Asymptomatic colonisation of the gastrointestinal tract by carbapenemase-producing Enterobacteriaceae is an important reservoir for transmission, which may precede infection. This retrospective observational case–control study was designed to identify risk factors for developing clinical infection with OXA-48-producing Klebsiella pneumoniae in rectal carriers during hospitalisation. Case patients (n = 76) had carbapenemase-producing K. pneumoniae (CPKP) infection and positive rectal culture for CPKP. Control patients (n = 174) were those with rectal colonisation with CPKP but without CPKP infection. Multivariate analysis identified the presence of a central venous catheter (OR 4·38; 95% CI 2·27–8·42; P = 0·008), the number of transfers between hospital units (OR 1·27; 95% CI (1·06–1·52); P < 0·001) and time at risk (OR 1·02 95% CI 1·01–1·03; P = 0·01) as independent risk factors for CPKP infection in rectal carriers. Awareness of these risk factors may help to identify patients at higher risk of developing CPKP infection.

Public health interest in norovirus (NoV) has increased in recent years following improved diagnostics, global burden estimates and the development of NoV vaccine candidates. This study aimed to describe the detection rate, clinical characteristics and environmental features associated with NoV detection in hospitalized children <5 years with diarrhoea in South Africa (SA). Between 2009 and 2013, prospective diarrhoeal surveillance was conducted at four sites in SA. Stool specimens were collected and screened for NoVs and other enteric pathogens using molecular and serological assays. Epidemiological and clinical data were compared in patients with or without detection of NoV. The study detected NoV in 15% (452/3103) of hospitalized children <5 years with diarrhoea with the majority of disease in children <2 years (92%; 417/452). NoV-positive children were more likely to present with diarrhoea and vomiting (odds ratio (OR) 1·3; 95% confidence interval (CI) 1·1–1·7; P = 0·011) with none-to-mild dehydration (adjusted OR 0·5; 95% CI 0·3–0·7) compared with NoV-negative children. Amongst children testing NoV positive, HIV-infected children were more likely to have prolonged hospitalization and increased mortality compared with HIV-uninfected children. Continued surveillance will be important to consider the epidemic trends and estimate the burden and risk of NoV infection in SA.

It has previously been suggested that southern Tunisian oases may be suitable areas for the circulation of flaviviruses. In order to anticipate and prevent possible epidemiological spread of flaviviruses in humans and domestic animals, the ecology of their transmission in the oasis system needs to be better understood. Thus, the aim of this study was to assess the seroprevalence of anti-flavivirus antibodies in the laughing dove (Spilopelia senegalensis), an abundant resident bird in Tunisian oases. Anti-flavivirus antibodies were detected in 17% of sampled doves. Ten per cent of the total tested doves were West Nile virus (WNV) seropositive and 4% were Usutu virus (USUV) seropositive, which provides the first evidence of USUV circulation in Tunisian birds. We also found that the occurrence probability of anti-flavivirus antibodies in dove plasma increased with decreasing distance to coast, suggesting that doves inhabiting coastal oases were more exposed to flaviviruses compared with those inhabiting inland oases. We also found significantly higher antibody occurrence probability in adult doves compared with young doves, which underlines the effect of exposure time. Overall, our results suggest that the laughing dove may be used for WNV and USUV surveillance in southern Tunisia. They also stress the need for investigations combining data on birds and mosquitoes to better understand the ecological factors governing the circulation of flaviviruses in this area.

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.

This observational study aims to investigate the microbiological quality of commercially prepared lightly cooked foods with a major component of food of animal origin and collected as would be served to a consumer. A total of 356 samples were collected from catering (92%), retail (7%) or producers (1%) and all were independent of known incidents of foodborne illness. Using standard methods, all samples were tested for: the presence of Campylobacter spp. and Salmonella spp. and enumerated for levels of, Bacillus spp. including B. cereus, Clostridium perfringens, Listeria spp. including L. monocytogenes, Staphylococcus aureus, Escherichia coli, Enterobacteriacea and aerobic colony count (ACC). Results were interpreted as unsatisfactory, borderline or satisfactory according to the Health Protection Agency guidelines for assessing the microbiological safety of ready-to-eat foods placed on the market. Amongst all samples, 70% were classified as satisfactory, 18% were borderline and 12% were of unsatisfactory microbiological quality. Amongst the unsatisfactory samples, six (2%) were potentially injurious to health due to the presence of: Salmonella spp. (one duck breast); Campylobacter spp. (two duck breast and one chicken liver pâté); L. monocytogenes at 4·3 × 103 cfu (colony-forming units)/g (one duck confit with foie gras ballotin) and C. perfringens at 2·5 × 105 cfu/g (one chicken liver pâté). The remaining unsatisfactory samples were due to high levels of indicator E. coli, Enterobacteriaceae or ACC.

This study aimed to examine the epidemiology and treatment outcomes of community-onset purulent staphylococcal skin and soft tissue infections (SSTI) in Central Australia. We performed a prospective observational study of patients hospitalised with community-onset purulent staphylococcal SSTI (n = 160). Indigenous patients accounted for 78% of cases. Patients were predominantly young adults; however, there were high rates of co-morbid disease. Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) was the dominant phenotype, accounting for 60% of cases. Hospitalisation during the preceding 6 months, and haemodialysis dependence were significant predictors of CA-MRSA infection on univariate analysis. Clinical presentation and treatment outcomes were found to be comparable for methicillin-susceptible S. aureus (MSSA) and methicillin-resistant cases. All MRSA isolates were characterised as non-multi-resistant, with this term used interchangeably with CA-MRSA in this analysis. We did not find an association between receipt of an active antimicrobial agent within the first 48 h, and progression of infection; need for further surgical debridement; unplanned General Practitioner or hospital re-presentation; or need for further antibiotics. At least one adverse outcome was experienced by 39% of patients. Clindamycin resistance was common, while rates of trimethoprim–sulfamethoxazole resistance were low. This study suggested the possibility of healthcare-associated transmission of CA-MRSA. This is the first Australian report of CA-MRSA superseding MSSA as the cause of community onset staphylococcal SSTI.

A total of 46 strains of Salmonella isolated from patients with sporadic diarrhoea or involved in foodborne outbreaks were analysed by PCR for genus identification and serotyping. Subtyping was performed using pulsed-field gel electrophoresis (PFGE) and multiple amplification of phage locus typing (MAPLT) for seven variable loci. Bacteria were identified as belonging to serotype Enteritidis (33 strains; 71·7%) or Typhimurium (13 strains; 28·3%). A high similarity coefficient (94·6%) was observed in the Salmonella Enteritidis group for which were found three related PFGE profiles and only one MAPLT; strains representing profile PA/P1/MI were prevalent (27; 81·8%). Two Salmonella Typhimurium isolates were untypeable by PFGE. The remaining 11 strains had eight PFGE and three MAPLT profiles. The discriminatory power of MAPLT was lower than that of PFGE. Salmonella Enteritidis of clonal nature is predominant in Paraná State, with the most prevalent profile PA/P1/M1 associated with sporadic diarrhoea and with seven of nine reported outbreaks. In conclusion, PFGE shows higher discriminatory power among Salmonella strains.

A legionellosis outbreak at an industrial site was investigated to identify and control the source. Cases were identified from disease notifications, workplace illness records, and from clinicians. Cases were interviewed for symptoms and risk factors and tested for legionellosis. Implicated environmental sources were sampled and tested for legionella. We identified six cases with Legionnaires’ disease and seven with Pontiac fever; all had been exposed to aerosols from the cooling towers on the site. Nine cases had evidence of infection with either Legionella pneumophila serogroup (sg) 1 or Legionella longbeachae sg1; these organisms were also isolated from the cooling towers. There was 100% DNA sequence homology between cooling tower and clinical isolates of L. pneumophila sg1 using sequence-based typing analysis; no clinical L. longbeachae isolates were available to compare with environmental isolates. Routine monitoring of the towers prior to the outbreak failed to detect any legionella. Data from this outbreak indicate that L. pneumophila sg1 transmission occurred from the cooling towers; in addition, L. longbeachae transmission was suggested but remains unproven. L. longbeachae detection in cooling towers has not been previously reported in association with legionellosis outbreaks. Waterborne transmission should not be discounted in investigations for the source of L. longbeachae infection.

Haemophilus influenzae is an important aetiological organism of both adult and child respiratory disease. The number of non-typeable (NTHi) invasive H. influenzae isolates referred to the Queensland (QLD) Public Health Microbiology laboratory has increased notably year-by-year. In this study we used whole-genome sequencing to molecularly characterise 100 referred invasive H. influenzae, including 74 NTHi isolates over a 15-year period, observing the carriage of capsular and putative virulence genes, including the major adhesins, antimicrobial resistance genes and population diversity. Encapsulated isolates were largely clonal, however NTHi isolates displayed high genetic variability by MLST and single nucleotide polymorphism typing with no dominant clone observed. The only mechanism for β-lactam resistance identified in the QLD isolates was β-lactamase production. No single set of virulence determinants was conclusively associated with invasive QLD NTHi isolates.

The seasonality and periodicity of infections, and the mechanisms underlying observed dynamics, can have implications for control efforts. This is particularly true for acute childhood infections. Among these, the dynamics of measles is the best understood and has been extensively studied, most notably in the UK prior to the start of vaccination. Less is known about the dynamics of other childhood diseases, particularly outside Europe and the United States. In this paper, we leverage a unique dataset to examine the epidemiology of six childhood infections – measles, mumps, rubella, varicella, scarlet fever and pertussis – across 32 states in Mexico from 1985 to 2007. This dataset provides us with a spatio-temporal probe into the dynamics of six common childhood infections, and allows us to compare them in the same setting over the same time period. We examine three key epidemiological characteristics of these infections – the age profile of infections, spatio-temporal dynamics, and seasonality in transmission – and compare them with predictions from existing theory and past findings. Our analysis reveals interesting epidemiological differences between the six pathogens, and variations across space. We find signatures of term-time forcing (reduced transmission during the summer) for measles, mumps, rubella, varicella, and scarlet fever; for pertussis, a lack of term-time forcing could not be rejected.

Several infections have been linked to telomere shortening and in some cases these associations have varied by sex. We assessed the association between seropositivity to four persistent pathogens (cytomegalovirus (CMV), herpes simplex virus-1, Helicobacter pylori, Chlamydia pneumoniae), and total pathogen burden on leukocyte telomere length in a diverse US sample. Data came from the Multi-Ethnic Study of Atherosclerosis, a population-based cohort study. We utilized cross-sectional survey data, and biological samples from participants tested for pathogens and telomere length (N = 163). Linear regression was used to examine the association between seropositivity for individual pathogens as well as total pathogen burden and telomere length, adjusting for various confounders. CMV seropositivity and increased total pathogen burden level were significantly associated with shorter telomere length among females (β = −0·1204 (standard error (s.e.) 0·06), P = 0·044) and (β = −0·1057 (s.e. = 0·05), P = 0·033), respectively. There was no statistically significant association among males. Our findings suggest that prevention or treatment of persistent pathogens, in particular CMV, may play an important role in reducing telomere shortening over the life course among women. Future research is needed to confirm these novel findings in larger longitudinal samples.

Campylobacter sp. are a globally significant cause of gastroenteritis. Although rates of infection in Australia are among the highest in the industrialized world, studies describing campylobacteriosis incidence in Australia are lacking. Using national disease notification data between 1998 and 2013 we examined Campylobacter infections by gender, age group, season and state and territory. Negative binomial regression was used to estimate incidence rate ratios (IRRs), including trends by age group over time, with post-estimation commands used to obtain adjusted incidence rates. The incidence rate for males was significantly higher than for females [IRR 1·20, 95% confidence interval (CI) 1·18–1·21], while a distinct seasonality was demonstrated with higher rates in both spring (IRR 1·18, 95% CI 1·16–1·20) and summer (IRR 1·17, 95% CI 1·16–1·19). Examination of trends in age-specific incidence over time showed declines in incidence in those aged <40 years combined with contemporaneous increases in older age groups, notably those aged 70–79 years (IRR 1998–2013: 1·75, 95% CI 1·63–1·88). While crude rates continue to be highest in children, our findings suggest the age structure for campylobacteriosis in Australia is changing, carrying significant public health implications for older Australians.

We sought to comprehensively assess the prevalence and outcomes of complications associated with Staphylococcus aureus bacteremia (SAB) in children. Secondarily, prevalence of methicillin resistance and outcomes of complications from methicillin-resistant S. aureus (MRSA) vs. methicillin-susceptible S. aureus SAB were assessed. This is a single-center cross-sectional study of 376 patients ⩽18 years old with SAB in 1990–2014. Overall, 197 (52%) patients experienced complications, the most common being osteomyelitis (33%), skin and soft tissue infection (31%), and pneumonia (25%). Patients with complications were older (median 3 vs. 0·7 years, P = 0·05) and more had community-associated SAB (66% vs. 34%, P = 0·001). Fewer patients with complications had a SAB-related emergency department or hospital readmission (10% vs. 19%, P = 0·014). Prevalence of methicillin resistance increased from 1990–1999 to 2000–2009, but decreased in 2010–2014. Complicated MRSA bacteremia resulted in more intensive care unit admissions (66% vs. 47%, P = 0·03) and led to increased likelihood of having ⩾2 foci (58% vs. 26%, P < 0·001). From multivariate analysis, community-associated SAB increased risk and concurrent infections decreased risk of complications (odds ratio (OR) 1·82 (1·1–3·02), P = 0·021) and (OR 0·58 (0·34–0·97), P = 0·038), respectively. In conclusion, children with SAB should be carefully evaluated for complications. Methicillin resistance remains associated with poor outcomes but have decreased in overall prevalence.

The objectives were to present three approaches for calculating antimicrobial (AM) use in pigs that take into account the rearing period and rearing site, and to study the association between these measurements and phenotypical resistance and abundance of resistance genes in faeces samples from 10 finisher batches. The AM use was calculated relative to the rearing period of the batches as (i) ‘Finisher Unit Exposure’ at unit level, (ii) ‘Lifetime Exposure’ at batch level and (iii) ‘Herd Exposure’ at herd level. A significant effect on the occurrence of tetracycline resistance measured by cultivation was identified for Lifetime Exposure for the AM class: tetracycline. Furthermore, for Lifetime Exposure for the AM classes: macrolide, broad-spectrum penicillin, sulfonamide and tetracycline use as well as Herd Unit Exposure for the AM classes: aminoglycoside, lincosamide and tetracycline use, a significant effect was observed on the occurrence of genes coding for the AM resistance classes: aminoglycoside, lincosamide, macrolide, β-lactam, sulfonamide and tetracycline. No effect was observed for Finisher Unit Exposure. Overall, the study shows that Lifetime Exposure is an efficient measurement of AM use in finisher batches, and has a significant effect on the occurrence of resistance, measured either by cultivation or metagenomics.

To characterize contacts in general wards, a prospective survey of healthcare workers (HCWs), patients and visitors was conducted using self-reported diary, direct observation and telephone interviews. Nurses, doctors and assorted HCWs reported a median of 14, 18 and 15 contact persons over one work shift, respectively. Within 1 h, we observed 3·5 episodes with 25·6 min of cumulative contact time for nurses, 2·9 episodes and 22·1 min for doctors and 5·0 episodes with 44·3 min for assorted-HCWs. In interactions with patients, nurses had multiple brief episodes of contact; doctors had fewer episodes and less cumulative contact time; assorted-HCWs had fewer contact episodes of longer durations (than for nurses and doctors). Assortative mixing occurred amongst HCWs: those of the same HCW type were the next most frequent class of contact after patients. Over 24-h, patients contacted 14 persons with 23 episodes and 314·5 min of contact time. Patient-to-patient contact episodes were rare, but a maximum of five were documented from one patient participant. 22·9% of visitors reported contact with patients other than the one they visited. Our study revealed differences in the characteristics of contacts among different HCW types and potential transmission routes from patients to others within the ward environment.

The 7 and 13-valent pneumococcal conjugate vaccines (PCVs) have reduced the incidence of invasive pneumococcal disease (IPD) in children in many countries. The objective of this work was to assess the impact of PCVs and potential herd-protection in older adults in Ireland. IPD notification and typing data from adults ⩾65 years of age from July 2007 to June 2016 was assessed using national surveillance data. There was a 94% reduction in PCV7 serotypes from 2007–2008 to 2015–2016, incidence rate ratio (IRR 0·05, P < 0·0001). However, there was no decline in the additional PCV13 (PCV13-7) serotypes over the same period (IRR 0·90) nor in comparison with the pre-PCV13 period 2009–2010 (IRR 0·92). The incidence of serotypes in the 23-valent pneumococcal polysaccharide vaccine only (PPV23-PCV13) and non-vaccine types (NVTs) increased significantly (IRR 2·17, P = 0·0002 and IRR 3·43, P = 0·0001 respectively). Consequently, the overall IPD incidence rate in adults has remained relatively unchanged (from 28·66/100 000 to 28·88/100 000, IRR 1·01, P = 0·9477). Serotype 19A and NVTs were mainly responsible for penicillin resistance in recent years. The decline of PCV7 serotypes indicate that the introduction of PCV7 resulted in herd-protection for adults. However, increases in PPV23-PCV13 and NVTs suggest that changes in vaccination strategy amongst older adults are needed to build on the success of PCVs in children.