In this study, we evaluated the association between high-risk human papillomavirus (hrHPV) and the vaginal microbiome. Participants were recruited in Nigeria between April and August 2012. Vaginal bacterial composition was characterized by deep sequencing of barcoded 16S rRNA gene fragments (V4) on Illumina MiSeq and HPV was identified using the Roche Linear Array® HPV genotyping test. We used exact logistic regression models to evaluate the association between community state types (CSTs) of vaginal microbiota and hrHPV infection, weighted UniFrac distances to compare the vaginal microbiota of individuals with prevalent hrHPV to those without prevalent hrHPV infection, and the Linear Discriminant Analysis effect size (LEfSe) algorithm to characterize bacteria associated with prevalent hrHPV infection. We observed four CSTs: CST IV-B with a low relative abundance of Lactobacillus spp. in 50% of participants; CST III (dominated by L. iners) in 39·2%; CST I (dominated by L. crispatus) in 7·9%; and CST VI (dominated by proteobacteria) in 2·9% of participants. LEfSe analysis suggested an association between prevalent hrHPV infection and a decreased abundance of Lactobacillus sp. with increased abundance of anaerobes particularly of the genera Prevotella and Leptotrichia in HIV-negative women (P < 0·05). These results are hypothesis generating and further studies are required.

The effects of temperature on reported cases of a number of foodborne illnesses in England and Wales were investigated. We also explored whether the impact of temperature had changed over time. Food poisoning, campylobacteriosis, salmonellosis, Salmonella Typhimurium infections and Salmonella Enteritidis infections were positively associated (P<0·01) with temperature in the current and previous week. Only food poisoning, salmonellosis and S. Typhimurium infections were associated with temperature 2–5 weeks previously (P<0·01). There were significant reductions also in the impact of temperature on foodborne illnesses over time. This applies to temperature in the current and previous week for all illness types (P<0·01) except S. Enteritidis infection (P=0·079). Temperature 2–5 weeks previously diminished in importance for food poisoning and S. Typhimurium infection (P<0·001). The results are consistent with reduced pathogen concentrations in food and improved food hygiene over time. These adaptations to temperature imply that current estimates of how climate change may alter foodborne illness burden are overly pessimistic.

A total of 1590 calves were investigated between May 1972 and December 1975. Twenty-two per cent were treated for respiratory disease and 2·5% died of pneumonia. Almost 80% of the respiratory illness occurred in six sharp outbreaks. Samples for virology were collected routinely from 127 healthy calves and from 354 calves treated for respiratory signs and comprised 1143 nasopharyngeal swabs and 1069 sera. Virus infections were detected on 540 occasions including 135 by parainfluenzavirus type 3 (Pi-3), 78 by respiratory syncytial virus (RSV), 103 by rhinovirus, 49 by bovine virus diarrhoea virus (BVDV), 29 by adenoviruses, 53 by reoviruses and 88 by enteroviruses. The seasonal and age distribution of infections differed between viruses. Only infections by RSV, Pi-3 and BVDV were significantly associated with disease.

Toxoplasmosis is a worldwide zoonosis due to Toxoplasma gondii, a ubiquitous protozoan parasite of warm-blooded animals including humans. In pregnant women, primary infection can cause congenital toxoplasmosis resulting in severe malformations in the newborn. Since 1978, public health authorities in France have implemented a congenital toxoplasmosis prevention programme, including monthly serological screening of all seronegative pregnant women, and treatment in case of seroconversion. However, this programme does not produce systematic surveillance data on incidence and prevalence. Our objective was to estimate the incidence and prevalence of T. gondii infection, and the incidence of seroconversion during pregnancy in women in France. We used a catalytic model to estimate incidence and prevalence of Toxoplasma infection between 1980 and 2020 in women of childbearing age. We used age- and time-specific seroprevalence data obtained from the National Perinatal Surveys (NPS) conducted in 1995, 2003 and 2010. We assumed that incidence depends both on age and calendar time, and can be expressed as the product of two unknown functions. We also estimated incidence of seroconversion during pregnancy in 2010 from the NPS and the National Surveillance of Congenital Toxoplasmosis (ToxoSurv). We combined data of 42208 women aged 15–45 years with serology available from the three NPS. For women aged 30 years the modelled incidence decreased from 7·5/1000 susceptible women in 1980 to 3·5/1000 in 2000. In 2010 the incidence was 2·4/1000. The predicted incidence and prevalence for 2020 was 1·6/1000 and 27%, respectively. The incidence of seroconversion during pregnancy in 2010 was estimated at 2·1/1000 susceptible pregnant women (95% CI 1·3–3·1) from the NPS and 1·9 (95% CI 1·8–2·1) from ToxoSurv. Incidence and prevalence of Toxoplasma infection has decreased markedly during the last 30 years. This decrease may be explained by a lower exposure to the parasite by changes in food habits and by improved hygiene practices in meat production. Modelled estimations were consistent with estimates observed in other studies conducted previously in France. The catalytic modelling provides reliable estimates of incidence and prevalence of Toxoplasma infection over time. This approach might be useful for evaluating preventive programme for toxoplasmosis.

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

Between 1 and 22 March 2003, a nosocomial outbreak of Severe Acute Respiratory Syndrome (SARS) occurred at the Communicable Disease Centre in Tan Tock Seng Hospital, Singapore, the national treatment and isolation facility for patients with SARS. A case-control study with 36 cases and 50 controls was conducted of factors associated with the transmission of SARS within the hospital. In univariate analysis, contact with respiratory secretions elevated the odds ratio to 6·9 (95% CI 1·4–34·6, P=0·02). Protection was conferred by hand washing (OR 0·06, 95% CI 0·007–0·5, P=0·03) and wearing of N95 masks (OR 0·1, 95% CI 0·03–0·4, P=0·001). Use of gloves and gowns had no effect. Multivariate analysis confirmed the strong role of contact with respiratory secretions (adjusted OR 21·8, 95% CI 1·7–274·8, P=0·017). Both hand washing (adjusted OR 0·07, 95% CI 0·008–0·66, P=0·02) and wearing of N95 masks (adjusted OR 0·1, 95% CI 0·02–0·86, P=0·04) remained strongly protective but gowns and gloves had no effect.

Systematic national surveillance of foodborne disease outbreaks effectively serves the development of public health policy on food safety. The Health Protection Agency has maintained a collaborative surveillance system for foodborne outbreaks in England and Wales since 1992. Up to 2008, 2429 foodborne outbreaks were identified, described and analysed for changes over time. Salmonella spp. accounted for half of the outbreaks, although the proportion of these decreased over the surveillance period. Similarly, the proportion of outbreaks caused by Clostridium perfringens decreased, while those attributed to Campylobacter spp. and Vero cytotoxin-producing Escherichia coli O157 increased. Although poultry meat was the most frequently implicated food vehicle in outbreaks followed by miscellaneous foods and red meats, the proportion of outbreaks attributed to meats in fact decreased over time but those linked to miscellaneous foods did not. Over the surveillance period, the proportion of outbreaks linked to eggs and S. Enteritidis non-phage-type 4, particularly in food service establishments, increased, highlighting the importance of this organism/setting/vehicle association. Contributory factors in most outbreaks were cross-contamination, inadequate heat treatment, and inappropriate food storage. This study describes the overall decline in foodborne outbreaks, providing evidence that the introduction and adherence to effective control measures provide the best means of minimizing the risk of foodborne infection.

1. Previous work on the antigenic structure of the cholera group of vibrios is experimentally reviewed, and the data amplified and systematised.

2. The cholera group is defined as consisting of vibrios with similar biochemical characters and having a common heat-labile antigenic component.

3. The heat-stable antigens are divisible into:

(a) A considerable number of specific antigens, best demonstrated by O sera and H-O suspensions, which serve as a basis of classification into O subgroups.

(b) A non-specific component, demonstrable with O sera and O suspensions.

4. The first subgroup contains all the standard cholera vibrios from central laboratories, and the majority of other epidemic strains. We consider that it represents the only class of vibrios known for certain to cause epidemic cholera.

5. The races of this subgroup I are further divisible into two (or perhaps three) “types”, as established by Japanese workers, according to differences in their subsidiary O antigens.

6. The haemolytic “El Tor” vibrios are serologically diverse. The term “El Tor” should, as Shousha suggests, be reserved for those that have the same specific O component as the standard cholera vibrios.

7. For the identification of the undoubted cholera vibrios a standard subgroup I O serum is recommended in conjunction with the haemolytic test. The serum should contain both the main and the subsidiary antigens of the subgroup.

8. As a working rule it is suggested that bacteriological proof of “cholera” or a cholera carrier should rest on the isolation of a non-haemolytic vibrio with the specific O antigen of subgroup I.

The studies and observations on which this paper is based were conducted while one of us (K. V. V.) was holding a Fellowship of the International Health Division of the Rockefeller Foundation.

Our thanks are due to Mr P. Bruce White for constant help and advice, and to the numerous bacteriologists in various lands who have kindly supplied us with cultures and sera.

Human respiratory syncytial virus (hRSV) transmission dynamics are inherently cyclical, and the observed genetic diversity (between groups A and B) also appears to have a repeating pattern. A key unknown is the extent to which genetic variants interact immunologically, and thus impact on epidemiology. We developed a novel mathematical model for hRSV transmission including seasonal forcing of incidence and temporary intra- and inter-group partial immunity. Simultaneous model fits to data from two locations (England & Wales, UK, and Turku, Finland) successfully reproduced the contrasting infection dynamics and group A/B dominance patterns. Parameter estimates are consistent with direct estimates. Differences in the magnitude and seasonal variation in contact rate between the two populations alone could account for the variation in dynamics between these populations. The A/B group dominance patterns are explained by reductions in susceptibility to and infectiousness of secondary homologous and heterologous infections. The consequences of the observed dynamic complexity are discussed.

Clostridium difficile (C. diff) is a major nosocomial problem. Epidemiological surveillance of the disease can be accomplished by microbiological or administrative data. Microbiological tracking is problematic since it does not always translate into clinical disease, and it is not always available. Tracking by administrative data is attractive, but ICD-9 code accuracy for C. diff is unknown. By using a large administrative database of hospitalized patients with C. diff (by ICD-9 code or cytotoxic assay), this study found that the sensitivity, specificity, positive, and negative predictive values of ICD-9 coding were 71%, 99%, 87%, and 96% respectively (using micro data as the gold standard). When only using symptomatic patients the sensitivity increased to 82% and when only using symptomatic patients whose test results were available at discharge, the sensitivity increased to 88%. C. diff ICD-9 codes closely approximate true C. diff infection, especially in symptomatic patients whose test results are available at the time of discharge, and can therefore be used as a reasonable alternative to microbiological data for tracking purposes.

Microsporidia are spore-forming intracellular parasites that infrequently cause disease in immunocompetent persons. This study describes the first report of a foodborne microsporidiosis outbreak which affected persons visiting a hotel in Sweden. Enterocytozoon bieneusi was identified in stool samples from 7/11 case-patients, all six sequenced samples were genotype C. To confirm that this was not a chance finding, 19 stool samples submitted by healthy persons from a comparable group who did not visit the hotel on that day were tested; all were negative for microsporidia. A retrospective cohort study identified 135 case-patients (attack rate 30%). The median incubation period was 9 days. Consumption of cheese sandwiches [relative risk (RR) 4·1, 95% confidence interval (CI) 1·4–12·2] and salad (RR 2·1, 95% CI 1·1–4) were associated with illness. Both items contained pre-washed, ready-to-eat cucumber slices. Microsporidia may be an under-reported cause of gastrointestinal outbreaks; we recommend that microsporidia be explored as potential causative agents in food- and waterborne outbreaks, especially when no other organisms are identified.

During epidemics of cholera in two rural sites (Bakerganj and Mathbaria), a much higher proportion of patients came for treatment with severe dehydration than was seen in previous years. V. cholerae O1 isolated from these patients was found to be El Tor in its phenotype, but its cholera toxin (CT) was determined to be that of classical biotype. Whether the observed higher proportion of severe dehydration produced by the El Tor biotype was due to a shift from El Tor to classical CT or due to other factors is not clear. However, if cholera due to strains with increased severity spread to other areas where treatment facilities are limited, there are likely to be many more cholera deaths.

Infection with thermophilic Campylobacter spp. usually leads to an episode of acute gastroenteritis. Occasionally, more severe diseases may be induced, notably Guillain–Barré syndrome and reactive arthritis. For some, the disease may be fatal. We have integrated available data in one public health measure, the Disability Adjusted Life Year (DALY). DALYs are the sum of Years of Life Lost by premature mortality and Years Lived with Disability, weighted with a factor between 0 and 1 for the severity of illness. The mean health burden of campylobacter-associated illness in the Dutch population in the period 1990–5 is estimated as 1400 (90% CI 900–2000) DALY per year. The main determinants of health burden are acute gastroenteritis (440 DALY), gastroenteritis related mortality (310 DALY) and residual symptoms of Guillain–Barré syndrome (340 DALY). Sensitivity analysis demonstrated that alternative model assumptions produced results in the above-mentioned range.

We examined multistate outbreaks attributed to raw tomatoes in the United States from 1990 to 2010. We summarized the demographic and epidemiological characteristics of 15 outbreaks resulting in 1959 illnesses, 384 hospitalizations, and three deaths. Most (80%) outbreaks were reported during 2000–2010; 73% occurred May–September. Outbreaks commonly affected adult (median age 34 years) women (median 58% of outbreak cases). All outbreaks were caused by Salmonella [serotypes Newport (n = 6 outbreaks), Braenderup (n = 2), Baildon, Enteritidis, Javiana, Montevideo, Thompson, Typhimurium (n = 1 each); multiple serotypes (n = 1)]. Red, round (69% of outbreaks), Roma (23%), and grape (8%) tomatoes were implicated. Most (93%) outbreaks were associated with tomatoes served predominantly in restaurants. However, traceback investigations suggested that contamination occurred on farms, at packinghouses, or at fresh-cut processing facilities. Government agencies, academia, trade associations, and the fresh tomato industry should consider further efforts to identify interventions to reduce contamination of tomatoes during production and processing.

Since April 2015, whole genome sequencing (WGS) has been the routine test for Salmonella identification, surveillance and outbreak investigation at the national reference laboratory in England and Wales. In May 2015, an outbreak of Salmonella Enteritidis cases was detected using WGS data and investigated. UK cases were interviewed to obtain a food history and links between suppliers were mapped to produce a food chain network for chicken eggs. The association between the food chain network and the phylogeny was explored using a network comparison approach. Food and environmental samples were taken from premises linked to cases and tested for Salmonella. Within the outbreak single nucleotide polymorphism defined cluster, 136 cases were identified in the UK and 18 in Spain. One isolate from a food containing chicken eggs was within the outbreak cluster. There was a significant association between the chicken egg food chain of UK cases and phylogeny of outbreak isolates. This is the first published Salmonella outbreak to be prospectively detected using WGS. This outbreak in the UK was linked with contemporaneous cases in Spain by WGS. We conclude that UK and Spanish cases were exposed to a common source of Salmonella-contaminated chicken eggs.

We investigated age- and gender-specific incidence of shingles reported in a large sentinel practice network monitoring a defined population over the years 1994–2001. In total, 5915 male and 8617 female incident cases were studied. For each age group, we calculated the relative risk of females to males presenting with shingles. Incidence rates of chickenpox and herpes simplex were examined similarly. Shingles incidence was greater in females in each age group (except for 15–24 years). Relative risks (female to male) were greatest in age groups 45–64 years (1·48) and 0–14 years (1·43). There were no gender differences in the incidence of chickenpox except in the 15–24 years age group (female excess): for herpes simplex there were female excesses in all age groups. Gender-specific age-standardized incidence rates of shingles were calculated for each year and showed a consistent female excess in each of the 8 years (average annual excess 28%).

The public health significance of giardiasis and cryptosporidiosis in sheep is currently unclear. Some research suggests that they are probably not an important zoonotic reservoir, whilst other research indicates this potential exists, and some outbreaks have also been associated with infections in sheep. Actions to limit water supply contamination by sheep have sometimes been severe, occasionally creating problems between farming and public health communities. Here our knowledge on these parasites in both sheep and goats is reviewed; although direct evidence of transmission to humans via water supply contamination is limited, the data accrued indicate that this is a real possibility. As cryptosporidiosis in sheep is generally more prevalent than giardiasis, and species/genotypes of Cryptosporidium infections in sheep are likely to be infectious to humans, this parasite may be considered the greater threat. Nevertheless, geographical variation in prevalence and genotypic distribution is extensive and as measures to limit sheep grazing can have a highly negative impact, it is important that cases are judged individually. If water contamination from a particular population of sheep/goats is suspected, then suitable investigations should be instigated, investigating both prevalence and species/genotype, before precautionary measures are imposed.

We retrospectively studied patients diagnosed with P. aeruginosa bloodstream infections (BSIs) in two Italian university hospitals. Risk factors for the isolation of multidrug-resistant (MDR) or non-MDR P. aeruginosa in blood cultures were identified by a case-case-control study, and a cohort study evaluated the clinical outcomes of such infections. We identified 106 patients with P. aeruginosa BSI over the 2-year study period; 40 cases with MDR P. aeruginosa and 66 cases with non-MDR P. aeruginosa were compared to 212 controls. Independent risk factors for the isolation of MDR P. aeruginosa were: presence of central venous catheter (CVC), previous antibiotic therapy, and corticosteroid therapy. Independent risk factors for non-MDR P. aeruginosa were: previous BSI, neutrophil count <500/mm3, urinary catheterization, and presence of CVC. The 21-day mortality rate of all patients was 33·9%. The variables independently associated with 21-day mortality were presentation with septic shock, infection due to MDR P. aeruginosa, and inadequate initial antimicrobial therapy.

Fresh produce is an important part of a healthy diet and is consumed in greater quantity in the United States than ever before. Consumption of cantaloupe has recently been associated with several large outbreaks of infections in North America, highlighting the need for a better understanding of practices and processes that may contribute to contamination. We reviewed all cantaloupe-associated outbreaks that were reported to the Centers for Disease Control and Prevention (CDC) and published in the literature. Twenty-three outbreaks occurred between 1984 and 2002; 1434 people became ill, 42 were hospitalized, and two died in these outbreaks. Aetiological agents in the outbreaks included five serotypes of Salmonella enterica, Campylobacter jejuni, Escherichia coli O157:H7, and norovirus. We reviewed processes contributing to cantaloupe contamination, conditions affecting survival and growth of bacterial pathogens on melons, and potential methods for sanitization. For maximum safety, industry, federal, and international partners must collaborate to ensure that appropriate interventions are in place to minimize the risk of contamination and prevent the growth of pathogens during cantaloupe production, processing, storage, and preparation.

Results of the Dutch laboratory surveillance of bacterial gastroenteritis between 1991 and 2001 are presented and compared with recent findings in general practices and in the community. Between 1996 and 2000 the mean annual number of stools screened by sentinel laboratories was about 1000 samples/100000 inhabitants, which is 4% of the estimated annual incidence of gastroenteritis in the Dutch population. Campylobacter (36/100000 inhabitants) and salmonella (24/100000 inhabitants) were the main pathogens isolated. Since 1996, the incidence of laboratory confirmed salmonellosis decreased by 30%, predominantly among young children. The incidence of campylobacter was highest in urban areas and Salmonella Enteritidis emerged as the predominant serotype in urban areas. Between 1991 and 2001, multi-resistant Salmonella Typhimurium DT104 emerged to comprise up to 15% of all salmonella isolates in 2001. Reported rates of Shigella spp. and Yersinia spp. varied little, with average annual incidences of 3·2 and 1·2 cases/100000 inhabitants, respectively. Escherichia coli O157 (90% STEC) was scarcely found (0·26/100000).