Human rotavirus strains from Kenya, from children with gastroenteritis in an urban area (Nairobi) and three rural areas were characterized by antigenic and genomic analysis. While in all areas strains with subgroups II and G serotype 1 antigens were most common, two unusual strains were detected. One strain (NK59: subgroup II. G serotype 4) possessed an additional RNA band on polyacrylamide gel electrophoresis, the other (D202) which had antigenic specificity of subgroup II and G serotype 1 showed a ‘short’ RNA pattern. The latter strain was adapted to growth in cell culture.

The coronavirus disease 2019 (COVID-19) pandemic is currently the most critical challenge in public health. An understanding of the factors that affect severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection will help fight the COVID-19 pandemic. This study sought to investigate the association between SARS-CoV-2 infection and blood type distribution. The big data provided by the World Health Organization (WHO) and Johns Hopkins University were used to assess the dynamics of the COVID-19 epidemic. The infection data in the early phase of the pandemic from six countries in each of six geographic zones divided according to the WHO were used, representing approximately 5.4 billion people around the globe. We calculated the infection growth factor, doubling times of infection and death cases, reproductive number and infection and death cases in relation to the blood type distribution. The growth factor of infection and death cases significantly and positively correlated with the proportion of the population with blood type A and negatively correlated with the proportion of the population with blood type B. Compared with the lower blood type A population (<30%), the higher blood type A population (⩾30%) showed more infection and death cases, higher growth factors and shorter case doubling times for infections and deaths and thus higher epidemic dynamics. Thus, an association exists between SARS-CoV-2 and the ABO blood group distribution, which might be useful for fighting the COVID-19 pandemic.

Various variables that might influence the rapid and sustained virological response to recombinant PEG-IFN-α-2a were explored in Iraqi HCV-infected patients with haemoglobinopathy. Forty-three patients were evaluated for the relationship between rapid virological response (RVR), IL-28B polymorphism, viral load, liver enzyme levels, blood group, ultrasound findings, or HCV genotype and the sustained virological response (SVR) achievement. The overall RVR was 55·81% while the overall SVR was 53·49%. SVR in patients that achieved RVR was 82·61% (P = 0·0004). A significant association was found between initial alanine transaminase levels and viral load with SVR achievement (P = 0·025) and (P = 0·004), respectively. Thirty-two (74%) out of 43 of our samples were host genotyped at the IL-28B locus as CC, a significant association was found between CC group and SVR achievement (P = 0·04). Of our samples, 23/43 (53%) were typed as HCV genotype 4, 10/43 (23%) as genotype 1, 9/43 (20·9%) as genotype 3 and 1/43 (2·3%) as genotype 2. A significant association was found between genotype 3 and SVR achievement (P = 0·006). Multivariate analysis showed that only RVR achievement independently associated with SVR in the Iraqi population (P = 0·00). These results can be used to classify the patients requiring the more expensive new direct-acting antiviral drugs.

1. A simple method for the long-term viable-preservation of samples of Leptospira suspensions is described. Quantities of about 25 μl., with the addition of 77·5 % glycerol, are introduced into capillary tubes, cooled slowly to −79° C. and stored at that temperature.

2. More than half the attempts were successful in re-establishing growth in culture after storage at −79° C. for periods up to 27 months.

3. The possibility that the method could be used for establishing ‘banks’ of standard Leptospira material for reference is discussed.

We performed two different approaches (broth enrichment step prior to culture (BEC) and PCR (BEPCR)) for detecting Streptococcus pneumoniae from nasopharyngeal specimens collected from 242 children aged <6 years attending one hospital (n = 140) and one childcare centre (n = 102) in a major urban area in Brazil. These specimens were collected immediately before the introduction of the 10-valent pneumococcal conjugate vaccine (PCV10) and the 13-valent vaccine (PCV13) for routine use in Brazil. Results were compared with previous findings obtained with direct culture (DC) on a selective medium. Colonisation prevalence was 58·3% (n = 141), being higher among children attending the childcare centre (62·7% vs. 55%). The culture-based methods (DC and BEC) enabled the detection of S. pneumoniae in 119 (49·2%) and 115 (47·5%) children, respectively. The PCR-based method (BEPCR) was more sensitive and 137 (56·6%) carriers were identified. Twenty-six serogroups/serotypes were identified, predominantly 6B, 19F, 14, 6A, 15C and 23F. Multiple colonisation was observed in 13 (5·4%) children. The estimated serotypes coverage of available PCVs was 40·4% for the 10-valent (included in the Brazilian immunisation programme) and 55·8% for the 13-valent (only available in private clinics). The use of robust approaches to obtain a more realistic insight about the asymptomatic carrier status is of paramount importance to estimate and assess the impact of vaccine implementation. The combination between culture-based and molecular methods constitutes a suitable strategy.

The names Citrobacter koseri, Levinea malonatica and Citrobacter diversus are synonymous. As a result of the study of representative strains of these organisms an antigenic scheme comprising seven O antigens has been proposed. The examination of a further 165 strains from clinical sources suggests that an additional seven antigens should be included in the scheme. The serological and biochemical reactions of the test strains for all 14 O antigens are described.

For some years past a careful record has been kept of the method of feeding, not only of all children dying of epidemic diarrhoea, but also of all babies under one year of age in the houses of the working classes, which are visited year by year in the course of routine house-to-house inspections by the sanitary inspectors in my department. It is impossible to ask the necessary questions at every house, but in most houses information has been given without difficulty, and it may be taken as certain that the 1259 babies living in 10,308 houses who are classified in the first four columns of Table I belong approximately to the same social stratum as the 121 babies dying from diarrhoea who are classified in the four last columins of the same table.

Pertussis morbidity is highest in infants too young to be fully protected by routine vaccination schedules. Alternate vaccine strategies are required to maximise protection in this age-group. To understand baseline pertussis epidemiology prior to the introduction of the maternal pertussis vaccination program in 2014, we conducted a retrospective case series analyses of 53 901 notifications and temporal trends from 1997 to 2014. Notifications were highest in infants younger than 4 months of age and highest annual notification rates in infants younger than 1 month of age (308/100 000 per year). Amongst Aboriginal and Torres Strait Islander infants aged younger than 1 month, this rate was 576/100 000 per year. Notification rates were 40% higher amongst women 15–44 years, 62·4/100 000 population compared with men (44·5/100 000) and 90% higher in Aboriginal and Torres Strait Islander women of the same age (38·2/100 000) compared with men (19·7/100 000). Six infant deaths were identified, all younger than 2 months of age. Monitoring epidemiology in at-risk groups – infants too young to be vaccinated, women of childbearing age and Aboriginal and Torres Strait Islander peoples – following implementation of the maternal pertussis vaccination program will be important to assess its impact and safety.

Antivirals are an important defence against novel strains of influenza. However, the impact of widespread drug usage on strain circulation across multiple epidemic waves – via their impact on host immunity – is unknown despite antivirals having the likelihood of extensive use during a pandemic. To explore how drug usage by individuals affects population strain dynamics, we embedded a two-strain model of within-host dynamics within an epidemic model. We found that when 40% of hosts took drugs early during the infectious period, transmission was reduced by 30% and average levels of immunity by 2·9-fold (comparable to antibody concentrations), relative to 14% and 1·5-fold reductions when drugs were taken late. The novel strain was more successful relative to the resident strain when drugs were not taken, and an intermediate level of drug coverage minimized incidence in subsequent waves. We discuss how drug regimens, coverage and R0 could impact pandemic preparedness.

Nipah virus (NiV) is a recently emerged zoonotic virus that causes severe disease in humans. The reservoir hosts for NiV, bats of the genus Pteropus (known as flying-foxes) are found across the Asia-Pacific including Australia. While NiV has not been detected in Australia, evidence for NiV infection has been found in flying-foxes in some of Australia's closest neighbours. A qualitative risk assessment was undertaken to assess the risk of NiV establishing in Australian flying-foxes through flying-fox movements from nearby regions. Events surrounding the emergence of new diseases are typically uncertain and in this study an expert opinion workshop was used to address gaps in knowledge. Given the difficulties in combining expert opinion, five different combination methods were analysed to assess their influence on the risk outcome. Under the baseline scenario where the median was used to combine opinions, the risk was estimated to be very low. However, this risk increased when the mean and linear opinion pooling combination methods were used. This assessment highlights the effects that different methods for combining expert opinion have on final risk estimates and the caution needed when interpreting these outcomes given the high degree of uncertainty in expert opinion. This work has provided a flexible model framework for assessing the risk of NiV establishment in Australian flying-foxes through bat movements which can be updated when new data become available.

To investigate the potential of poultry products as the source of human infections associated with quinolone-resistant campylobacters, 140 human and 75 poultry isolates of nalidixic acid-resistant campylobacters were collected between 1996 and 1998, and analysed by two molecular typing methods. By the analysis of restriction fragment length polymorphism of the flagellin gene, 33 distinct patterns were obtained, with 18 of which shared by both human (89%) and poultry (93%) isolates. By the pulsed-field gel electrophoresis of SmaI-restricted macrofragments, 105 different profiles were obtained, and 11 were found in both human (40%) and poultry (23%) isolates. When the two typing methods were combined, 112 unique genotypes were obtained, 11 of which were shared by both populations, including 53 (38%) human isolates and 14 (19%) poultry isolates. Although domestic poultry products are still important sources of the quinolone-resistant campylobacter infections in humans, there are other factors that might contribute to these increasing infections simultaneously. A more stringent policy in the use of antimicrobial agents in food animals can no longer be ignored.

Salmonella Paratyphi A (SPA) is rapidly becoming a common cause of enteric fever in South East Asia. A large outbreak of SPA occurred in a boarding middle school in China in 2004. There were 394 suspected cases; 95·5% were students. The highest incidence was in the youngest children (7th grade). Forty-four of 151 (29%) blood cultures and 4/54 (7·4%) rectal swabs were positive for SPA; three were from kitchen workers. The geometric mean levels of serum IgG anti-lipopolysaccharide (anti-LPS) from patients was higher than from healthy individuals [35·25 vs. 5·20 ELISA units (EU), P<0·001]. A kitchen worker with a positive rectal swab, negative blood culture and a high level of serum IgG anti-LPS (529·65 EU), was identified as a possible SPA carrier. No SPA was isolated from water or food samples. A survey of students' habits indicated drinking unboiled water as being the main reason for contracting the disease. Hand washing was the second most important factor. A food handler with possible SPA carriage could also have been a risk factor. Attention to maintaining a safe water supply, enhancing food-handler hygiene and proper hand washing can help to prevent similar outbreaks in the future.

The bacterial populations of six freshwater streams in populated areas of the Hong Kong New Territories were studied. There is considerable faecal contamination of these streams, with coliform counts as high as 105 c.f.u./ml and the contaminating organisms show a high prevalence of antibiotic resistance and multiple resistance. With direct plating of water samples onto antibioticcontaining media, an average of 49% of the gram-negative bacteria were ampicillinresistant, 3% chloramphenicol-resistant and 1% gentamicin-resistant. At individual sites resistance to these three drugs was as high as 98%, 8% and 3% respectively. More than 70% of strains were resistant to two or more antibiotics, 29% to five or more and 2% to eight or more. A total of 98 patterns of antibiotic resistance were detected with no one pattern predominating. Twenty-eight gram-negative bacterial species were identified as stream contaminants. Escherichia coli was the commonest bacterial species isolated and other frequent isolates were Enterobacter sp., Klebsiella sp. and Citrobacter sp., but no enteric pathogens were detected. The greatest prevalence of resistance and multiple resistance was associated with the heaviest contamination by E. coli. Analysis of selected stream isolates revealed multiple plasmid bands arranged in many different patterns, but multiple antibiotic resistances were shown to be commonly mediated by single transferable plasmids. Faecally-contaminated freshwater streams in Hong Kong may be reservoirs of antibiotic resistance plasmids for clinically-important bacteria.

For studies examining risk factors of sexually transmitted infections (STIs), confounding can stem from characteristics of partners of study subjects, and persist after adjustment for the subjects’ individual-level characteristics. Two conditions that can result in confounding by the subjects’ partners are: (C1) partner choice is assortative by the risk factor examined and, (C2) sexual activity is associated with the risk factor. The objective of this paper is to illustrate the potential impact of the assortativity bias in studies examining STI risk factors, using smoking and human papillomavirus (HPV) as an example. We developed an HPV transmission-dynamic mathematical model in which we nested a cross-sectional study assessing the smoking–HPV association. In our base case, we assumed (1) no effect of smoking on HPV, and (2) conditions C1–C2 hold for smoking (based on empirical data). The assortativity bias caused an overestimation of the odds ratio (OR) in the simulated study after perfect adjustment for the subjects’ individual-level characteristics (adjusted OR 1·51 instead of 1·00). The bias was amplified by a lower basic reproductive number (R0), greater mixing assortativity and stronger association of smoking with sexual activity. Adjustment for characteristics of partners is needed to mitigate assortativity bias.

To study whether African-Americans are less likely than whites to present with cryptosporidiosis as an AIDS-defining condition (ADC), a case-control study was conducted using a large, population-based surveillance registry of AIDS patients in California. Data from January 1980 through June 1999 were analysed using risk factor stratification and multivariate logistic regression to evaluate confounding by other risk factors such as gender, injection drug use (IDU), CD4 counts, age and sexual orientation. Cases included 1373 subjects with cryptosporidiosis as an ADC and controls included 97419 subjects with other ADC. The results indicate a significantly lower risk for presentation with cryptosporidiosis as an ADC among African-Americans compared with whites (OR vs. whites = 0·5, 95% CI 0·4, 0·7). Additionally, there is evidence that heterosexuals are less likely than homosexual/bisexual males to present with cryptosporidiosis (OR = 0·5, 95% CI 0·4, 0·7). Our analyses also suggest a decreasing risk with increasing age. The possibility that there may be biologic factors or differential lifetime exposures that account for the difference between the racial/ethnic groups merits further investigation.

Aeromonas caviae, an enteropathogen associated with gastroenteritis, displays several virulence characteristics. Studies on the kinetics of growth of A. caviae and expression of β–haemolytic toxin revealed that A. caviae produced maximum haemolytic activity extracellularly during the stationary phase. Preliminary studies on the properties of A. caviae haemolysin suggested that divalent cations (Mg2+ and Ca2+) and thiol compounds, dithiothreitol and mercaptoethanol enhanced the haemolytic activity. Addition of L–cysteine, glutathione and EDTA reduced the haemolytic activity. The iron chelator, 2–2' bipyridyl, significantly inhibited the growth of A. caviae possibly by iron limitation, with parallel enhancement of haemolysin production compared to A. caviae grown in excess of iron. These results suggest that A. caviae produces only β-haemolysin, which resembles the haemolysins reported for several other bacteria and the activity might be regulated by environmental factors especially iron.

1. When chick embryo cell monolayers were infected with ultrasonically treated elementary body suspension by a short period of adsorption some of the adsorbed virus lost infectivity in a few minutes. This was followed by a more gradual loss during incubation of the cultures. The lowest point was reached at 4–6 hr. followed by a rise in titre due to production of new virus at 7–8 hr. The quantitative assessment of these changes is discussed.

2. In such cultures, titration of intact and disintegrated cells after incubation for 4–5 hr., indicated an eclipse phase by showing an absence of infective virus in cells which ultimately produced it. The process of eclipse continued for several hours. With inoculum that had not been subjected to ultrasonic treatment it was not possible to show this by infecting HeLa cell monolayers.

3. Ultrasonically treated inoculum, compared with a similar, but untreated inoculum, had a three to flvefold higher titre. The virus units in it were more uniformly capable of infecting cells. After its adsorption to monolayers a rapid loss of some infective virus occurred within a few minutes which was not demonstrable with untreated inoculum. During incubation of monolayers infected with treated inoculum the loss of infectivity was faster, there was a more rapid production of new virus and a greater yield. The nature of the changes in the virus which were brought about by ultrasonic treatment have not been explained, but the use of such an inoculum markedly affected the results of experiments.

4. Treatment of infected monolayers with trypsin or EDTA caused the cells to shed as much as half their virus. This virus would not be released spontaneously into the medium or removed from monolayers by washing. This applied to all periods of incubation up to 24 hr. or more when marked increase of virus had occurred.

5. The disintegration of infected cells by ultrasonic treatment was efficient in releasing infective virus from them, although it was not possible to be certain all the virus in the cells was rendered detectable by this technique.

6. The effect of some technical procedures on the interpretation of results is discussed.

This article describes an outbreak of Q fever involving 24 men (five prison officers and nineteen detainees) in one of H.M. Detention Centres. The evidence collected points strongly to the consumption of raw milk as the route of infection. This appears to be the first milk-borne outbreak of Q fever to be reported in Britain.

This study investigated the incidence and risk to staff groups for sustaining needlestick injuries (NSIs) in the National University Hospital (NUH), Singapore. A retrospective cohort review of incident NSI cases was undertaken to determine the injury rate, causation, and epidemiological profile of such injuries. Analysis of the risk of sustaining recurrent NSI by occupation and location was done using the Cox proportional hazards model. There were 244 NSI cases in 5957 employees in NUH in 2014, giving an incidence rate of 4·1/100 healthcare workers (HCWs) per year. The incidence rate was highest for doctors at 21·3, and 2·7 for nurses; 40·6% of injuries occurred in wards, and 32·8% in operating theatres. There were 27 cases of repeated NSI cases. The estimated cost due to NSIs in NUH ranged from US$ 109 800 to US$ 563 152 in 2014. We conclude that creating a workplace environment where top priority is given to prevention of NSIs in HCWs, is essential to address the high incidence of reported NSIs. The data collected will be of value to inform the design of prevention programmes to reduce further the risk of NSIs in HCWs.

Resistance to carbapenems in human pathogens is a growing clinical and public health concern. The carbapenems are in an antimicrobial class considered last-resort, they are used to treat human infections caused by multidrug-resistant Enterobacterales, and they are classified by the World Health Organization as ‘High Priority Critically Important Antimicrobials’. The presence of carbapenem-resistant Enterobacterales (CREs) of animal-origin is of concern because targeted studies of Canadian retail seafood revealed the presence of carbapenem resistance in a small number of Enterobacterales isolates. To further investigate this issue, a risk profile was developed examining shrimp and salmon, the two most important seafood commodities consumed by Canadians and Escherichia coli, a member of the Enterobacterales order. Carbapenem-resistant E. coli (CREc) isolates have been identified in shrimp and other seafood products. Although carbapenem use in aquaculture has not been reported, several classes of antimicrobials are utilised globally and co-selection of antimicrobial-resistant microorganisms in an aquaculture setting is also of concern. CREs have been identified in retail seafood purchased in Canada and are currently thought to be uncommon. However, data concerning CRE or CREc occurrence and distribution in seafood are limited, and argue for implementation of ongoing or periodic surveillance.