investigations of network changes. Comparing network characteristics over time offers additional insights into transmission dynamics. We examined confirmed COVID-19 patients from an eastern Chinese province, analyzing social mixing and network characteristics using transmission network topology before and after widespread interventions. Between the two time periods, the percentage of singleton networks increased from 38.9$ \% $ to 62.8$ \% $$ (p<0.001) $; the average shortest path length decreased from 1.53 to 1.14 $ (p<0.001) $; the average betweenness reduced from 0.65 to 0.11$ (p<0.001) $; the average cluster size dropped from 4.05 to 2.72 $ (p=0.004) $; and the out-degree had a slight but nonsignificant decline from 0.75 to 0.63 $ (p=0.099). $ Results show that nonpharmaceutical interventions effectively disrupted transmission networks, preventing further disease spread. Additionally, we found that the networks’ dynamic structure provided more information than solely examining infection curves after applying descriptive and agent-based modeling approaches. In summary, we investigated social mixing and network characteristics of COVID-19 patients during different pandemic stages, revealing transmission network heterogeneities.

We conducted a retrospective cross-sectional population-based survey among recovered COVID-19 cases in Uganda to establish the case presentations of the second wave SARS-CoV-2 infections. We interviewed 1,120 recovered COVID-19 cases from 10 selected districts in Uganda. We further conducted 38 key informant interviews with members of the COVID-19 District Taskforce and 19 in-depth interviews among COVID-19 survivors from March to June 2021. Among them, 62% were aged 39 years and below and 51.5% were female with 90.9% under home-based care management. Cases were more prevalent among businesspeople (25.9%), students (16.2%), farmers (16.1%), and health workers (12.4%). Being asymptomatic was found to be associated with not seeking healthcare (APR 2, P < 0.001). The mortality rate was 3.6% mostly among the elderly (6.3%) and 31.3% aged 40 years and above had comorbidities of high blood pressure, diabetes, and asthma. Being asymptomatic, or under home-based care management (HBCM), working/operating/studying at schools, and not being vaccinated were among the major drivers of the second wave of the resurgence of COVID19 in Uganda. Managing future COVID-19 waves calls for proactive efforts for improving homebased care services, ensuring strict observation of SOPs in schools, and increasing the uptake of COVID-19 vaccination.

Bacterial antimicrobial resistance (AMR) is among the leading global health challenges of the century. Animals and their products are known contributors to the human AMR burden, but the extent of this contribution is not clear. This systematic literature review aimed to identify studies investigating the direct impact of animal sources, defined as livestock, aquaculture, pets, and animal-based food, on human AMR. We searched four scientific databases and identified 31 relevant publications, including 12 risk assessments, 16 source attribution studies, and three other studies. Most studies were published between 2012 and 2022, and most came from Europe and North America, but we also identified five articles from South and South-East Asia. The studies differed in their methodologies, conceptual approaches (bottom-up, top-down, and complex), definitions of the AMR hazard and outcome, the number and type of sources they addressed, and the outcome measures they reported. The most frequently addressed animal source was chicken, followed by cattle and pigs. Most studies investigated bacteria–resistance combinations. Overall, studies on the direct contribution of animal sources of AMR are rare but increasing. More recent publications tailor their methodologies increasingly towards the AMR hazard as a whole, providing grounds for future research to build on.

In Beijing, the capital of China, routine measles mass vaccination has been in place for decades with high coverage; and since the 2000s, catch-up vaccination programmes have been implemented for migrant workers coming to the city. However, measles epidemics in Beijing persisted. Here, we explored the contributing factors of persistent measles transmission in Beijing using an epidemic model in conjunction with a particle filter. Model inputs included data on birth, death, migration, and vaccination. We formulated a series of hypotheses covering the impact of migrant influx, early waning of maternal immunity, and increased mixing among infants; we compared the plausibility of the hypotheses based on model fit to age-grouped, weekly measles incidence data from January 2005 to December 2014, and out-of-fit prediction during 2015–2019. Our best models showed close agreement with the data, and the out-of-fit prediction generally captured the trend of measles incidence from 2015 to 2019. We found that large influx of migrants with considerably higher susceptibility likely contributed to the persistent measles transmission in Beijing. Our findings suggest that stronger catch-up vaccination programmes for migrants may help eliminate measles transmission in Beijing.

Post COVID-19 condition (PCC) refers to persistent or recurring symptoms (>8 weeks) occurring ≤12 weeks following acute COVID-19. The objective of this systematic review was to assess the evidence on the risk of PCC with vaccination before or after COVID-19 or after developing PCC, and the safety of vaccination among those already experiencing PCC. A search was conducted up to 13 December 2022 and standard systematic review methodology was followed. Thirty-one observational studies were included. There is moderate confidence that two doses of vaccine given pre-infection reduced the odds of PCC (pooled OR (pOR) 0.67, 95% CI 0.60–0.74, I2 = 59.9%), but low confidence that one dose may not reduce the odds (pOR 0.64, 95% CI 0.31#x2013;1.31, I2 = 99.2%), and the evidence is very uncertain about the effect of three doses (pOR 0.45, 95% CI 0.10#x2013;1.99, I2 = 30.9%). One of three studies suggested vaccination shortly after COVID-19 may offer additional protection from developing PCC compared to unvaccinated individuals, but this evidence was very uncertain. For those with PCC, vaccination was not associated with worsening PCC symptoms (10 studies) and appears safe (3 studies), but it is unclear if vaccination may change established PCC symptoms.

Antifungal susceptibility of Candida species is decreasing. Successful treatment for antifungal-resistant candida infection is challenging and associated with significant mortality. We performed a prospective observational study to identify the species and antifungal susceptibilities of invasive isolates of Candida species over a 5-year period at a university hospital in southern Thailand. Between 2017 and 2021, the species distribution was 39.1% Candida tropicalis, 24.8% Candida albicans, 20.3% Candida parapsilosis complex, 10.5% Candida glabrata, and 5.2% miscellaneous Candida spp. Notable observations include elevated minimal inhibitory concentration (MIC) and decrease susceptibility of C. tropicalis and C. glabrata to echinocandin and all tested triazoles. A shift of MIC90 value in the COVID-19 era was seen in C. albicans and C. tropicalis with azoles and echinocandins. Azole resistance increased among C. tropicalis isolates, and echinocandin resistance also increased among C. parapsilosis and C. glabrata isolates. Novel alterations in FKS1 HS1 and HS2 were detected in both isolates of anidulafungin-resistant C. parapsilosis. As Candida species have become more resistant to azoles and less susceptible to echinocandin development, the need arose to observe the emergence of resistance to both antifungal classes in candida clinical isolates, for a more effective infection control in the hospital.

Stepwise non-pharmaceutical interventions and health system changes implemented as part of the COVID-19 response have had implications on the incidence, diagnosis, and reporting of other communicable diseases. Here, we established the impact of the COVID-19 outbreak response on gastrointestinal (GI) infection trends using routinely collected surveillance data from six national English laboratory, outbreak, and syndromic surveillance systems using key dates of governmental policy to assign phases for comparison between pandemic and historic data. Following decreases across all indicators during the first lockdown (March–May 2020), bacterial and parasitic pathogens associated with foodborne or environmental transmission routes recovered rapidly between June and September 2020, while those associated with travel and/or person-to-person transmission remained lower than expected for 2021. High out-of-season norovirus activity was observed with the easing of lockdown measures between June and October 2021, with this trend reflected in laboratory and outbreak systems and syndromic surveillance indicators. Above expected increases in emergency department (ED) attendances may have reflected changes in health-seeking behaviour and provision. Differential reductions across specific GI pathogens are indicative of the underlying routes of transmission. These results provide further insight into the drivers for transmission, which can help inform control measures for GI infections.

For many deaths associated with influenza and Omicron infections, those viruses are not detected. We applied previously developed methodology to estimate the contribution of influenza and Omicron infections to all-cause mortality in France for the 2014–2015 through the 2018–2019 influenza seasons, and the period between week 33, 2022 and week 12, 2023. For the 2014–2015 through the 2018–2019 seasons, influenza was associated with annual average of 15,654 (95% CI (13,013, 18,340)) deaths, while between week 33, 2022 and week 12, 2023, we estimated 7,851 (5,213, 10,463) influenza-associated deaths and 32,607 (20,794, 44,496) SARS-CoV-2 associated deaths. For many Omicron-associated deaths for cardiac disease, mental&behavioural disorders, and other causes, Omicron infections are not characterised as a contributing cause of death – for example, between weeks 33–52 in 2022, we estimated 23,983 (15,307, 32,620) SARS-CoV-2-associated deaths in France, compared with 12,811 deaths with COVID-19 listed on death certificate. Our results suggest the need for boosting influenza vaccination coverage in different population groups in France, and for wider detection of influenza infections in respiratory illness episodes (including pneumonia) in combination with the use of antiviral medications. For Omicron epidemics, wider detection of Omicron infections in persons with underlying health conditions is needed.

This study aimed to summarise the findings of the studies assessing the effectiveness of ultraviolet C (UV-C) room disinfection in reducing the incidence rate of healthcare-associated multi-drug-resistant organism (MDRO) infections. A systematic screening was conducted using PubMed, EMBASE, and Scopus for randomised controlled trials (RCTs), quasi-experimental studies, and before–after studies, which assessed the efficacy of the UV-C disinfectant system in reducing the incidence of MDRO infections. A random-effects model was used for the analysis. Effect sizes were described as incidence rate ratio (IRR) with 95% confidence intervals (CI). Nine studies were included, all of which were conducted in the USA. No statistically significant reduction in Clostridioides difficile (CD) (IRR: 0.90, 95% CI; 0.62–1.32) and vancomycin-resistant enterococcal (VRE) infection rates (IRR 0.72, 95% CI; 0.38–1.37) was observed with the use of UV-C, but the risk of Gram-negative rod infection was reduced (IRR 0.82, 95% CI; 0.68–0.99).

A foodborne outbreak related to milk cartons served in school lunches occurred in June 2021, which involved more than 1,800 cases from 25 schools. The major symptoms were abdominal pain, diarrhoea, vomiting, and fever. Although major foodborne toxins and pathogens were not detected, a specific Escherichia coli strain, serotype OUT (OgGp9):H18, was predominantly isolated from milk samples related to the outbreak and most patients tested. The strains from milk and patient stool samples were identified as the same clone by core genome multilocus sequence typing and single-nucleotide polymorphism analysis. The strain was detected in milk samples served for two days related to the foodborne outbreak at a rate of 69.6% and levels of less than ten most probable number/100 mL but not on days unrelated to the outbreak. The acid tolerance of the strain for survival in the stomach was similar to that of enterohaemorrhagic E. coli O157:H7, and the same inserts in the chu gene cluster in the acid fitness island were genetically revealed. The pathogenicity of the strain was not clear; however, it was indicated that the causative pathogen was atypical diarrhoeagenic E. coli OUT (OgGp9):H18.

Laboratory-based case confirmation is an integral part of measles surveillance programmes; however, logistical constraints can delay response. Use of RDTs during initial patient contact could enhance surveillance by real-time case confirmation and accelerating public health response. Here, we evaluate performance of a novel measles IgM RDT and assess accuracy of visual interpretation using a representative collection of 125 sera from the Brazilian measles surveillance programme. RDT results were interpreted visually by a panel of six independent observers, the consensus of three observers and by relative reflectance measurements using an ESEQuant Reader. Compared to the Siemens anti-measles IgM EIA, sensitivity and specificity of the RDT were 94.9% (74/78, 87.4–98.6%) and 95.7% (45/47, 85.5-99.5%) for consensus visual results, and 93.6% (73/78, 85.7–97.9%) and 95.7% (45/47, 85.5-99.5%), for ESEQuant measurement, respectively. Observer agreement, determined by comparison between individuals and visual consensus results, and between individuals and ESEQuant measurements, achieved average kappa scores of 0.97 and 0.93 respectively. The RDT has the sensitivity and specificity required of a field-based test for measles diagnosis, and high kappa scores indicate this can be accomplished accurately by visual interpretation alone. Detailed studies are needed to establish its role within the global measles control programme.

Turkeys are important sources of antimicrobial-resistant Campylobacter. A total of 1063 isolates were obtained from 293 turkey flocks across Canada between 2016 and 2021 to evaluate their antimicrobial resistance (AMR) prevalence, patterns, distribution, and association with antimicrobial use (AMU). A high proportion of C. jejuni and C. coli isolates were resistant to tetracyclines and fluoroquinolones, despite the very low use of these drugs. C. jejuni isolates had a higher probability of being resistant to tetracyclines than C. coli isolates. The chance of C. jejuni isolates being resistant to fluoroquinolones, macrolides, and lincosamides was lower compared to C. coli. Isolates from the western region had a higher probability of being resistant to fluoroquinolones than isolates from Ontario. Isolates from Ontario had higher odds of being resistant to tetracyclines than isolates from Quebec. No associations were noted between the resistance and use of the same antimicrobial, but the use of certain antimicrobial classes may have played a role in the maintenance of resistance in Campylobacter (fluoroquinolone resistance – bacitracin and streptogramin use, tetracycline resistance – flavophospholipids and streptogramins use, macrolide resistance – flavophospholipid use). Low-level multidrug-resistant Campylobacter was observed indicating a stable AMR in turkeys. This study provided insights aiding future AMU and AMR surveillance.

Scabies is a parasitic infestation with high global burden. Mass drug administrations (MDAs) are recommended for communities with a scabies prevalence of >10%. Quantitative analyses are needed to demonstrate the likely effectiveness of MDA recommendations. In this study, we developed an agent-based model of scabies transmission calibrated to demographic and epidemiological data from Monrovia. We used this model to compare the effectiveness of MDA scenarios for achieving scabies elimination and reducing scabies burden, as measured by time until recrudescence following delivery of an MDA and disability-adjusted-life-years (DALYs) averted. Our model showed that three rounds of MDA delivered at six-month intervals and reaching 80% of the population could reduce prevalence below 2% for three years following the final round, before recrudescence. When MDAs were followed by increased treatment uptake, prevalence was maintained below 2% indefinitely. Increasing the number of and coverage of MDA rounds increased the probability of achieving elimination and the number of DALYs averted. Our results suggest that acute reduction of scabies prevalence by MDA can support a transition to improved treatment access. This study demonstrates how modelling can be used to estimate the expected impact of MDAs by projecting future epidemiological dynamics and health gains under alternative scenarios.

Clostridium botulinum causes infant botulism by colonising the intestines and producing botulinum neurotoxin in situ. Previous reports have linked infant botulism cases to C. botulinum spores in household dust, yet the baseline incidence of C. botulinum spores in residential households is currently unknown. Vacuum cleaner dust from 963 households in 13 major Canadian cities was tested for C. botulinum using a novel real-time PCR assay directed against all known subtypes of the botulinum neurotoxin gene. None of the samples tested positive for C. botulinum. Analysis of a random subset of samples by MALDI Biotyper revealed that the most common anaerobic bacterial isolates were of the genus Clostridium and the most common species recovered overall was Clostridium perfringens. Dust that was spiked with C. botulinum spores of each toxin type successfully produced positive real-time PCR reactions. These control experiments indicate that this is a viable method for the detection of C. botulinum spores in household dust. We make several recommendations for future work that may help discover a common environmental source of C. botulinum spores that could lead to effective preventative measures for this rare but deadly childhood disease.

Longitudinal studies on the variations of phenotypic and genotypic characteristics of K. pneumoniae across two decades are rare. We aimed to determine the antimicrobial susceptibility and virulence factors for K. pneumoniae isolated from patients with bacteraemia or urinary tract infection (UTI) from 1999 to 2022. A total of 699 and 1,267 K. pneumoniae isolates were isolated from bacteraemia and UTI patients, respectively, and their susceptibility to twenty antibiotics was determined; PCR was used to identify capsular serotypes and virulence-associated genes. K64 and K1 serotypes were most frequently observed in UTI and bacteraemia, respectively, with an increasing frequency of K20, K47, and K64 observed in recent years. entB and wabG predominated across all isolates and serotypes; the least frequent virulence gene was htrA. Most isolates were susceptible to carbapenems, amikacin, tigecycline, and colistin, with the exception of K20, K47, and K64 where resistance was widespread. The highest average number of virulence genes was observed in K1, followed by K2, K20, and K5 isolates, which suggest their contribution to the high virulence of K1. In conclusion, we found that the distribution of antimicrobial susceptibility, virulence gene profiles, and capsular types of K. pneumoniae over two decades were associated with their clinical source.

The global prevalence and spread of multidrug-resistant organisms (MDROs) represent an emerging public health threat. Day care centre (DCC) attendance is a risk factor for MDRO carriage in children and their environment. This study aimed to map the epidemiology of carriage and potential transmission of these organisms within 18 Flemish DDCs (Belgium). An MDRO prevalence survey was organised between November 2018 and February 2019 among children attending the centres. Selective chromogenic culture media were used for the detection of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E), carbapenemase-producing Enterobacterales (CPE), and vancomycin-resistant Enterococci (VRE) in faecal swabs obtained from diapers or jars (n = 448). All isolated MDROs were subjected to resistance gene sequencing. A total of 71 of 448 samples (15.8%) yielded isolates of ESBL-E with a predominance of Escherichia coli (92.2% of ESBL-E) and ESBL resistance gene blaCTX-M-15 (50.7% of ESBL coding genes in E. coli). ESBL-E prevalence varied between DCCs, ranging from 0 to 50%. Transmission, based on the clonal relatedness of ESBL-E strains, was observed. CPE was identified in only one child carrying an E. coli with an OXA-244 gene. VRE was absent from all samples. The observed prevalence of ESBL-E in Flemish DCCs is high compared with previous studies, and our findings re-emphasise the need for rigorous hygiene measures within such centres to control the further spread of MDROs in the community.

Hepatitis E virus infection is a major cause of acute hepatitis, typically self-limiting but occasionally leading to liver failure. Understanding disease progression factors could inform prevention strategies. This study aimed to analyse the characteristics of a large cohort of hospitalised hepatitis E patients in Tianjin, China, and explore factors influencing their progression to liver failure. A total of 1279 hospitalised patients with hepatitis E were included in this cross-sectional study in Tianjin, China. Student's t-test and the Mann–Whitney U-test were used for comparisons. Multiple logistic regression analysis was used to explore the association. Among these 1279 patients, 107 (8.4%) developed liver failure. Patients with diabetes mellitus (DM) (95% confidence interval [CI] 1.150–2.887, p = 0.011), liver cirrhosis (95% [CI] 2.229–7.224, p < 0.001), and hepatitis B (95% [CI] 1.159–4.512, p = 0.017) were more likely to progress to liver failure. Hepatitis E patients with comorbid DM, liver cirrhosis, or hepatitis B virus co-infection have higher risks of developing liver failure. Hepatitis E vaccination may be recommended for these vulnerable patients to curb disease severity.

The SARS-CoV-2 pandemic persists with global repercussions. Initial COVID-19 symptoms encompass pneumonia, fever, myalgia, and fatigue. The human immune system produces IgM and IgG antibodies in response to SARS-CoV-2. Despite previous research, a comprehensive understanding of the interplay between clinical manifestations and humoral immune responses remains elusive. This study aims to scrutinize this association. 134 COVID-19 patients were enrolled, and stratified into mild, moderate, and severe symptom groups. Serum IgM and IgG levels were assessed thrice at one-month intervals using ELISA. The findings reveal significant elevation in serum IgG levels in moderate compared to mild cases (P < 0.001). Additionally, IgG production was significantly heightened in severe cases compared to both mild (P < 0.0001) and moderate (P < 0.05) groups. IgM and IgG levels peaked initially and diminished over time. While anti-SARS-CoV-2 antibodies are expected to confer protection, the direct correlation between IgG levels and symptom severity may arise from delayed immune activation, resulting in an intense antibody response in severe cases. Given evidence linking delayed immune function with a dysregulated innate immune response, comprehensive data collection should encompass not only serum IgG and IgM, but also early measurement of type I interferons at symptom onset. This could provide a more thorough understanding of COVID-19 progression.

Coronaviruses of the human variety have been the culprit of global epidemics of varying levels of lethality, including COVID-19, which has impacted more than 200 countries and resulted in 5.7 million fatalities as of May 2022. Effective clinical management necessitates the allocation of sufficient resources and the employment of appropriately skilled personnel. The elderly population and individuals with diabetes are at increased risk of more severe manifestations of COVID-19. Countries with a higher gross domestic product (GDP) typically exhibit superior health outcomes and reduced mortality rates. Here, we suggest a predictive model for the density of medical doctors and nursing personnel for 134 countries using a support vector machine (SVM). The model was trained in 107 countries and tested in 27, with promising results shown by the kappa statistics and ROC analysis. The SVM model used for predictions showed promising results with a high level of agreement between actual and predicted cluster values.

Haemolytic uraemic syndrome (HUS) caused by infection with Shiga toxin-producing Escherichia coli (STEC) is a relatively rare but potentially fatal multisystem syndrome clinically characterised by acute kidney injury. This study aimed to provide robust estimates of paediatric HUS incidence in England, Wales, Northern Ireland, and the Republic of Ireland by using data linkage and case reconciliation with existing surveillance systems, and to describe the characteristics of the condition. Between 2011 and 2014, 288 HUS patients were included in the study, of which 256 (89.5%) were diagnosed as typical HUS. The crude incidence of paediatric typical HUS was 0.78 per 100,000 person-years, although this varied by country, age, gender, and ethnicity. The majority of typical HUS cases were 1 to 4 years old (53.7%) and female (54.0%). Clinical symptoms included diarrhoea (96.5%) and/or bloody diarrhoea (71.9%), abdominal pain (68.4%), and fever (41.4%). Where STEC was isolated (59.3%), 92.8% of strains were STEC O157 and 7.2% were STEC O26. Comparison of the HUS case ascertainment to existing STEC surveillance data indicated an additional 166 HUS cases were captured during this study, highlighting the limitations of the current surveillance system for STEC for monitoring the clinical burden of STEC and capturing HUS cases.