Investigating whether high-risk human papillomavirus (HR-HPV) types tend to become grouped in a particular way and whether factors are associated with such grouping is important for measuring the real impact of vaccination. In total, 219 women proving positive for HPV as detected by real-time PCR were included in the study. Each sample was analysed for detecting and quantifying six viral types and the hydroxymethylbilane synthase gene. Multiple correspondence analysis led to determining grouping patterns for six HR-HPV types and simultaneous association with multiple variables and whether viral load was related to the coexistence of other viral types. Two grouping profiles were identified: the first included HPV-16 and HPV-45 and the second profile was represented by HPV-31, HPV-33 and HPV-58. Variables such as origin, contraceptive method, births and pregnancies, educational level, healthcare affiliation regime, atypical squamous cells of undetermined significance and viral load were associated with these grouping profiles. Different socio-demographic characteristics were found when coinfection occurred by phylogenetically related HPV types and when coinfection was due to non-related types. Biological characteristics, the number of viral copies, temporality regarding acquiring infection and competition between viral types could influence the configuration of grouping patterns. Characteristics related to women and HPV, influence such interactions between coexisting HPV types reflecting the importance of their evaluation.

Established methods of recruiting population controls for case–control studies to investigate gastrointestinal disease outbreaks can be time consuming, resulting in delays in identifying the source or vehicle of infection. After an initial evaluation of using online market research panel members as controls in a case–control study to investigate a Salmonella outbreak in 2013, this method was applied in four further studies in the UK between 2014 and 2016. We used data from all five studies and interviews with members of each outbreak control team and market research panel provider to review operational issues, evaluate risk of bias in this approach and consider methods to reduce confounding and bias. The investigators of each outbreak reported likely time and cost savings from using market research controls. There were systematic differences between case and control groups in some studies but no evidence that conclusions on the likely source or vehicle of infection were incorrect. Potential selection biases introduced by using this sampling frame and the low response rate are unclear. Methods that might reduce confounding and some bias should be balanced with concerns for overmatching. Further evaluation of this approach using comparisons with traditional methods and population-based exposure survey data is recommended.

Little is known about Clostridium difficile infection (CDI) in Asia. The aims of our study were to explore (i) the prevalence, risk factors and molecular epidemiology of CDI and colonization in a tertiary academic hospital in North-Eastern Peninsular Malaysia; (ii) the rate of carriage of C. difficile among the elderly in the region; (iii) the awareness level of this infection among the hospital staffs and students. For stool samples collected from hospital inpatients with diarrhea (n = 76) and healthy community members (n = 138), C. difficile antigen and toxins were tested by enzyme immunoassay. Stool samples were subsequently analyzed by culture and molecular detection of toxin genes, and PCR ribotyping of isolates. To examine awareness among hospital staff and students, participants were asked to complete a self-administered questionnaire. For the hospital and community studies, the prevalence of non-toxigenic C. difficile colonization was 16% and 2%, respectively. The prevalence of CDI among hospital inpatients with diarrhea was 13%. Out of 22 C. difficile strains from hospital inpatients, the toxigenic ribotypes 043 and 017 were most common (both 14%). In univariate analysis, C. difficile colonization in hospital inpatients was significantly associated with greater duration of hospitalization and use of penicillin (both P < 0·05). Absence of these factors was a possible reason for low colonization in the community. Only 3% of 154 respondents answered all questions correctly in the awareness survey. C. difficile colonization is prevalent in a Malaysian hospital setting but not in the elderly community with little or no contact with hospitals. Awareness of CDI is alarmingly poor.

We report an outbreak of confirmed Mycoplasma pneumoniae community-acquired pneumonia (CAP) in Nord Franche-Comté Hospital, France, from 14 November 2023 to 31 January 2024. All 13 inpatients (11 adults with a mean age of 45.5 years and 2 children) were diagnosed with positive serology and/or positive reverse transcription polymerase chain reaction (RT-PCR) on respiratory specimens. All patients were immunocompetent and required oxygen support with a mean duration of oxygen support of 6.2 days. Two patients were transferred to the intensive care unit (ICU) but were not mechanically ventilated. Patients were treated with macrolides (n = 12, 92.3%) with recovery in all cases. No significant epidemiological link was reported in these patients.

Cyclospora cayetanensis is an emerging food- and waterborne pathogen that causes cyclosporiasis, a gastrointestinal disease in humans. The parasite is endemic in tropical and subtropical regions; however, its prevalence is largely dependent on environmental factors, such as climate and rainfall patterns. The objective of this paper was to conduct a systematic review and meta-analysis to determine the prevalence of C. cayetanensis in water and to determine if geography, water source and other variables influence this prevalence. A literature search was performed using search terms relating to water and C. cayetanensis in MEDLINE®, CAB Direct, Food Science and Technology Abstracts, Agricola databases and Environmental Science Index. Observational studies published in English after 1979 were eligible. Screening, data extraction and risk-of-bias assessment were performed independently by two reviewers. A multi-level random-effects meta-analysis was completed to determine the prevalence of C. cayetanensis in water and subgroup meta-analyses were performed to explore between-study heterogeneity. The search identified 828 unique articles, and after the screening, 33 articles were included in the review. The pooled prevalence of C. cayetanensis in water was 6.90% [95% confidence interval (CI) 2.25%–13.05%, I2 = 84.38%]. Subgroup meta-analyses revealed significant differences in the prevalence between continents. Additionally, laboratory methods between studies were highly variable and these findings highlight the need for further environmental research on C. cayetanensis in water using detection methods that include PCR and sequencing to accurately identify the organism. The results of this study can be used to help assess the risk of waterborne cyclosporiasis.

The English HCV lookback programme has identified some individuals with transfusion-transmitted HCV infection. The path from the collection of donations from HCV-infected donors to the identification of infected recipients was constructed. The probability of different outcomes at each branch was derived from data collected during this programme. This path of probabilities was then used to produce a complete estimate of the number of recipients infected by blood transfusions (dead and alive at the end of 1995) by re-entry of blood components that fell out of the lookback at various steps prior to recipient testing, and entry of components from HCV-infected donations that were never identified for lookback. Less than 14 000 recipients were estimated to have been infected with HCV during the decade prior to the start of donation testing. Over 60% of these were expected to have died by the end of 1995. Transfusion has infected a large group of individuals. However, this group constitutes a very small, and declining, proportion of all HCV infections in the population.

Few population-based studies have investigated the epidemiology of adult community-acquired pneumonia (CAP). We aimed to determine the incidence of CAP in a population at high-risk for pneumococcal disease and to evaluate a standardized method for interpreting chest radiographs adapted from the World Health Organization paediatric chest radiograph interpretation guidelines. We reviewed radiology records at the two healthcare facilities serving the White Mountain Apache tribe to identify possible pneumonia cases ⩾40 years of age. We categorized patients with clinical criteria and a physician diagnosis of pneumonia as clinical CAP and those with clinical criteria and an acute infiltrate as radiographic CAP. We identified 100 (27/1000 person-years) and 60 (16/1000 person-years) episodes of clinical and radiographic CAP, respectively. The incidence of CAP increased with age. Both radiographic and clinical CAP were serious illnesses with more than half of patients hospitalized. Our case definitions and methods may be useful for comparing data across studies and conducting vaccine trials.

The Salmonella Bio-EnzaBead Screening Kit, in its modified form with both the MOPC 467 and the 6H4 antibodies, was used for the detection of salmonellas in naturally contaminated foods and animal feeding stuffs in parallel with a traditional cultural procedure.

Initial results showed an 82% agreement between the enzyme immunoassay (EIA) and cultural methods when using the criterion recommended by the manufacturer as a cut-off for all types of foods. By adjusting the cut-off for each type of food, the number of EIA positive, culture negative samples was reduced although the number of EIA negative, culture positive samples increased. The EIA may be more sensitive than the cultural methods as in many cases the EIA positive, culture negative results could be real positives which were not detected by the cultural methods.

The screening kit provides a simple and convenient method for the detection of salmonella in foods and feeds and a presumptive positive result can be reported within 48 h. The advantages and disadvantages of the method are discussed.

Antimicrobial resistance (AMR) in Neisseria gonorrhoeae compromises patient treatment and disease control. Epidemiologically based surveillance of AMR in gonococci is needed to optimize standard treatment regimens. Validation of AMR surveillance data depends on external quality assurance schemes (EQAS). AMR surveillance data quality in India during 2001–2007 was assessed by participants testing panels of reference strains and repeated re-challenge with identical controls, accompanied by educative feedback. Overall, correct results were obtained for 944 (82%) of 1030 tests performed for five ‘core’ antibiotics. Aggregated error rates decreased from 33% (123 tests) in 2001 to 4·4% (180 tests) in 2007 with improvements in individual laboratory performance. Cephalosporin test results produced high error rates without improvement. Reference centre and network laboratory collaboration produced marked improvements in test performance through annual EQAS integrating proficiency testing and participant education. More frequent EQAS cycles would assist this process. These experiences may be applicable in similar settings elsewhere.

Because of recent reports of abortion in farmers' wives following infection with ovine strains of Chlamydia psittaci during pregnancy, the distribution of chlamydial antibodies was studied in rural populations in north-west England, where endemic chalamydial infection with abortion in common in sheep. Immunoperoxidase assays with C. treachomatis and ovine C. psittaci showed no significant differences in either the frequency or titres of antibodies between sheep farmers and other types of farmer or non-farming adults living in the same areas. The frequency and titers of antibodies in farmers' wives were no greater than in farmers, and were unrelated to their previous obstetric history or type of farming. Overall, 62/255 (24%) of this rural population had antibody detected by C. trachomatis antigen and only 30/255 (13%) detected by C.Psittaci antigen. The possible significance of these findings is discussed. This survey does not suggest that the risk of infection with C.psittaci is especially high in people working with sheep, but the complications following infection during pregnancy deserve the specific instructions that have been given to pregnant women to avoid exposure, especially during lambing, in farming and veterinary work.

Analysis by epidemiological methods of the spread of the common cold among office workers and their families has failed to account for more than a fraction of the infections as a consequence of known exposure to infected individuals. Infections too mild to be recorded as colds, survival of the virus in the environment and its subsequent dispersal are considered as possible explanations of this.

The distribution of serial intervals between colds suffered by members of the same family indicates that the median interval between the onset of an infection and the first symptom in infection apparently arising from it as cross-infections was between 21½ and 31½ days. This is only slightly longer than the median interval, 2·4 days, observed between nasal installation and the onset of symptoms in experimental infections.

There is some epidemiological evidence that susceptibility to the common cold is reduced during the weeks following a cold.

We should like to repeat, in this the second paper in this series, our thanks to the Ministry of Pensions and National Insurance and to the Shell Petroleum Company, to those members of their staffs and to the nurses and others who helped us in this investigation.

A prospective survey was conducted in patients admitted to 11 randomly selected general practices and eight hospitals located in six provinces of Poland. For each patient meeting the international acute gastrointestinal infection (AGI) case definition criteria, information was collected on healthcare resources used. Antibacterial drug consumption was assessed using defined daily doses (DDD) and extrapolated to the national level using results from a parallel study of AGI incidence in the community. Additionally, a logistic multivariable model was fitted assessing determinants of antibacterial drug administration. Valid questionnaires were collected from 385 general practitioner (GP) consultations and 504 hospital admissions. Antibacterials for systemic use were prescribed during 60 (16%) GP consultations and 179 (36%) hospital admissions. The estimated societal AGI-related consumption of antibacterials amounted to 5·48 million DDD (95% uncertainty interval 1·56–14·12 million DDD). Antibacterial prescription was associated with work in large practices [adjusted odds ratio (aOR) 3·16] and hospital wards (aOR 2·87), compared to small general practices, referral for microbiological testing (aOR 2·88), presence of fever (aOR 2·50), presence of mucus or blood in stool (aOR 1·94), age >65 years vs. <5 years (aOR 1·88), and rural vs. urban residence (aOR 1·53). Despite the fact that antibacterials were prescribed to a minority of consulted AGI patients, their consumption in society was not negligible due to the high prevalence of AGI symptoms. Prescription of antibacterial drugs should be restricted to cases with specific indications, preferably following microbiological investigation of AGI aetiology. To achieve this, clear national recommendations should be widely disseminated to physicians, and included in medical training curricula.

In an established burns centre which moved from an old building to new purpose-designed premises, colonization rates of patients' burns with Staphylococcus aureus, Pseudomonas aeruginosa and other Gram-negative bacilli were not reduced. Colonization rates with Streptococcus pyogenes increased but the increase was mainly due to multiple importations in the new premises of a strain of higher communicability than any seen in the old.

In the first 32 months in the new environment 10 patients were found colonized with pseudomonas on admission and 20 became colonized in the unit. A much higher proportion of patients with burns of more than 30% body surface became colonized than of patients with less. About one-third of the above 20 patients became colonized with strains already isolated from another patient; all but one of them had small area burns. Cross-infection was not observed from numerous heavily colonized patients with high percentage burns. This paradox is discussed in detail. Basin outflows in the new premises became colonized with P. aeruginosa of two serotypes not found on patients in this unit.

Outbreaks of soft tissue or skin infection due to non-tuberculous mycobacteria are reported frequently in scientific journals but in general the infection source in these outbreaks remains unknown. In Venezuela, in two distinct outbreaks, one after breast augmentation surgery and another after hydrolipoclasy therapy, 16 patients contracted a soft tissue infection due to Mycobacterium abscessus subsp. abscessus. Searching for the possible environmental infection sources in these outbreaks, initially the tap water (in the hydrolipoclasy therapy outbreak) and a surgical skin marker (in the breast implant surgery outbreak), were identified as the infection sources. Molecular typing of the strains with a variable number tandem repeat typing assay confirmed the tap water as the infection source but the molecular typing technique excluded the skin marker. We discuss the results and make a call for the implementation of stringent hygiene and disinfection guidelines for cosmetic procedures in Venezuela.

African horse sickness (AHS) and equine encephalosis (EE) viruses are endemic to southern Africa. AHS virus causes severe epidemics when introduced to naive equine populations, resulting in severe restrictions on the movement of equines between AHS-positive and negative countries. Recent zoning of South Africa has created an AHS-free zone to facilitate equine movement, but the transmission dynamics of these viruses are not fully understood. Here, we present further analyses of serosurveys of donkeys in South Africa conducted in 1983–5 and in 1993–5. Age-prevalence data are used to derive estimates of the force of infection, λ. For both viruses, λ was highest in the northeastern part of the country and declined towards the southwest. In most of the country, EE virus had a higher transmission rate than AHS. The force of infection increased for EE virus between 1985 and 1993, but decreased for AHS virus. Both viruses showed high levels of variation in transmission between districts within the same province, particularly in areas of intermediate transmission. These data emphasize the focal nature of these viruses, and indicate areas where further data will assist in understanding the geographical variation in transmission.

Risk factors for cervical infection with human papillomavirus (HPV) were assessed among 236 Italian women at risk for human immunodeficiency virus (HIV) infection (intravenous drug users (IVDU) or sexual partners of males at risk for HIV infection). All study participants underwent a structured interview, determination of HIV serostatus and detection of HPV cervical infection by means of polymerase chain reaction (PCR). Overall, the cervical presence of HPV DNA was ascertained in 86 of these 236 women (36·4%), while squamous intraepithelial lesions (SIL) were diagnosed in 57 (24·1%). HPV-infected and non-infected women did not differ in age, education and cigarette smoking. A statistically significant trend in the risk of HPV infection with increasing number of lifetime sexual partners was noted (P=0·01), but such trend was attenuated in multivariate analysis (multiple logistic regression (MLR) odds ratio (OR) for [ges ]20 partners vs 1=1·6, 95% confidence intervals (CI): 0·4–5·9). A nearly threefold higher risk of HPV cervical infection emerged among IVDU women (MLR–OR: 2·7, 95% CI: 1·4–5·0), and this difference was not influenced by HIV serostatus. The prevalence of HIV infection was higher among HPV-positive than HPV-negative women (62·8% and 54·0%, respectively) (MLR–OR=1·9, 95% CI: 0·9–3·8), and the proportion of women with less than 200 CD4+ cells/mm3 was slightly and not significantly higher among HPV-positive (47·1%) than negative women (37·2%).

Better control of highly pathogenic avian influenza (HPAI) outbreaks requires deeper understanding of within-flock virus transmission dynamics. For such fatal diseases, daily mortality provides a proxy for disease incidence. We used the daily mortality data collected during the 2015 H5N2 HPAI outbreak in Minnesota turkey flocks to estimate the within-flock transmission rate parameter (β). The number of birds in Susceptible, Exposed, Infectious and Recovered compartments was inferred from the data and used in a generalised linear mixed model (GLMM) to estimate the parameters. Novel here was the correction of these data for normal mortality before use in the fitting process. We also used mortality threshold to determine HPAI-like mortality to improve the accuracy of estimates from the back-calculation approach. The estimated β was 3.2 (95% confidence interval (CI) 2.3–4.3) per day with a basic reproduction number of 12.8 (95% CI 9.2–17.2). Although flock-level estimates varied, the overall estimate was comparable to those from other studies. Sensitivity analyses demonstrated that the estimated β was highly sensitive to the bird-level latent period, emphasizing the need for its precise estimation. In all, for fatal poultry diseases, the back-calculation approach provides a computationally efficient means to obtain reasonable transmission parameter estimates from mortality data.

The course of experimental infection in groups of 6-month-old castrated lambs with field isolates of Mycoplasma agalactiae from France was followed culturally and serologically for 7 months. Infection with an ovine field isolate following inoculation by different routes and contact exposure was compared with that caused similarly by a caprine field isolate. The prolonged infections produced were symptomless apart from limited arthritis in one animal inoculated with the isolate from sheep and increased lachrymation in another associated with the goat isolate. The ovine isolate was more virulent in that ante- and post-mortem recoveries of the organism were more consistent and the serological responses more pronounced. Serological responses varied between animals and between strain infections, and the results of the film inhibition test were more consistent than those of the complement fixation test. The limitations of both these tests for detecting carrier infections are discussed.

In one locality in Italy where the incidence of psittacosis has increased rapidly since 1980, a hospital-based study and a seroepidemiological survey were carried out in order to define the clinical and epidemiological features of psittacosis in that area.

Registers of the Virology Unit of the University of Ancona, Italy, were reviewed and all hospitalized patients with a serological diagnosis of psittacosis were identified. A total of 76 cases were found and studied. A presumptive bird source was identified in 80% of 62 patients, on whom a detailed investigation had been possible. Poultry represented the most frequent probable source of infection. Clinically, the predominant pattern of illness was a moderately severe lower respiratory tract infection, with chest X-rays showing pulmonary shadowings in 68 patients (89%).

In the seroepidemiological study, 51 out of 143 subjects were exposed to birds (35·7%), but only 7 out of 90 urban adult blood donors (7·3%) were positive for chlamydial antibodies using the microimmunofluorescence test.

Understanding endemic infectious disease risk factors through traditional epidemiological tools is challenging. Population-based case–control studies are costly and time-consuming. A case–case analyses using surveillance data addresses these limitations by using resources more efficiently. We conducted a case–case analyses using routine surveillance data reported by 16 U.S. states (2005–2015), wherein reported cases of salmonellosis were used as a comparison group to identify exposure associations with reported cases of cryptosporidiosis and giardiasis. Odds ratios adjusted for age and reporting state (aOR) and 95% confidence intervals (95% CI) were calculated. A total of 10 704 cryptosporidiosis cases, 17 544 giardiasis cases, and 106 351 salmonellosis cases were included in this analyses. When compared with cases of salmonellosis, exposure to treated recreational water (aOR 4.7, 95% CI 4.3–5.0) and livestock (aOR: 3.2; 95% CI: 2.9–3.5) were significantly associated with cryptosporidiosis and exposure to untreated drinking (aOR 4.1, 95% CI 3.6–4.7) and recreational water (aOR 4.1, 95% CI 3.7–4.5) were associated with giardiasis. Our analyses shows that routine surveillance data with standardised exposure information can be used to identify associations of interest for cryptosporidiosis and giardiasis.