In epidemiological investigations, pathogen genomics can provide insights and test epidemiological hypotheses that would not have been possible through traditional epidemiology. Tools to synthesize genomic analysis with other types of data are a key requirement of genomic epidemiology. We propose a new ‘phylepic’ visualization that combines a phylogenomic tree with an epidemic curve. The combination visually links the molecular time represented in the tree to the calendar time in the epidemic curve, a correspondence that is not easily represented by existing tools. Using an example derived from a foodborne bacterial outbreak, we demonstrated that the phylepic chart communicates that what appeared to be a point-source outbreak was in fact composed of cases associated with two genetically distinct clades of bacteria. We provide an R package implementing the chart. We expect that visualizations that place genomic analyses within the epidemiological context will become increasingly important for outbreak investigations and public health surveillance of infectious diseases.

Influenza and other acute respiratory viral infections (ARVIs) are among the most common human diseases. In recent decades, the discovery of cytokines and their significance in the pathogenesis of diseases has led to extensive research on these compounds in various pathologies including ARVIs. The aim of the research was to study the cytokine profile in patients with ARVIs. The cases of 30 patients were investigated. Etiological diagnosis was performed by polymerase chain reaction. Different classes of cytokines in the serum were defined by the enzyme-linked immunosorbent assay (ELISA). The level of cytokines depended on the number of pathogens. The highest levels of pro-inflammatory interleukins and the lowest levels of anti-inflammatory IL-4 were observed in patients with a combination of five or more viruses compared to those with a monoinfection. Analysis of the data showed that in the acute phase, the levels of all studied pro-inflammatory cytokines – IL-2, IL-6, and TNF-α – increased by 8, 39, and 9 times, respectively, compared to those in healthy individuals. In the acute phase of ARVI, the levels of pro-inflammatory cytokines were significantly higher and depended on the severity of the disease. The imbalance of cytokines in the serum has been established in cases of ARVIs, depending on the severity of the disease.

Globally, there is seasonal variation in tuberculosis (TB) incidence, yet the biological and behavioural or social factors driving TB seasonality differ across countries. Understanding season-specific risk factors that may be specific to the UK could help shape future decision-making for TB control. We conducted a time-series analysis using data from 152,424 UK TB notifications between 2000 and 2018. Notifications were aggregated by year, month, and socio-demographic covariates, and negative binomial regression models fitted to the aggregate data. For each covariate, we calculated the size of the seasonal effect as the incidence risk ratio (IRR) for the peak versus the trough months within the year and the timing of the peak, whilst accounting for the overall trend. There was strong evidence for seasonality (p < 0.0001) with an IRR of 1.27 (95% CI 1.23–1.30). The peak was estimated to occur at the beginning of May. Significant differences in seasonal amplitude were identified across age groups, ethnicity, site of disease, latitude and, for those born abroad, time since entry to the UK. The smaller amplitude in older adults, and greater amplitude among South Asians and people who recently entered the UK may indicate the role of latent TB reactivation and vitamin D deficiency in driving seasonality.

In December 2018, an outbreak of Salmonella Enteritidis infections was identified in Canada by whole-genome sequencing (WGS). An investigation was initiated to identify the source of the illnesses, which proved challenging and complex. Microbiological hypothesis generation methods included comparisons of Salmonella isolate sequence data to historical domestic outbreaks and international repositories. Epidemiological hypothesis generation methods included routine case interviews, open-ended centralized re-interviewing, thematic analysis of open-ended interview data, collection of purchase records, a grocery store site visit, analytic comparison to healthy control groups, and case–case analyses. Food safety hypothesis testing methods included food sample collection and analysis, and traceback investigations. Overall, 83 cases were identified across seven provinces, with onset dates from 6 November 2018 to 7 May 2019. Case ages ranged from 1 to 88 years; 60% (50/83) were female; 39% (22/56) were hospitalized; and three deaths were reported. Brand X profiteroles and eclairs imported from Thailand were identified as the source of the outbreak, and eggs from an unregistered facility were hypothesized as the likely cause of contamination. This study aims to describe the outbreak investigation and highlight the multiple hypothesis generation methods that were employed to identify the source.

An investigation into an outbreak of Salmonella Newport infections in Canada was initiated in July 2020. Cases were identified across several provinces through whole-genome sequencing (WGS). Exposure data were gathered through case interviews. Traceback investigations were conducted using receipts, invoices, import documentation, and menus. A total of 515 cases were identified in seven provinces, related by 0–6 whole-genome multi-locus sequence typing (wgMLST) allele differences. The median age of cases was 40 (range 1–100), 54% were female, 19% were hospitalized, and three deaths were reported. Forty-eight location-specific case sub-clusters were identified in restaurants, grocery stores, and congregate living facilities. Of the 414 cases with exposure information available, 71% (295) had reported eating onions the week prior to becoming ill, and 80% of those cases who reported eating onions, reported red onion specifically. The traceback investigation identified red onions from Grower A in California, USA, as the likely source of the outbreak, and the first of many food recall warnings was issued on 30 July 2020. Salmonella was not detected in any tested food or environmental samples. This paper summarizes the collaborative efforts undertaken to investigate and control the largest Salmonella outbreak in Canada in over 20 years.

Varicella is a vaccine-preventable infectious disease. Since 1 December 2018, the varicella vaccine has been included in the local Expanded Programme on Immunization (EPI) in Wuxi, China, and children born after 1 December 2014 are eligible for free vaccination. To evaluate the effect of varicella vaccination in Wuxi city, we selected 382 397 children born from 2012 to 2016 as subjects. Their disease data were obtained from the Chinese Disease Prevention and Control Information System, and their vaccination data were obtained from the Jiangsu Province Vaccination Integrated Service Management Information System. The incidence of breakthrough varicella cases increased in the first 4 years and reached the peak in the fifth year. With the increase of vaccination rate, the incidence of varicella decreased significantly. The vaccine effectiveness (VE) was found to be 88.17%–95.78% for one dose and 98.65%–99.93% for two doses. Although the VE per dose decreased from 99.57% in the first year to 93.04% in the eighth year, it remained high. These findings confirmed the effectiveness of varicella vaccination in children, supported the use of a two-dose varicella vaccination strategy to achieve better protection, and provided important insights into the optimal vaccination strategy for varicella prevention in children.

We hypothesized that the incubation for urethral gonorrhoea would be longer for men with oropharyngeal gonorrhoea than those without oropharyngeal gonorrhoea. We conducted a chart review of men who have sex with men with urethral gonorrhoea symptoms at a sexual health clinic between 2019 and 2021. The incubation period was defined as the number of days between men’s last sexual contact and onset of symptoms. We used a Mann–Whitney U test to compare differences in the median incubation for urethral gonorrhoea between men with and men without oropharyngeal gonorrhoea. There were 338 men with urethral symptoms (median age = 32 years; IQR: 28–39), and of these, 307 (90.1%) were tested for oropharyngeal gonorrhoea, of whom 124 (40.4%, 95% CI: 34.9–46.1) men had oropharyngeal and urethral gonorrhoea. We analyzed incubation data available for 190 (61.9%) of the 307 men, with 38.9% (74/190) testing positive for oropharyngeal gonorrhoea. The incubation for urethral gonorrhoea did not differ between 74 men (39%) with oropharyngeal gonorrhoea (median = 4 days; IQR: 2–6) and 116 men (61%) without oropharyngeal gonorrhoea (median = 2.5 days; IQR: 1–5) (p = 0.092). Research is needed to investigate gonorrhoea transmission from the oropharynx to the urethra.

Since early 2022, routine testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on symptoms and exposure history has largely ceased in Canada. Consequently, seroprevalence studies, particularly longitudinal studies, have become critical for monitoring the rate of incident SARS-CoV-2 infections and the proportion of the population with evidence of immunity. EnCORE is a longitudinal SARS-CoV-2 seroprevalence study comprising five rounds of serology testing from October 2020 to June 2023, in a sample of 2- to 17-year-olds (at baseline), recruited from daycares and schools in four neighbourhoods of Montreal, Canada. We report on SARS-CoV-2 incidence and seroprevalence among the 509 participants in the fifth and final round of the study. Seroprevalence of antibodies from either infection or vaccination was 98% (95 per cent confidence interval [CI]: 97, 99). The infection-acquired seroprevalence was 78% (95% CI: 73–82), and the incidence rate was 113 per 100 person-years (95% CI: 94–132), compared to the seroprevalence of 58% and the incidence rate of 133 per 100 person-years, respectively, in the fourth round of testing (mid–late 2022). Of the 131 participants newly seropositive for infection in Round 4, only 18 were seronegative for infection in Round 5 (median follow-up: 326 days).

On 19 January 2020, the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was identified in the United States, with the first cases in South Carolina confirmed on 06 March 2020. Due to initial limited testing capabilities and potential for asymptomatic transmission, it is possible that SARS-CoV-2 may have been present earlier than previously thought, while the immune status of at-risk populations was unknown. Saliva from 55 South Carolina emergency healthcare workers (EHCWs) was collected from September 2019 to March 2020, pre- and post-healthcare shifts, and stored frozen. To determine the presence of SARS-CoV-2-reactive antibodies, saliva-acquired post-shift was analysed by enzyme-linked immunosorbent assay (ELISA) with a repeat of positive or inconclusive results and follow-up testing of pre-shift samples. Two participants were positive for SARS-CoV-2 N/S1-reactive IgG, confirmed by follow-up testing, with S1 receptor binding domain (RBD)-specific IgG present in one individual. Positive samples were collected from medical students working in emergency medical services (EMSs) in October or November 2019. The presence of detectable anti-SARS-CoV-2 antibodies in 2019 suggests that immune responses to the virus existed in South Carolina, and the United States, in a small percentage of EHCWs prior to the earliest documented coronavirus disease 2019 (COVID-19) cases. These findings suggest the feasibility of saliva as a noninvasive tool for surveillance of emerging outbreaks, and EHCWs represent a high-risk population that should be the focus of infectious disease surveillance.

Campylobacter spp. are leading bacterial gastroenteritis pathogens. Infections are largely underreported, and the burden of outbreaks may be underestimated. Current strategies of testing as few as one isolate per sample can affect attribution of cases to epidemiologically important sources with high Campylobacter diversity, such as chicken meat. Multiple culture method combinations were utilized to recover and sequence Campylobacter from 45 retail chicken samples purchased across Norwich, UK, selecting up to 48 isolates per sample. Simulations based on resampling were used to assess the impact of Campylobacter sequence type (ST) diversity on outbreak detection. Campylobacter was recovered from 39 samples (87%), although only one sample was positive through all broth, temperature, and plate combinations. Three species were identified (Campylobacter jejuni, Campylobacter coli, and Campylobacter lari), and 33% of samples contained two species. Positive samples contained 1–8 STs. Simulation revealed that up to 87 isolates per sample would be required to detect 95% of the observed ST diversity, and 26 isolates would be required for the average probability of detecting a random theoretical outbreak ST to reach 95%. An optimized culture approach and selecting multiple isolates per sample are essential for more complete Campylobacter recovery to support outbreak investigation and source attribution.

Surveillance of SARS-CoV-2 through reported positive RT-PCR tests is biased due to non-random testing. Prevalence estimation in population-based samples corrects for this bias. Within this context, the pooled testing design offers many advantages, but several challenges remain with regards to the analysis of such data. We developed a Bayesian model aimed at estimating the prevalence of infection from repeated pooled testing data while (i) correcting for test sensitivity; (ii) propagating the uncertainty in test sensitivity; and (iii) including correlation over time and space. We validated the model in simulated scenarios, showing that the model is reliable when the sample size is at least 500, the pool size below 20, and the true prevalence below 5%. We applied the model to 1.49 million pooled tests collected in Switzerland in 2021–2022 in schools, care centres, and workplaces. We identified similar dynamics in all three settings, with prevalence peaking at 4–5% during winter 2022. We also identified differences across regions. Prevalence estimates in schools were correlated with reported cases, hospitalizations, and deaths (coefficient 0.84 to 0.90). We conclude that in many practical situations, the pooled test design is a reliable and affordable alternative for the surveillance of SARS-CoV-2 and other viruses.

Studies on climate variables and food pathogens are either pathogen- or region-specific, necessitating a consolidated view on the subject. This study aims to systematically review all studies on the association of ambient temperature and precipitation on the incidence of gastroenteritis and bacteraemia from Salmonella, Shigella, Campylobacter, Vibrio, and Listeria species. PubMed, Ovid MEDLINE, Scopus, and Web of Science databases were searched up to 9 March 2023. We screened 3,204 articles for eligibility and included 83 studies in the review and three in the meta-analysis. Except for one study on Campylobacter, all showed a positive association between temperature and Salmonella, Shigella, Vibrio sp., and Campylobacter gastroenteritis. Similarly, most of the included studies showed that precipitation was positively associated with these conditions. These positive associations were found regardless of the effect measure chosen. The pooled incidence rate ratio (IRR) for the three studies that included bacteraemia from Campylobacter and Salmonella sp. was 1.05 (95 per cent confidence interval (95% CI): 1.03, 1.06) for extreme temperature and 1.09 (95% CI: 0.99, 1.19) for extreme precipitation. If current climate trends continue, our findings suggest these pathogens would increase patient morbidity, the need for hospitalization, and prolonged antibiotic courses.

International travel is thought to be a major risk factor for developing gastrointestinal (GI) illness for UK residents. Here, we present an analysis of routine laboratory and exposure surveillance data from North East (NE) England, describing the destination-specific contribution that international travel makes to the regional burden of GI infection.

Laboratory reports of common notifiable enteric infections were linked to exposure data for cases reported between 1 January 2013 and 31 December 2022. Demographic characteristics of cases were described, and rates per 100,000 visits were determined using published estimates of overseas visits from the Office for National Statistics (ONS) International Passenger Survey (IPS).

About 34.9% of cases reported international travel during their incubation period between 2013 and 2022, although travel-associated cases were significantly reduced (>80%) during the COVID-19 pandemic. Between 2013 and 2019, half of Shigella spp. and non-typhoidal Salmonella infections and a third of Giardia sp., Cryptosporidium spp., and Shiga toxin-producing Escherichia coli (STEC) infections were reported following travel. Rates of illness were highest in travellers returning from Africa and Asia (107.8 and 61.1 per 100,000 visits), with high rates also associated with tourist resorts like Turkey, Egypt, and the Dominican Republic (386.4–147.9 per 100,000 visits).

International travel is a major risk factor for the development of GI infections. High rates of illness were reported following travel to both destinations, which are typically regarded as high-risk and common tourist resorts. This work highlights the need to better understand risks while travelling to support the implementation of guidance and control measures to reduce the burden of illness in returning travellers.

Shiga toxin-producing Escherichia coli (STEC) transmission occurs in ruminant contact settings and can lead to post-diarrheal hemolytic uremic syndrome (HUS). We investigated whether exposure setting (ruminant exposure from living or working on a farm, visiting a farm or animal contact venue, or both) influenced HUS development among individuals with laboratory-confirmed STEC infections using Minnesota surveillance data from 2010 to 2019. Logistic regression was performed to determine whether exposure setting was associated with HUS independent of age, gender, stx2 gene detection, and county ruminants per capita. Among confirmed STEC cases, ruminant exposure only from living or working on a farm was not significantly associated with HUS compared to cases without any ruminant exposure (OR: 1.25; 95% CI: 0.51, 3.04). However, ruminant exposure only from visiting a farm or public animal contact venue was associated with HUS (OR: 2.53; 95% CI: 1.50, 4.24). Exposure from both settings was also associated with HUS (OR: 3.71; 95% CI: 1.39, 9.90). Exposure to ruminants when visiting farms or animal contact venues is an important predictor of HUS, even among people who live or work on farms with ruminants. All people, regardless of routine ruminant exposure, should take care in settings with ruminants to avoid infection with STEC.

This retrospective study compared central line-associated bloodstream infection (CLABSI) rates per 1 000 central line days, and overall mortality before and during the COVID-19 pandemic in adult, paediatric, and neonatal ICU patients at King Abdul-Aziz Medical City-Riyadh who had a central line and were diagnosed with CLABSI according to the National Healthcare Safety Network standard definition. The study spanned between January 2018 and December 2019 (pre-pandemic), and January 2020 and December 2021 (pandemic). SARS-CoV-2 was confirmed by positive RT-PCR testing. The study included 156 CLABSI events and 46 406 central line days; 52 and 22 447 (respectively) in pre-pandemic, and 104 and 23 959 (respectively) during the pandemic. CLABSI rates increased by 2.02 per 1 000 central line days during the pandemic period (from 2.32 to 4.34, p < 0.001). Likewise, overall mortality rates increased by 0.86 per 1 000 patient days (from 0.93 to 1.79, p = 0.003). Both CLABSI rates (6.18 vs. 3.7, p = 0.006) and overall mortality (2.72 vs. 1.47, p = 0.014) were higher among COVID-19 patients compared to non-COVID-19 patients. The pandemic was associated with a substantial increase in CLABSI-associated morbidity and mortality.

The COVID-19 pandemic modified the epidemiology and the transmission of respiratory syncytial virus (RSV). We collected data on RSV positivity and incidence from children hospitalized in the largest tertiary paediatric hospital in Greece before (2018–2020, period A), during (2020–2021, period B), and after (2021–2023, period C) the COVID-19 lockdown. A total of 9,508 children were tested for RSV. RSV positivity (%) was 17.6% (552/3,134) for period A, 2.1% (13/629) for period B, and 13.4% (772/5,745) for period C (p < 0.001). The mean age (±SD) of RSV-positive children among the three periods was A: 5.9(±9.3), B: 13.6 (±25.3), and C: 16.7 (±28.6) months (p < 0.001). The peak of RSV epidemiology was shifted from January–March (period A) to October–December (period C). RSV in-hospital incidence per 1,000 hospitalizations in paediatric departments was A:16.7, B:1.0, and C:28.1 (p < 0.001), and the incidence in the intensive care unit was A: 17.3, B: 0.6, and C: 26.6 (p < 0.001). A decrease in RSV incidence was observed during the COVID-19 lockdown period, whereas a significant increase was observed after the lockdown. A change in epidemiological patterns was identified after the end of the lockdown, with an earlier seasonal peak and an age shift of increased RSV incidence in older children.

Syphilis remains a serious public health problem in mainland China that requires attention, modelling to describe and predict its prevalence patterns can help the government to develop more scientific interventions. The seasonal autoregressive integrated moving average (SARIMA) model, long short-term memory network (LSTM) model, hybrid SARIMA-LSTM model, and hybrid SARIMA-nonlinear auto-regressive models with exogenous inputs (SARIMA-NARX) model were used to simulate the time series data of the syphilis incidence from January 2004 to November 2023 respectively. Compared to the SARIMA, LSTM, and SARIMA-LSTM models, the median absolute deviation (MAD) value of the SARIMA-NARX model decreases by 352.69%, 4.98%, and 3.73%, respectively. The mean absolute percentage error (MAPE) value decreases by 73.7%, 23.46%, and 13.06%, respectively. The root mean square error (RMSE) value decreases by 68.02%, 26.68%, and 23.78%, respectively. The mean absolute error (MAE) value decreases by 70.90%, 23.00%, and 21.80%, respectively. The hybrid SARIMA-NARX and SARIMA-LSTM methods predict syphilis cases more accurately than the basic SARIMA and LSTM methods, so that can be used for governments to develop long-term syphilis prevention and control programs. In addition, the predicted cases still maintain a fairly high level of incidence, so there is an urgent need to develop more comprehensive prevention strategies.

Nontuberculous mycobacteria (NTM) is a large group of mycobacteria other than the Mycobacterium tuberculosis complex and Mycobacterium leprae. Epidemiological investigations have found that the incidence of NTM infections is increasing in China, and it is naturally resistant to many antibiotics. Therefore, studies of NTM species in clinical isolates are useful for understanding the epidemiology of NTM infections. The present study aimed to investigate the incidence of NTM infections and types of NTM species. Of the 420 samples collected, 285 were positive for M. tuberculosis, 62 samples were negative, and the remaining 73 samples contained NTM, including 35 (8.3%) only NTM and 38 (9%) mixed (M. tuberculosis and NTM). The most prevalent NTM species were Mycobacterium intracellulare (30.1%), followed by Mycobacterium abscessus (15%) and M. triviale (12%). M. gordonae infection was detected in 9.5% of total NTM-positive cases. Moreover, this study reports the presence of Mycobacterium nonchromogenicum infection and a high prevalence of M. triviale for the first time in Henan. M. intracellulare is the most prevalent, accompanied by some emerging NTM species, including M. nonchromogenicum and a high prevalence of M. triviale in Henan Province. Monitoring NTM transmission and epidemiology could enhance mycobacteriosis management in future.

Development of gastrointestinal illness after animal contact at petting farms is well described, as are factors such as handwashing and facility design that may modify transmission risk. However, further field evidence on other behaviours and interventions in the context of Cryptosporidium outbreaks linked to animal contact events is needed. Here, we describe a large outbreak of Cryptosporidium parvum (C. parvum) associated with a multi-day lamb petting event in the south-west of England in 2023 and present findings from a cohort study undertaken to investigate factors associated with illness. Detailed exposure questionnaires were distributed to email addresses of 647 single or multiple ticket bookings, and 157 complete responses were received. The outbreak investigation identified 23 laboratory-confirmed primary C. parvum cases. Separately, the cohort study identified 83 cases of cryptosporidiosis-like illness. Associations between illness and entering a lamb petting pen (compared to observing from outside the pen; odds ratio (OR) = 2.28, 95 per cent confidence interval (95% CI) 1.17 to 4.53) and self-reported awareness of diarrhoeal and vomiting disease transmission risk on farm sites at the time of visit (OR = 0.40, 95% CI 0.19 to 0.84) were observed. In a multivariable model adjusted for household clustering, awareness of disease transmission risk remained a significant protective factor (adjusted OR (aOR) = 0.07, 95% CI 0.01 to 0.78). The study demonstrates the likely under-ascertainment of cryptosporidiosis through laboratory surveillance and provides evidence of the impact that public health messaging could have.