Hepatitis C virus (HCV) infection was frequent in human immunodeficiency virus (HIV) patients in Yunnan province. We studied the epidemic characteristics of HCV in HIV/HCV co-infected patients. Serum from 894 HIV-1 patients was collected, together with basic information and biochemical features. All samples were infected with HIV through injecting drug users (IDUs) and sexual transmission (ST). The NS5B gene was amplified and sequenced to affirm HCV genotype. In total, 202 HIV patients were co-infected with HCV, and most (81.19%) of co-infected patients were IDUs. Genotype 3b was predominant (37.62%) in these samples, and its frequency was similar in patients with IDU and ST. The frequencies of genotypes 1a, 1b, 3a, 6a, 6n, 2a and 6u were 3.96%, 16.34%, 23.76%, 6.93%, 10.40%, 0.50% and 0.50%, respectively. However, genotype 3a showed significantly different frequency in HCV patients with IDU and ST (P = 0.019). When HCV patients were divided into subgroups, the haemoglobin (HGB) level was significantly higher in patients with genotype 3a than in patients with 3b (P = 0.033), 6a (P = 0.006) and 6n (P = 0.007), respectively. Although no difference existed among HCV subgroups, HIV-viral load was identified to be positively correlated with the HGB level and CD4+ cells when dividing HCV/HIV co-infected persons into male and female groups. In conclusion, genotype 3b was the predominant HCV genotype in Yunnan HIV/HCV co-infected persons. The HGB level was higher in patients with genotype 3a than others. HIV-viral load was positively correlated with the HGB level and CD4+ cells in the male or female HCV-infected group.

The spread of the Zika virus (ZIKV) in the Americas led to large outbreaks across the region and most of the Southern hemisphere. Of greatest concern were complications following acute infection during pregnancy. At the beginning of the outbreak, the risk to unborn babies and their clinical presentation was unclear. This report describes the methods and results of the UK surveillance response to assess the risk of ZIKV to children born to returning travellers. Established surveillance systems operating within the UK – the paediatric and obstetric surveillance units for rare diseases, and national laboratory monitoring – enabled rapid assessment of this emerging public health threat. A combined total of 11 women experiencing adverse pregnancy outcomes after possible ZIKV exposure were reported by the three surveillance systems; five miscarriages, two intrauterine deaths and four children with clinical presentations potentially associated with ZIKV infection. Sixteen women were diagnosed with ZIKV during pregnancy in the UK. Amongst the offspring of these women, there was unequivocal laboratory evidence of infection in only one child. In the UK, the number and risk of congenital ZIKV infection for travellers returning from ZIKV-affected countries is very small.

Increasing hospital admissions for pneumonia have been reported recently but it is not known whether pneumonia incidence rates have increased in the community. To determine whether incidence rates of pneumonia increased in primary care in the United Kingdom from 2002 to 2017, an open cohort study was conducted using electronic health records from the UK Clinical Practice Research Datalink. Clinically diagnosed pneumonia, influenza pneumonia, pleural infection and clinically suspected pneumonia, defined as chest infection treated with antibiotics, were evaluated. Age-standardised and age-specific rates were estimated. Joinpoint regression models were fitted and annual percentage changes (APC) were estimated. There were 70.7 million person-years of follow-up with 120 662 episodes of clinically diagnosed pneumonia, 1 831 005 of clinically suspected pneumonia, 23 814 episodes of influenza pneumonia and 2644 pleural infections over 16 years. The incidence of clinically diagnosed pneumonia increased from 1.50 per 1000 person-years in 2002 to 2.22 per 1000 in 2017. From 2010 to 2017, the APC in age-standardised incidence was 5.1% (95% confidence interval 3.4–6.9) compared with 0.3% (−0.6 to 1.2%) before 2010. Clinically suspected pneumonia incidence rates increased from 2002 to 2008 with an APC 3.8% (0.8–6.9) but decreased with an APC −4.9% (−6.7 to −3.1) from 2009 to 2017. Influenza pneumonia increased in the epidemic year of 2009. There was no overall trend in pleural infection. The results show that clinically diagnosed pneumonia has increased in primary care but there was a contemporaneous decline in recording of clinically suspected pneumonia or ‘chest infection’. Changes in disease labelling practice might partly account for these trends.

Foodborne salmonellosis causes approximately 1 million illnesses annually in the United States. In the summer of 2017, we investigated four multistate outbreaks of Salmonella infections associated with Maradol papayas imported from four Mexican farms. PulseNet initially identified a cluster of Salmonella Kiambu infections in June 2017, and early interviews identified papayas as an exposure of interest. Investigators from Maryland, Virginia and Food and Drug Administration (FDA) collected papayas for testing. Several strains of Salmonella were isolated from papayas sourced from Mexican Farm A, including Salmonella Agona, Gaminara, Kiambu, Thompson and Senftenberg. Traceback from two points of service associated with illness sub-clusters in two states identified Farm A as a common source of papayas, and three voluntary recalls of Farm A papayas were issued. FDA sampling isolated four additional Salmonella strains from papayas sourced from Mexican Farms B, C and D. In total, four outbreaks were identified, resulting in 244 cases with illness onset dates from 20 December 2016 to 20 September 2017. The sampling of papayas and the collaborative work of investigative partners were instrumental in identifying the source of these outbreaks and preventing additional illnesses. Evaluating epidemiological, laboratory and traceback evidence together during investigations is critical to solving and stopping outbreaks.

We studied trends in the incidence of health care-associated infections (HAIs) in LTCFs between 2009 and 2015 and determined the effect of participation in our network. Elder-care physicians reported weekly the number of cases of influenza-like illness, gastroenteritis, (probable) pneumonia, urinary tract infections (UTIs) and all-cause mortality. Trends in the incidence of infection and mortality in relation to LTCF characteristics were calculated using multilevel univariate and multivariate logistic regression. Thirty LTCF participated for 3 years or more, 16 for 2 years and the remaining 12 LTCF for 1 year. During the study period, the median number of beds decreased from 158 to 139, whereas the percentage of residents with private bedrooms increased from 14% to 87%. UTIs were the most frequently reported infections, followed by (probable) pneumonia and gastroenteritis. Adjusted for calendar year and season, we observed a statistically significant decrease in the incidence of influenza-like illness (odds ratio (OR) = 0.8, P < 0.01) and (probable) pneumonia (OR = 0.8, P < 0.01) for each extra year an LTCF participated. Although there are other likely contributors, such as more private rooms and enhanced infection control measures, the decreasing trend of HAI in LTCFs participating in surveillance implies that surveillance is a valuable addition to current strategies to optimise infection control.

In 2016, we reviewed preventive control measures for secondary transmission of Shiga-toxin producing Escherichia coli (STEC) in humans in European Union (EU)/European Free Trade Association (EEA) countries to inform the revision of the respective Norwegian guidelines which at that time did not accommodate for the varying pathogenic potential of STEC. We interviewed public health experts from EU/EEA institutes, using a semi-structured questionnaire. We revised the Norwegian guidelines using a risk-based approach informed by the new scientific evidence on risk factors for HUS and the survey results. All 13 (42%) participating countries tested STEC for Shiga toxin (stx) 1, stx2 and eae (encoding intimin). Five countries differentiated their control measures based on clinical and/or microbiological case characteristics, but only Denmark based their measures on routinely conducted stx subtyping. In all countries, but Norway, clearance was obtained with ⩽3 negative STEC specimens. After this review, Norway revised the STEC guidelines and recommended only follow-up of cases infected with high-virulent STEC (determined by microbiological and clinical information); clearance is obtained with three negative specimens. Implementation of the revised Norwegian guidelines will lead to a decrease of STEC cases needing follow-up and clearance, and will reduce the burden of unnecessary public health measures and the socioeconomic impact on cases. This review of guidelines could assist other countries in adapting their STEC control measures.

Social outings can trigger influenza transmission, especially in children and elderly. In contrast, school closures are associated with reduced influenza incidence in school-aged children. While influenza surveillance modelling studies typically account for holidays and mass gatherings, age-specific effects of school breaks, sporting events and commonly celebrated observances are not fully explored. We examined the impact of school holidays, social events and religious observances for six age groups (all ages, ⩽4, 5–24, 25–44, 45–64, ⩾65 years) on four influenza outcomes (tests, positives, influenza A and influenza B) as reported by the City of Milwaukee Health Department Laboratory, Milwaukee, Wisconsin from 2004 to 2009. We characterised holiday effects by analysing average weekly counts in negative binomial regression models controlling for weather and seasonal incidence fluctuations. We estimated age-specific annual peak timing and compared influenza outcomes before, during and after school breaks. During the 118 university holiday weeks, average weekly tests were lower than in 140 school term weeks (5.93 vs. 11.99 cases/week, P < 0.005). The dampening of tests during Winter Break was evident in all ages and in those 5–24 years (RR = 0.31; 95% CI 0.22–0.41 vs. RR = 0.14; 95% CI 0.09–0.22, respectively). A significant increase in tests was observed during Spring Break in 45–64 years old adults (RR = 2.12; 95% CI 1.14–3.96). Milwaukee Public Schools holiday breaks showed similar amplification and dampening effects. Overall, calendar effects depend on the proximity and alignment of an individual holiday to age-specific and influenza outcome-specific peak timing. Better quantification of individual holiday effects, tailored to specific age groups, should improve influenza prevention measures.

Risk factors and prevalence of pulmonary nontuberculous mycobacterial (NTM) diseases were retrospectively evaluated in 1208 suspected pulmonary TB patients seeking care at the Affiliated Hospital of Hangzhou Normal University between July 2018 and December 2018. Further analysis of 390 culture-positive cases demonstrated that 358 (358/390, 91.8%) were infected with Mycobacterium tuberculosis (MTB), 24 (24/390, 6.2%) with NTM and eight (8/390, 2.0%) with both MTB and NTM. M. intracellulare was the most prevalent NTM isolated (16/24, 66.7%), followed by M. abscessus (3/24), M. kansasii (2/24), M. avium (1/24), M. szulgai (1/24) and M. fortuitum (1/24). The difference between NTM and TB case rates for the ⩾65-year-old age group significantly exceeded the difference for the reference group (patients aged 25–44 years) (OR (95% CI): 4.63 (1.03–20.90)). Pulmonary NTM diseases incidence positively correlated with prior TB history (OR (95% CI): 12.92 (3.24–31.82)). Moreover, pulmonary NTM patients were significantly more likely to exhibit underlying bronchiectasis than pulmonary TB patients (OR (95% CI): 18.89 (7.54–47.88)). In conclusion, approximately one-tenth of culture-positive suspected pulmonary TB patients are infected with NTM (most frequently M. intracellulare) in Zhejiang Province, China. The elderly and those with bronchiectasis or a history of TB are at the greatest risk of contracting pulmonary NTM disease.

We investigated a large multistate outbreak that occurred in the United States in 2015–2016. Epidemiologic, laboratory, and traceback studies were conducted to determine the source of the infections. We identified 907 case-patients from 40 states with illness onset dates ranging from July 3, 2015 to March 2, 2016. Sixty-three percent of case-patients reported consuming cucumbers in the week before illness onset. Ten illness sub-clusters linked to events or purchase locations were identified. All sub-clusters investigated received cucumbers from a single distributor which were sourced from a single grower in Mexico. Seventy-five cucumber samples were collected, 19 of which yielded the outbreak strain. Whole genome sequencing performed on 154 clinical isolates and 19 cucumber samples indicated that the sequenced isolates were closely related genetically to one another. This was the largest US foodborne disease outbreak in the last ten years and the third largest in the past 20 years. This was at least the fifth multistate outbreak caused by contaminated cucumbers since 2010. The outbreak is noteworthy because a recall was issued only 17 days after the outbreak was identified, which allowed for the removal of the contaminated cucumbers still available in commerce, unlike previous cucumber associated outbreaks. The rapid identification and response of multiple public health agencies resulted in preventing this from becoming an even larger outbreak.

With the aim to elucidate gonococcal antimicrobial resistance (AMR)–risk factors, we undertook a retrospective analysis of the molecular epidemiology and AMR of 104 Neisseria gonorrhoeae isolates from clinical samples (urethra, rectum, pharynx and cervix) of 94 individuals attending a sexually transmitted infection clinic in Madrid (Spain) from July to October 2016, and explored potential links with socio-demographic, behavioural and clinical factors of patients. Antimicrobial susceptibility was determined by E-tests, and isolates were characterised by N. gonorrhoeae multi-antigen sequence typing. Penicillin resistance was recorded for 15.4% of isolates, and most were susceptible to tetracycline, cefixime and azithromycin; a high incidence of ciprofloxacin resistance (~40%) was found. Isolates were grouped into 51 different sequence types (STs) and 10 genogroups (G), with G2400, ST5441, ST2318, ST12547 and G2992 being the most prevalent. A significant association (P = 0.015) was evident between HIV-positive MSM individuals and having a ciprofloxacin-resistant strain. Likewise, a strong association (P = 0.047) was found between patient age of MSM and carriage of isolates expressing decreased susceptibility to azithromycin. A decrease in the incidence of AMR gonococcal strains and a change in the strain populations previously reported from other parts of Spain were observed. Of note, the prevalent multi-drug resistant genogroup G1407 was represented by only three strains in our study, while the pan-susceptible clones such as ST5441, and ST2318, associated with extragenital body sites were the most prevalent.

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic disease transmitted from dromedary camels to people, which can result in outbreaks with human-to-human transmission. Because it is a subclinical infection in camels, epidemiological measures other than prevalence are challenging to assess. This study estimated the force of infection (FOI) of MERS-CoV in camel populations from age-stratified serological data. A cross-sectional study of MERS-CoV was conducted in Kenya from July 2016 to July 2017. Seroprevalence was stratified into four age groups: <1, 1–2, 2–3 and >3 years old. Age-independent and age-dependent linear and quadratic generalised linear models were used to estimate FOI in pastoral and ranching camel herds. Models were compared based on computed AIC values. Among pastoral herds, the age-dependent quadratic FOI was the best fit model, while the age-independent FOI was the best fit for the ranching herd data. FOI provides an indirect estimate of infection risk, which is especially valuable where direct estimates of incidence and other measures of infection are challenging to obtain. The FOIs estimated in this study provide important insight about MERS-CoV dynamics in the reservoir species, and contribute to our understanding of the zoonotic risks of this important public health threat.

We examined the prevalence and correlates of Helicobacter pylori (H. pylori) infection according to cytotoxin-associated gene A (CagA) phenotype, a main virulence antigen, among the ethnically diverse population groups of Jerusalem. A cross-sectional study was undertaken in Arab (N = 959) and Jewish (N = 692) adults, randomly selected from Israel's national population registry in age-sex and population strata. Sera were tested for H. pylori immunoglobulin G (IgG) antibodies. Positive samples were tested for virulence IgG antibodies to recombinant CagA protein, by enzyme-linked immunosorbent assay. Multinomial regression models were fitted to examine associations of sociodemographic factors with H. pylori phenotypes. H. pylori IgG antibody sero-prevalence was 83.3% (95% confidence interval (CI) 80.0%–85.5%) and 61.4% (95% CI 57.7%–65.0%) among Arabs and Jews, respectively. Among H. pylori positives, the respective CagA IgG antibody sero-positivity was 42.3% (95% CI 38.9%–45.8%) and 32.5% (95% CI 28.2%–37.1%). Among Jews, being born in the Former Soviet Union, the Middle East and North Africa, vs. Israel and the Americas, was positively associated with CagA sero-positivity. In both populations, sibship size was positively associated with both CagA positive and negative phenotypes; and education was inversely associated. In conclusion, CagA positive and negative infection had similar correlates, suggesting shared sources of these two H. pylori phenotypes.

This study aimed to evaluate the clinical characteristics, risk factors and outcomes of adult patients with candidaemia caused by C. albicans vs. non-albicans Candida spp. (NAC). All adult hospitalised cases of candidaemia (2012–2017) at a tertiary hospital in Shenyang were included in the retrospective study, and a total of 180 episodes were analysed. C. parapsilosis was the most frequently isolated species (38.3%), followed by C. albicans (35.6%), C. glabrata (13.9%), C. tropicalis (10%) and others (2.2%). As initial antifungal therapy, 75.0%, 3.9%, 5.6% and 2.2% of patients received fluconazole, caspofungin, micafungin and voriconazole, respectively. Multivariate analyses revealed that total parenteral nutrition was associated with an increased risk of NAC bloodstream infections (BSI) (OR 2.535, 95% CI (1.066–6.026)) vs. C. albicans BSI. Additionally, the presence of a urinary catheter was associated with an increased risk of C. albicans BSI (OR 2.295 (1.129–4.666)) vs. NAC BSI. Moreover, ICU stay (OR 4.013 (1.476–10.906)), renal failure (OR 3.24 (1.084–9.683)), thrombocytopaenia (OR 7.171 (2.152–23.892)) and C. albicans (OR 3.629 (1.352–9.743)) were independent risk factors for candidaemia-related 30-day mortality, while recent cancer surgery was associated with reduced mortality risk (OR 26.479 (2.550–274.918)). All these factors may provide useful information to select initial empirical antifungal agents.

This study aimed to characterise children and adults diagnosed with influenza who were admitted to three medical centres in northern Israel in the winter of 2015–2016, a unique season due to infection with three types of influenza strains: A/H1N1, A/non-H1N1 and B. Data were collected retrospectively from medical records. Influenza A/H1N1 infected mainly adults (61% vs. 16% in children, P < 0.001) while influenza B was the common type in children (54% vs. 28% in adults, P < 0.001). Adults (36% vs. 5% in children, P < 0.001) and patients infected with A/H1N1 had higher rates of pneumonia (34% vs. 16% and 14% in influenza B and A/non-H1N1, respectively, P = 0.002). Treatment with oseltamivir was prescribed to 90% of patients; adults had higher rates of treatment (96% vs. 84% in children, P = 0.002) as well as patients infected with A/H1N1 (96% vs. 86% in influenza B and A/non-H1N1, respectively, P = 0.04). Oseltamivir was given after a mean of 3.6 days of symptoms. Preferential infection of adults by A/H1N1 was evident in Israel in 2015–2016; pneumonia rates were higher in adults and in A/H1N1-infected patients. Oseltamivir was prescribed to most patients but especially to those infected with A/H1N1, and was given relatively late in the course of the disease.

Seasonal influenza virus epidemics have a major impact on healthcare systems. Data on population susceptibility to emerging influenza virus strains during the interepidemic period can guide planning for resource allocation of an upcoming influenza season. This study sought to assess the population susceptibility to representative emerging influenza virus strains collected during the interepidemic period. The microneutralisation antibody titers (MN titers) of a human serum panel against representative emerging influenza strains collected during the interepidemic period before the 2018/2019 winter influenza season (H1N1-inter and H3N2-inter) were compared with those against influenza strains representative of previous epidemics (H1N1-pre and H3N2-pre). A multifaceted approach, incorporating both genetic and antigenic data, was used in selecting these representative influenza virus strains for the MN assay. A significantly higher proportion of individuals had a ⩾four-fold reduction in MN titers between H1N1-inter and H1N1-pre than that between H3N2-inter and H3N2-pre (28.5% (127/445) vs. 4.9% (22/445), P < 0.001). The geometric mean titer (GMT) of H1N1-inter was significantly lower than that of H1N1-pre (381 (95% CI 339–428) vs. 713 (95% CI 641–792), P < 0.001), while there was no significant difference in the GMT between H3N2-inter and H3N2-pre. Since A(H1N1) predominated the 2018–2019 winter influenza epidemic, our results corroborated the epidemic subtype.

Enteric illness outbreaks are complex events, therefore, outbreak investigators use many different hypothesis generation methods depending on the situation. This scoping review was conducted to describe methods used to generate a hypothesis during enteric illness outbreak investigations. The search included five databases and grey literature for articles published between 1 January 2000 and 2 May 2015. Relevance screening and article characterisation were conducted by two independent reviewers using pretested forms. There were 903 outbreaks that described hypothesis generation methods and 33 papers which focused on the evaluation of hypothesis generation methods. Common hypothesis generation methods described are analytic studies (64.8%), descriptive epidemiology (33.7%), food or environmental sampling (32.8%) and facility inspections (27.9%). The least common methods included the use of a single interviewer (0.4%) and investigation of outliers (0.4%). Most studies reported using two or more methods to generate hypotheses (81.2%), with 29.2% of studies reporting using four or more. The use of multiple different hypothesis generation methods both within and between outbreaks highlights the complexity of enteric illness outbreak investigations. Future research should examine the effectiveness of each method and the contexts for which each is most effective in efficiently leading to source identification.