Reducing the risk of human immunodeficiency virus type 1 (HIV-1) transmission is still a public health priority. The development of effective control strategies relies on the quantification of the effects of prophylactic and therapeutic measures in disease incidence. Although several assays can be used to estimate HIV incidence, these estimates are limited by the poor performance of these assays in distinguishing recent from long-standing infections. To address such limitation, we have developed an assay to titrate p24-specific IgG3 antibodies as a marker of recent infection. The assay is based on a recombinant p24 protein capable to detect total IgG antibodies in sera using a liquid micro array and enzyme-linked immunosorbent assay. Subsequently, the assay was optimised to detect and titrate anti-p24 IgG3 responses in a panel of sequential specimens from seroconverters over 24 months. The kinetics of p24-specific IgG3 titres revealed a transient peak in the 4 to 5-month period after seroconversion. It was followed by a sharp decline, allowing infections with less than 6 months to be distinguished from older ones. The developed assay exhibited a mean duration of recent infection of 144 days and a false-recent rate of ca. 14%. Our findings show that HIV-1 p24-specific IgG3 titres can be used as a tool to evaluate HIV incidence in serosurveys and to monitor the efficacy of vaccines and other transmission control strategies.

High-throughput sequencing technologies now allow for rapid cost-effective surveys of multiple pathogens in many host species including rodents, but it is currently unclear if the organ chosen for screening influences the number and identity of bacteria detected. We used 16S rRNA amplicon sequencing to identify bacterial pathogens in the heart, liver, lungs, kidneys and spleen of 13 water voles (Arvicola terrestris) collected in Franche-Comté, France. We asked if bacterial pathogen assemblages within organs are similar and if all five organs are necessary to detect all of the bacteria present in an individual animal. We identified 24 bacteria representing 17 genera; average bacterial richness for each organ ranged from 1·5 ± 0·4 (mean ± standard error) to 2·5 ± 0·4 bacteria/organ and did not differ significantly between organs. The average bacterial richness when organ assemblages were pooled within animals was 4·7 ± 0·6 bacteria/animal; Operational Taxonomic Unit accumulation analysis indicates that all five organs are required to obtain this. Organ type influences bacterial assemblage composition in a systematic way (PERMANOVA, 999 permutations, pseudo-F4,51 = 1·37, P = 0·001). Our results demonstrate that the number of organs sampled influences the ability to detect bacterial pathogens, which can inform sampling decisions in public health and wildlife ecology.

To assess the relationship between the neutrophil-to-lymphocyte ratio (NLR) and related parameters to the severity of coronavirus disease 2019 (COVID-19) symptoms. Clinical data from 38 COVID-19 patients who were diagnosed, treated and discharged from the Qishan Hospital in Yantai over the period from January to February 2020 were analysed. NLR and procalcitonin (PCT) were determined in the first and fourth weeks after their admission, along with the clinical characteristics and laboratory test results of these patients. Based on results as obtained on the first and fourth weeks after admission, five indices consisting of NLR, white blood cells, neutrophils, lymphocytes (LY) and monocytes (MON) were selected to generate receiver operating characteristic curves, while optimal cutoff values, sensitivities and specificities were obtained according to the Yuden index. Statistically significant differences in neutrophils, LY and the NLR were present in the severe vs. moderate COVID-19 group from the first to the fourth week of their hospitalisation. The cut-off value of NLR for predicting the severity of COVID-19 was 4.425, with a sensitivity of 0.855 and a specificity of 0.979. A statistically significant positive correlation was present between PCT and NLR in the severe group as determined within the first week of admission. NLR can serve as a predictor of COVID-19 disease severity as patients' progress from the first to the fourth week of their hospitalisation. The statistically significant positive correlation between levels of NLR and PCT in severe patients indicated that increases in NLR were accompanied with gradual increases in PCT.

The objective of the study was to assess whether genotypic characterization by means of DNA-fingerprinting pattern (DFP) and multilocus enzyme electrophoresis (MEE) profile as compared to phenotypic characterization would improve the differentiation of Neisseria meningitidis strains associated with outbreaks from strains associated with sporadic cases of meningococcal disease. In addition, the differentiation of serogroup C carrier strains from those associated with an outbreak of serogroup C meningococcal disease was investigated.

A total of 118 N. meningitidis strains were available for the study: 59 from patients involved in outbreaks of meningococcal disease (2 serogroup B and 2 serogroup C), 37 from patients considered to be sporadic cases and 22 serogroup C carrier strains.

Among the 59 strains from patients involved in outbreaks the 4 strains isolated from the patient registered as the first in each outbreak were designated the index strains. Among the remaining 55 outbreak strains 52 were either DFP-identical or DFP-indistinguishable when compared with the one relevant out of the 4 index strains. This was only the case for 17 of the 37 strains isolated from sporadic cases caused by the same serogroup of meningococci during the outbreak periods, and 5 of the 22 meningococcal strains isolated from healthy carriers. Among the 56 (52 + 4) DFP-identical or DFP-indistinguishable outbreak strains 5 different electrophoretic types were identified by MEE.

Among 59 assumed outbreak strains a total of 4 were identified as genotypically distinct. Among the 37 mainly DFP-indistinguishable or DFP-different strains from sporadic cases 17 different ETs were identified, and among the 22 mainly DFP-different carrier strains 13 different ETs were identified. Two strains among those selected from sporadic cases were identical to the outbreak strain. None of the local serogroup C carrier strains isolated during the outbreak of serogroup C disease were identical to the outbreak strain.

Both DNA-fingerprinting and MEE improved the differentiation of meningococci when compared with phenotypic characterization. The results indicate that tracing a virulent strain within an open group of contacts is irrelevant.

The objective of this study was to assess the use of statistical algorithms in identifying significant clusters of Salmonella spp. across different sectors of the food chain within an integrated surveillance programme. Three years of weekly Salmonella serotype data from farm animals, meat, and humans were used to create baseline models (first two years) and identify weeks with counts higher than expected using surveillance algorithms in the third (test) year. During the test year, an expert working group identified events of interest reviewing descriptive analyses of same data. The algorithms did not identify Salmonella events presenting as gradual increases or seasonal patterns as identified by the working group. However, the algorithms did identify clusters for further investigation, suggesting they could be a valuable complementary tool within an integrated surveillance system.

Healthcare-associated infections in veterinary hospitals are commonly attributed to Salmonella enterica, particularly in large animal facilities, and are characteristically associated with widespread environmental contamination. The objective of this study was to investigate factors influencing the likelihood of identifying environmental contamination of a veterinary hospital with S. enterica, while exploring different analytic methods to model complex factors that may influence this ecology. Environmental surveillance samples were collected in a large veterinary hospital as part of a long-term infection control programme. Data were collected retrospectively from the electronic medical records database. Many easily measured variables were complex in nature (i.e., they represented variance that is unmeasured or unidentified as a specific factor) necessitating the use of alternative analytic methods (variable cluster and principal components analyses) to provide perspective regarding the complex data structure and latent factors that may be contributing to this ecology. Subsequently, multivariable logistic regression was performed using generalised estimating equations. Results suggest the probability of detecting Salmonella in the environment increased as demand on personnel increased (e.g., in a busy hospital). Veterinary personnel need to remain vigilant in implementing practices that we believe empirically will mitigate risk for widespread environmental contamination and sustained transmission among patients (i.e., rigorous hygiene for personnel and the environment).

Although pneumonic plague is listed by the Centers of Disease Control in the leading ‘critical biological agents’, very few studies exist on this subject. In this study, a mathematical compartment model was used to describe the geographical and temporal spread of an epidemic of pneumonic plague following its use as a biological weapon. Univariate and multivariate analyses were performed in order to assess the key parameters for the control of an outbreak in France. If interventions were taken 10 days after an attack, a reference scenario of 1000 index cases in Paris would lead to 2500 deaths. The results of the study indicate that the rapidity of onset of interventions has the largest effect on the final size of the epidemic, followed by wearing masks, treating contacts preventively and quarantine. Limiting inter-regional mixing does little to reduce casualties, although it does confine them to a single region.

Dengue virus, commonly transmitted by mosquitoes, causes a human disease of significant social impact and presents a serious public health problem in Brazil. This report describes the unusual emergence of DENV-4 in northern Brazil after a nearly 30-year-long absence. DENV-4 genotype I is of Asian origin and was identified in the serum of patients receiving treatment at a hospital serving the Salvador area (Brazilian state of Bahia). The identification of dengue virus serotypes through molecular and phylogenetic analysis is essential for predicting disease severity or fatal illness, principally in endemic countries such as Brazil.

A total of 160 consecutive isolates of Neisseria gonorrhoeae was collected over a 3-month period. They were tested for their susceptibility to penicillin, erythromycin and spectinomycin and the auxotype and the serotype determined. We have evaluated two sampling methods, the collection of every fifth isolate and the first 20 isolates (10 male and 10 female) each month, to determine whether either is representative of the total population. There was no significant difference between either method of sampling and the total for detecting the predominant auxotypes and serovars or the distributions in antibiotic susceptibility. It is possible to monitor major changes in a gonococcal population, particularly susceptibility to antibiotics, using a sample of the total population.

Estimates of the proportion of illness transmitted by food for different enteric pathogens are essential for foodborne burden-of-disease studies. Owing to insufficient scientific data, a formal synthesis of expert opinion, an expert elicitation, is commonly used to produce such estimates. Eleven experts participated in an elicitation to estimate the proportion of illnesses due to food in Australia for nine pathogens over three rounds: first, based on their own knowledge alone; second, after being provided with systematic reviews of the literature and Australian data; and finally, at a workshop where experts reflected on the evidence. Estimates changed significantly across the three rounds (P = 0·002) as measured by analysis of variance. Following the workshop in round 3, estimates showed smoother distributions with significantly less variation for several pathogens. When estimates were combined to provide combined distributions for each pathogen, the width of these combined distributions reflected experts’ perceptions of the availability of evidence, with narrower intervals for pathogens for which evidence was judged to be strongest. Our findings show that the choice of expert elicitation process can significantly influence final estimates. Our structured process – and the workshop in particular – produced robust estimates and distributions appropriate for inclusion in burden-of-disease studies.

Considerable difference of opinion has existed as to whether the incidence of cancer is at all affected by the habits of life of different classes of the community. There is of course no doubt that in certain occupations particular forms of malignant disease are exceptionally prevalent, the case of chimney sweeps being notorious; but the more general question as to the incidence on large groups of occupations has not been so definitely determined. The present research was suggested by the apparently contradictory results obtained by Heron from his study of London statistics, and by Maynard from an analysis of United States data.

Gas production by coliform organisms and Escherichia coli from lauryl tryptose lactose broth (LTLB) was compared with that from brilliant green (lactose) bile broth (BGB). These media were compared with lauryl tryptose mannitol broth (LTMB) with and without added tryptophan for both gas and indole production. At 37 °C, LTLB and BGB were both satisfactory for gas production, but at 44 °C, LTLB gave fewer false-negative results and was thus significantly less inhibitory than BGB. However when LTLB and LTMB were compared as single-tube confirmatory media, LTLB give a high proportion of false-negative reactions in the indole test at 44 °C. The substitution of mannitol for lactose and the addition of tryptophan yielded a satisfactory medium for both confirmation of gas production and the demonstration of indole at 44 °C.

Toxoplasma gondii (T. gondii) is an important human disease-causing parasite. In the USA, T. gondii infects >10% of the population, accrues economic losses of US$3.6 billion/year, and ranks as the second leading culprit of foodborne illness-related fatalities. We assessed toxoplasmosis risk among the Old Order Amish, a mostly homogenous population with a high prevalence of T. gondii seropositivity, using a questionnaire focusing on food consumption/preparation behaviours and environmental risk factors. Analyses were conducted using multiple logistic regression. Consuming raw meat, rare meat, or unpasteurised cow or goat milk products was associated with increased odds of seropositivity (unadjusted Odds Ratios: 2.192, 1.613, and 1.718 , respectively). In separate models by sex, consuming raw meat, or consuming unpasteurised cow or goat milk products, was associated with increased odds of seropositivity among women; washing hands after touching meat with decreased odds of seropositivity among women (adjusted OR (AOR): 0.462); and cleaning cat litterbox with increased odds of seropositivity among men (AOR: 5.241). This is the first study to assess associations between behavioural and environmental risk factors and T. gondii seropositivity in a US population with high seroprevalence for T. gondii. Our study emphasises the importance of proper food safety behaviours to avoid the risk of infection.

Epidemiological research on respiratory syncytial virus (RSV) infections in children was carried out at the Virology Laboratory, University Teaching Hospital (UTH), in Lusaka, Zambia, from January–December 1996. Specimens including 736 nasal washings and 2424 throat swabs were collected from children with acute respiratory infections (ARI) and tested for RSV by enzyme immunoassay and by virus isolation. RSV was isolated in 62 (4·1%) of 1496 throat swabs collected from March to September and was detected in 99 (16·3%) of 609 nasal washings from March to November. The average RSV isolation rate was 2·6% and the average RSV detection rate was 13·5%. The highest RSV isolation (8·1%) and detection (30·5%) rates were in June 1996. RSV antibody in the 278 serum specimens collected from Zambian children, who were hospitalized in the paediatric ward, UTH, was detected using a standard neutralization test. The antibody positive rate was 60–80% in children >4 years. It is evident that RSV is one of the main causal agents of ARI in children in Zambia.

Trimethoprim resistance was examined in faecal bacteria obtained from chickens, sheep, cattle and pigs. The incidence of trimethoprim resistance in porcine strains was 17% (157/922) and, whereas 15·8% (146/922) of these bacteria were highly resistant, only 4% (37/922) of the isolates possessed trimethoprim resistance plasmids. Highly resistant porcine strains were obtained from 44% of the pig farms (41/93) but transferable trimethoprim resistance was found in isolates from 11% (10/93) of the farms. There was an association between the carriage of trimethoprim resistance plasmids and certain farms. Most of the resistance plasmids were not identical with those found in human clinical bacteria but one porcine plasmid was the same as the most ubiquitous trimethoprim resistance plasmid in Edinburgh.

Ticks recovered from dogs in rural villages around Madrid (Spain) were processed to isolate rickettsiae. One sample containing mixtures of ticks and four containing eggs, in which rickettsiae had been detected by indirect immunofluorescence with a human serum highly reactive to Rickettsia conorii, were decontaminated, homogenized and inoculated onto Vero cells. Two egg samples yielded a cytopathic agent that reacted positively by immunofluorescence. One sample (14H) was successfully subcultured and identified as a member of the spotted fever group rickettsia. Tick eggs provide suitable material for isolation of rickettsia.

We present data on pneumococcal isolates collected from deep and superficial sites over a 16-year period at the Edinburgh City Hospital. The 10 most frequent serotypes overall were 6, 19, 11, 9, 3, 14, 1, 15 and 18 in children and 19, 23, 6, 6, 9, 11, 3, 15, 14, 22 and 4 in adults. Over 88% (2588/2932, 88·3%) of these pneumococci were of serotypes represented in the 23-valent polysaccharide pneumococcal vaccine. Within the 20–45 years age group, 228/434 (52·5%) of specimens were from HIV-infected individuals. The isolations showed a seasonal distribution with peaks in February and troughs in September. The annual numbers of blood culture isolates showed an upward trend. Recurrent isolations were more frequent in HIV-infected individuals (49/132, 37%) than in non-HIV-infected individuals (218/2421, 9·9%) (relative risk = 5·05, 95% confidence interval, 3·46–7·03). The prevalence of resistance to penicillin and erythromycin was lower than that reported in other parts of the UK.

From 21 January 2020 to 9 February 2020, three family clusters involving 31 patients with coronavirus disease 2019 were identified in Wenzhou, China. The epidemiological and clinical characteristics of the family cluster patients were analysed and compared with those of 43 contemporaneous sporadic cases. The three index cases transmitted the infection to 28 family members 2–10 days before illness onset. Overall, 28 of the 41 sporadic cases and three of 31 patients in the family clusters came back from Wuhan (65.12 vs. 9.68%, P< 0.001). In terms of epidemiological characters and clinical symptoms, no significant differences were observed between the family cluster and sporadic cases. However, the lymphocyte counts of sporadic cases were significantly lower than those of family cluster cases ((1.32 ± 0.55) × 109/l vs. (1.63 ± 0.70) × 109/l, P = 0.037), and the proportion of hypoalbuminaemia was higher in sporadic cases (18/43, 41.86%) than in the family clusters (6/31, 19.35%) (P < 0.05). Within the family cluster, the second- and third-generation cases had milder clinical manifestations, without severe conditions, compared with the index and first-generation cases, indicating that the virulence gradually decreased following passage through generations within the family clusters. Close surveillance, timely recognition and isolation of the suspected or latent patient is crucial in preventing family cluster infection.

Fifteen and five of 20 volunteers challenged with the enterotoxigenic Escherichia coli strain O 78·H11 showed a fourfold titre increase of serum ELISA antibody to the homologous O 78 and the heterologous O 8 lipopolysaccharide antigen, respectively. Sixty-three of 191 sera from 1- to 48-month-old German children showed serum antibody reactive with O 78 antigen, all but two of these O 78-positive sera also showed reactivity with at least one further O antigen. Only 14 of the O 78 reactive sera also showed antibody to heat-labile enterotoxin. In addition, soluble O 8 antigen could inhibit the binding of serum antibody to absorbed O 78 in 68% of the German children. Antibody reactive with O 78 antigen is thus not a reliable serological marker for enterotoxigenic E. coli infection in German children.