Porphyromonas gingivalis has been linked to the development and progression of oesophageal squamous cell carcinoma (ESCC), and is considered to be a high-risk factor for ESCC. Currently, the commonly used methods for P. gingivalis detection are culture or DNA extraction-based, which are either time and labour intensive especially for high-throughput applications. We aimed to establish and evaluate a rapid and sensitive direct quantitative polymerase chain reaction (qPCR) protocol for the detection of P. gingivalis without DNA extraction which is suitable for large-scale epidemiological studies. Paired gingival swab samples from 192 subjects undergoing general medical examinations were analysed using two direct and one extraction-based qPCR assays for P. gingivalis. Tris-EDTA buffer-based direct qPCR (TE-direct qPCR), lysis-based direct qPCR (lysis-direct qPCR) and DNA extraction-based qPCR (kit-qPCR) were used, respectively, in 192, 132 and 60 of these samples for quantification of P. gingivalis. The sensitivity and specificity of TE-direct qPCR was 95.24% and 100% compared with lysis-direct qPCR, which was 100% and 97.30% when compared with kit-qPCR; TE-direct qPCR had an almost perfect agreement with lysis-direct qPCR (κ = 0.954) and kit-qPCR (κ = 0.965). Moreover, the assay time used for TE-direct qPCR was 1.5 h. In conclusion, the TE-direct qPCR assay is a simple and efficient method for the quantification of oral P. gingivalis and showed high sensitivity and specificity compared with routine qPCR.

Plasmid profile analysis by agarose gel electrophoresis was carried out on 37 drug-resistant strains of Shigella dysenteriae types 2, 3, 4, 6 and 7. These strains were collected between 1976 and 1985 in Addis Ababa, Ethiopia.

The plasmid profile of S. dysenteriae type 2 strains with R-type CSSuT did not show middle-sized plasmids likely to code for CSSuT resistance. All strains contained a large plasmid of about 120 megadaltons (MDa), and a cryptic plasmid of about 2·2 MDa. The plasmid profiles of S. dysenteriae type 3 with R-types ACSSuT, SSuT and SSu showed a 4·2 MDa SSu-determinant, which was demonstrated in Escherichia coli K12 recipients resulting from triparental crosses. The ACT determinant in S. dysenteriae type 3 with R-type ACSSuT is probably chromosomally mediated. Cryptic plasmids of about 3·0 and 2·2 MDa were found in all S. dysenteriae type 3 isolates. The 4·2 MDa plasmid featured prominently in the plasmid profiles of S. dysenteriae types 4, 6 and 7 with R-types SSuT and SSu. However, this plasmid was not mobilizable by triparental crosses. There was a relative paucity of transferable plasmids in non-Shiga bacillus isolates. However, incompatibility group N plasmids, coding for tetracycline resistance, were detected.

To characterize post-treatment clearance of young forms of Plasmodium falciparum from the blood, three differential equation models, a linear decline, a linear then logarithmic decline, and the Michaelis–Menten (MM) kinetic equation, were fitted to log-transformed serial parasite counts from 30 semi-immune patients with synchronous parasitaemias allocated one of six antimalarial drug regimens. The first two equations were solved analytically. The MM equation was solved numerically using a fifth-order Runge–Kutta method. For each equation, parasite clearance was assumed stochastic and log-transformed parasite counts were assumed to be normally distributed at each time-point. Comparisons between models were by Minimum Akaike Information Criterion Estimate. A constrained MM equation fitted the data at least as well as the other two models in 5 of 6 drug groups and also when pooled data were analysed, providing a single index which could be used in drug efficacy studies in similar situations or as part of more complex models that encompass asynchronous, complicated infections.

During the 2014–2016 Ebola epidemic in West Africa, some communities reacted hostilely to the implementation of quarantine measures. This study's aim was to examine the views of lay people in Guinea on the acceptability of community quarantine. From June to August 2016, 302 adults indicated the acceptability of quarantine in 36 scenarios varying as a function of four factors: the infectious disease's level of contagiousness, its level of lethality, the number of cases in the community and whether persons in quarantine are provided with support services. Five clusters were identified: (1) for 18% of the participants, quarantine is never acceptable; (2) 16% considered, in contrast, that quarantine is always acceptable; (3) for 14%, it depends on the disease's level of contagiousness and lethality; (4) 36% based their judgement not only on the levels of contagiousness and lethality, but also on whether those in quarantine are provided with support services; and (5) 16% had no opinion. Interventions to increase voluntary compliance with community quarantine in Guinea must not be ‘one size fits all’, but must be multifaceted and tailored in design and implementation to match the diversity of people's concerns and needs.

The discriminatory power of multiple-locus variable-number tandem-repeat analysis (MLVA) needs to be evaluated for all Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) phage types so that the power of this methodology is understood and results can be interpreted correctly during outbreak investigations. We evaluated the ability of MLVA to characterize four definitive phage types (DT) problematic in New Zealand. MLVA discriminated between DT104 isolates although there was very limited variation in the MLVA profiles for isolates with an RDNC phage type (reacts but does not conform to a recognized Typhimurium phage pattern) first observed in New Zealand's Enteric Reference Laboratory in May 2006. Most DT101 isolates had indistinguishable MLVA profiles or profiles that differed at one or two loci. This was also observed in DT160 isolates. MLVA may not identify all common-source outbreaks although it provided valuable data when applied to case isolates from two S. Typhimurium outbreaks.

1. The methods used for clearing a vaccine substrain of 17 D yellow fever virus of contaminant avian leucosis viruses are described.

2. Tests in animals and human subjects showed that the characteristics of the virus remained unchanged.

We conducted a retrospective observational study in patients with laboratory-confirmed coronavirus disease (COVID-19) who received medical care in 688 COVID-19 ambulatory units and hospitals in Mexico City between 24 February 2020 and 24 December 2020, to study if the elderly seek medical care later than younger patients and their severity of symptoms at initial medical evaluation. Patients were categorised into eight groups (<20, 20–29, 30–39, 40–49, 50–59, 60–69, 70–79 and ≥80 years). Symptoms at initial evaluation were classified according to a previously validated classification into respiratory and non-respiratory symptoms. Comparisons between time from symptom onset to medical care for every age category were performed through variance analyses. Logistic regression models were applied to determine the risk of presenting symptoms of severity according to age, and mortality risk according to delays in medical care. In total, 286 020 patients were included (mean age: 42.8, s.d.: 16.8 years; 50.4% were women). Mean time from symptom onset to medical care was 4.04 (s.d.: 3.6) days and increased with older age categories (P < 0.0001). Mortality risk increased by 6.4% for each day of delay in medical care from symptom onset. The risk of presenting with the symptoms of severity was greater with increasing age categories. In conclusion, COVID-19 patients with increasing ages tend to seek medical care later, with higher rates of symptoms of severity at initial presentation in both ambulatory units and hospitals.

French Guiana, a tropical country, is characterised by a young and multi-ethnic population. Difficulties in accessing safe water sources lead to outbreaks of gastroenteritis. The objectives of this study were (1) to describe the microbiological profile of shigella strains isolated in western French Guiana, including antimicrobial susceptibility and the distribution of strains in terms of species and serotypes and (2) to estimate the incidence of shigellosis in children under 5 years old. A retrospective observational study was conducted of 213 cases of shigellosis diagnosed in the biology department of the hospital centre for western French Guiana between 2000 and 2012 in children under 5 years old. The serogroups (formerly known as species) that predominates in French Guiana was Shigella flexneri. No resistance was observed to fluoroquinolones or to third-generation cephalosporins. The average incidence of shigellosis in children under 5 years old in western French Guiana was estimated at 189.6 cases per 100 000 inhabitants per year. Shigellosis is a public health problem in western French Guiana. These infections suggest the difficulties in accessing safe water sources and the lack of public sanitation. A quadrivalent vaccine containing Shigella sonnei and three serotypes of S. flexneri (S. flexneri 2a, 3a and 6) could provide broad coverage against shigella infections.

West Nile neuroinvasive disease (WNND) is a severe neurological illness that can result from West Nile virus (WNV) infection, with long-term disability and death being common outcomes. Although WNV arrived in North America over two decades ago, risk factors for WNND are still being explored. The objective of this study was to identify WNND comorbid risk factors in the Ontario population using a retrospective, population-based cohort design. Incident WNV infections from laboratory records between 1 January 2002 – 31 December 2012 were individually-linked to health administrative databases to ascertain WNND outcomes and comorbid risk factors. WNND incidence was compared among individuals with and without comorbidities using risk ratios (RR) calculated with log binomial regression.

Three hundred and forty-five individuals developed WNND (18.3%) out of 1884 WNV infections. West Nile encephalitis was driving most associations with comorbidities. Immunocompromised (aRR 2.61 [95% CI 1.23–4.53]) and male sex (aRR 1.32 [95% CI 1.00–1.76]) were risk factors for encephalitis, in addition to age, for which each 1-year increase was associated with a 2% (aRR 1.02 [95% CI 1.02–1.03]) relative increase in risk. Our results suggest that individuals living with comorbidities are at higher risk for WNND, in particular encephalitis, following WNV infection.

Seventy-five clinical isolates of Pseudomonas aeruginosa collected in a tertiary teaching hospital in Thailand were investigated for susceptibility to antimicrobials including imipenem. Metallo-β-lactamase (MBL) enzymes were detected by E-test MBL assay and PCR; class 1 integron genes were also detected by PCR. Strains positive for blaIMP and blaVIM genes were further characterized by DNA sequencing and examined for clonality by pulsed-field gel electrophoresis. High rates of resistance to anti-pseudomonal agents were found. MBL enzymes were found in 13 (17·3%) strains and 24 (32%) carried class 1 integron genes. Twelve of the latter strains harboured the blaIMP-14 gene and one strain the blaVIM-2 gene. All of the IMP-14 strains were identical or closely related suggesting clonal dissemination of these genes.

Two hundred and fourteen patients who had a cough illness lasting at least 2 weeks were studied to investigate Bordetella pertussis as a cause of prolonged cough in adolescents and adults. Medical history and nasopharyngeal swab specimens for culture and polymerase chain reaction (PCR) were obtained at presentation. Three (1·4%) patients were B. pertussis culture-positive; 15 (7%) were B. pertussis PCR-positive (including the culture-positive patients) and 11 (5·1%) were Bordetella spp. PCR-positive. Symptom combinations were significantly high both in patients with pertussis and patients with indeterminate results (P < 0·05). We conclude that B. pertussis should be considered among differential diagnoses of prolonged cough in adolescents and adults and PCR and culture should be used to detect these cases and facilitate public health response.

The Biofire® Film Array Meningitis Encephalitis (FAME) panel can rapidly diagnose common aetiologies but its impact in Colombia is unknown. A retrospective study of adults with CNS infections in one tertiary hospital in Colombia. The cohort was divided into two time periods: before and after the implementation of the Biofire® FAME panel in May 2016. A total of 98 patients were enrolled, 52 and 46 were enrolled in the Standard of Care (SOC) group and in the FAME group, respectively. The most common comorbidity was human immunodeficiency virus infection (47.4%). The median time to a change in therapy was significantly shorter in the FAME group than in the SOC group (3 vs. 137.3 h, P < 0.001). This difference was driven by the timing to appropriate therapy (2.1 vs. 195 h, P < 0.001) by identifying viral aetiologies. Overall outcomes and length of stay were no different between both groups (P > 0.2). The FAME panel detected six aetiologies that had negative cultures but missed identifying one patient with Cryptococcus neoformans. The introduction of the Biofire FAME panel in Colombia has facilitated the identification of viral pathogens and has significantly reduced the time to the adjustment of empirical antimicrobial therapy.

1. The types of strains of tubercle bacilli isolated from fifty cases of non-pulmonary tuberculosis in children, 0–14 years of age, in Eire have been determined. In cervical gland disease ten (71·4%) out of fourteen strains were bovine, in bone and joint disease four (18·2%) out of twenty-two were bovine and in meningitis three (25%) out of twelve were bovine. Only two cases of primary abdominal tuberculosis were examined. Both yielded human strains.

2. The difficulties in assessing the true significance of the results recorded are briefly discussed.

3. The technique used and some bacteriological observations made are described.

A one-year field-study has been carried out in a diarrhoea-endemic area in West Africa to determine the relationship between the bacteriostatic activity of fresh human milk for Escherichia coli in vitro and freedom from diarrhoea of the infant recipients of the milk. The specific contribution of E. coli gastroenteritis to gastrointestinal diseases of infants in general is not known, nor is its particular role in the Gambian infants studied. During the study period, however, both enteropathogenic and toxigenic strains of E. coli were isolated.

The incidence of diarrhoea in Gambian infants of seven age-groups from 2 days to 12 months was not significantly correlated with the bacteriostatic activity of milk. This was due rather to absence of diarrhoea in babies fed on low-activity milk than illness in those receiving highly bacteriostatic milk. Indeed, very active milk appeared to protect recipients almost completely, including seven babies of over 3 months of age, five of them during the rainy season, when the risk was high. Babies receiving lower-activity milk experienced more diarrhoea. In a situation where diarrhoeal disease is multifactorial, field evaluation of the protective action by one antibacterial property of milk is difficult. A better understanding of in vivo protection is important, and the factors which have to be taken into account are discussed.

As the corona virus disease 2019 (COVID-19) pandemic continues around the world, understanding the transmission characteristics of COVID-19 is vital for prevention and control. We conducted the first study aiming to estimate and compare the relative risk of secondary attack rates (SARs) of COVID-19 in different contact environments. Until 26 July 2021, epidemiological studies and cluster epidemic reports of COVID-19 were retrieved from SCI, Embase, PubMed, CNKI, Wanfang and CBM in English and Chinese, respectively. Relative risks (RRs) were estimated in pairwise comparisons of SARs between different contact environments using the frequentist NMA framework, and the ranking of risks in these environments was calculated using the surface under the cumulative ranking curve (SUCRA). Subgroup analysis was performed by regions. Thirty-two studies with 68 260 participants were identified. Compared with meal or gathering, transportation (RR 10.55, 95% confidence interval (CI) 1.43–77.85), medical care (RR 11.68, 95% CI 1.58–86.61) and work or study places (RR 10.15, 95% CI 1.40–73.38) had lower risk ratios for SARs. Overall, the SUCRA rankings from the highest to the lowest were household (95.3%), meal or gathering (81.4%), public places (58.9%), daily conversation (50.1%), transportation (30.8%), medical care (18.2%) and work or study places (15.3%). Household SARs were significantly higher than other environments in the subgroup of mainland China and sensitive analysis without small sample studies (<100). In light of the risks, stratified personal protection and public health measures need to be in place accordingly, so as close contacts categorising and management.

An investigation of Salm. saint-paul infection in England and Wales in 1959 is described. In one-third of the human incidents the infection was attributed to home-produced meat coming from two infected abattoirs.

Animal infection was demonstrated and was probably due to contaminated imported animal feedingstuffs.

The clinical histories of 55 of the 89 cases reported during the year were studied. There was one death. In ten patients the illness commenced with fever and malaise and diarrhoea was absent or did not occur until 24–48 hr. later. One patient developed meningitis and another an abdominal abscess.

Several methods were used to obtain serologically active materials from cultures of Micropolyspora faeni. From the results of immunodiffusion and immunoelectrophoresis tests on these materials it is suggested that preparations for the laboratory diagnosis of farmer's lung disease (FLD) should contain concentrated culture supernatant (CS) and extracts of mycelium obtained by ultrasonic treatment (MU). Although CS and MU have many serological activities in common they also possess activities unique to each.

Extraction of mycelium with trichloracetic acid, boiling water or methanol yielded a product which gave simple patterns in immunodiffusion tests. The products contained little protein but were rich in carbohydrates, particularly arabinose, galactose and glucosamine. A similar material was obtained from a cell-wall preparation by treatment with lysozyme. Antibodies to the serologically active substances in these materials occurred more frequently in sera of patients with FLD than antibodies to any other M. faeni antigen.

Attempts to obtain serologically active materials from spores were unsuccessful. Moreover antibodies to M. faeni could not be removed from patients' sera by absorption with partially purified spore preparations. It is suggested that the hypersensitivity in FLD arises from exposure to mycelial antigens.

This investigation of the incidence of tumours of the respiratory tract in Leeds was prompted by a paper read by Duguid before the Pathological Society of Great Britain and Ireland in January 1927, and published in the Lancet later in the same year. He analysed all the available post mortem records of the Manchester Royal Infirmary and showed that the incidence of intrathoracic cancer at autopsy in Manchester has steadily increased during the period of years 1886–1926 from 1·58 per cent, to 2·57 per cent.

Three time-series models (regression, decomposition, and Box–Jenkins autoregressive integrated moving averages) were applied to national surveillance data for campylobacteriosis with the goal of disease forecasting in three US states. Datasets spanned 1998–2007 for Minnesota and Oregon, and 1999–2007 for Georgia. Year 2008 was used to validate model results. Mean absolute percent error, mean square error and coefficient of determination (R2) were the main evaluation fit statistics. Results showed that decomposition best captured the temporal patterns in disease risk. Training dataset R2 values were 72·2%, 76·3% and 89·9% and validation year R2 values were 66·2%, 52·6% and 79·9% respectively for Georgia, Oregon and Minnesota. All three techniques could be utilized to predict monthly risk of infection for Campylobacter sp. However, the decomposition model provided the fastest, most accurate, user-friendly method. Use of this model can assist public health personnel in predicting epidemics and developing disease intervention strategies.