Burden of bacteraemia is rising due to increased average life expectancy in developed countries. This study aimed to compare the epidemiology and outcomes of bacteraemia in two similarly ageing populations with different ethnicities in Singapore and Denmark. Historical cohorts from the second largest acute-care hospital in Singapore and in the hospitals of two Danish regions included patients aged 15 and above who were admitted from 1 January 2006 to 31 December 2016 with at least 1 day of hospital stay and a pathogenic organism identified. Among 13 144 and 39 073 bacteraemia patients from Singapore and Denmark, similar 30-day mortality rates (16.5%; 20.3%), length of hospital stay (median 14 (IQR: 9–28) days; 11 (6–21)), and admission rate to ICU (15.5%; 15.6%) were observed, respectively. Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus ranked among the top four in both countries. However, Singaporeans had a higher proportion of patients with diabetes (46.8%) and renal disease (29.5%) than the Danes (28.0% and 13.7%, respectively), whilst the Danes had a higher proportion of patients with chronic pulmonary disease (18.0%) and malignancy (35.3%) than Singaporeans (9.7% and 16.2%, respectively). Our study showed that top four causative organisms and clinical outcomes were similar between the two cohorts despite pre-existing comorbidities differed.

Salmonella enterica continues to be a leading cause of foodborne morbidity worldwide. A quantitative risk assessment model was developed to evaluate the impact of pathogen enumeration and serotyping strategies on public health after consumption of undercooked contaminated ground turkey in the USA. The risk assessment model predicted more than 20,000 human illnesses annually that would result in ~700 annual reported cases. Removing ground turkey lots contaminated with Salmonella exceeding 10 MPN/g, 1 MPN/g, and 1 MPN/25 g would decrease the mean number of illnesses by 38.2, 73.1, and 95.0%, respectively. A three-class mixed sampling plan was tested to allow the detection of positive lots above threshold levels with 2–6 (c = 1) and 3–8 samples per lot (c = 2) using 25-g and 325-g sample sizes for a 95% probability of rejecting a contaminated lot. Removal of positive lots with the presence of highly virulent serotypes would decrease the number of illnesses by 44.2–87.0%. Based on these model prediction results, risk management strategies should incorporate pathogen enumeration and/or serotyping. This would have a direct impact on illness incidence linking public health outcomes with measurable food safety objectives, at the cost of diverting production lots.

Toxigenic diphtheria is rare in Australia with generally fewer than 10 cases reported annually; however, since 2020, there has been an increase in toxin gene-bearing isolates of Corynebacterium diphtheriae cases in North Queensland, with an approximately 300% escalation in cases in 2022. Genomic analysis on both toxin gene-bearing and non-toxin gene-bearing C. diphtheriae isolated from this region between 2017 and 2022 demonstrated that the surge in cases was largely due to one sequence type (ST), ST381, all of which carried the toxin gene. ST381 isolates collected between 2020 and 2022 were highly genetically related to each other, and less closely related to ST381 isolates collected prior to 2020. The most common ST in non-toxin gene-bearing isolates from North Queensland was ST39, an ST that has also been increasing in numbers since 2018. Phylogenetic analysis demonstrated that ST381 isolates were not closely related to any of the non-toxin gene-bearing isolates collected from this region, suggesting that the increase in toxigenic C. diphtheriae is likely due to the expansion of a toxin gene-bearing clone that has moved into the region rather than an already endemic non-toxigenic strain acquiring the toxin gene.

In August 2019, public health surveillance systems in Scotland and England identified seven, geographically dispersed cases infected with the same strain (defined as isolates that fell within the same five single nucleotide polymorphism single linage cluster) of Shiga toxin-producing Escherichia coli O157:H7. Epidemiological analysis of enhanced surveillance questionnaire data identified handling raw beef and shopping from the same national retailer (retailer A) as the common exposure. Concurrently, a microbiological survey of minced beef at retail identified the same strain in a sample of minced beef sold by retailer A, providing microbiological evidence of the link. Between September and November 2019, a further four primary and two secondary cases infected with the same strain were identified; two cases developed haemolytic uraemic syndrome. None of the four primary cases reported consumption of beef from retailer A and the transmission route of these subsequent cases was not identified, although all four primary cases visited the same petting farm. Generally, outbreaks of STEC O157:H7 in the UK appear to be distinct, short-lived events; however, on-going transmission linked to contaminated food, animals or environmental exposures and person-to-person contact do occur. Although outbreaks of STEC caused by contaminated fresh produce are increasingly common, undercooked meat products remain a risk of infection.

In April 2018, Public Health England was notified of cases of Shigella sonnei who had eaten food from three different catering outlets in England. The outbreaks were initially investigated as separate events, but whole-genome sequencing (WGS) showed they were caused by the same strain. The investigation included analyses of epidemiological data, the food chain and microbiological examination of food samples. WGS was used to determine the phylogenetic relatedness and antimicrobial resistance profile of the outbreak strain. Ultimately, 33 cases were linked to this outbreak; the majority had eaten food from seven outlets specialising in Indian or Middle Eastern cuisine. Five outlets were linked to two or more cases, all of which used fresh coriander although a shared supplier was not identified. An investigation at one of the venues recorded that 86% of cases reported eating dishes with coriander as an ingredient or garnish. Four cases were admitted to hospital and one had evidence of treatment failure with ciprofloxacin. Phylogenetic analysis showed that the outbreak strain was part of a wider multidrug-resistant clade associated with travel to Pakistan. Poor hygiene practices during cultivation, distribution or preparation of fresh produce are likely contributing factors.

In August 2015, Public Health England detected an outbreak of Shiga toxin-producing Escherichia coli (STEC) serotype O157:H7 caused by contaminated salad leaves in a mixed leaf prepacked salad product from a national retailer. The implicated leaves were cultivated at five different farms and the zoonotic source of the outbreak strain was not determined. In March 2016, additional isolates from new cases were identified that shared a recent common ancestor with the outbreak strain. A case–case study involving the cases identified in 2016 revealed that ovine exposures were associated with illness (n = 16; AOR 8·24; 95% CI 1·55–39·74). By mapping the recent movement of sheep and lambs across the United Kingdom, epidemiological links were established between the cases reporting ovine exposures. Given the close phylogenetic relationship between the outbreak strain and the isolates from cases with ovine exposures, it is plausible that ovine faeces may have contaminated the salad leaves via untreated irrigation water or run-off from fields nearby. Timely and targeted veterinary and environmental sampling should be considered during foodborne outbreaks of STEC, particularly where ready to eat vegetables and salads are implicated.

Giardiasis is a treatable disease, caused by the flagellated protozoan parasite, Giardia duodenalis (G. duodenalis). It is one of the most common enteric parasites found globally to cause gastrointestinal disturbances, and infections may result in long-term irritable bowel syndrome-like symptoms. It is a common misconception that giardiasis is associated with foreign travel, which results in locally acquired cases in the UK being underdiagnosed. This report highlights the findings from one large Scottish Health Board, arising from a change in testing methodology, which resulted in the screening of all stools submitted for enteric investigations for G. duodenalis. Previous selection criteria were restricted to patients with a travel history to specific regions of the world, or on the basis of certain clinical details. In this report, clinical details were recorded from samples shown to be positive using two methods: an ELISA-based antigen detection assay and microscopy. Clinical details were assessed for a total of 28 laboratory-confirmed positive cases against the original selection criteria. Twenty-six cases (93%) would have been excluded from Giardia testing if the previous selection criteria had been applied. Although nine cases stated foreign travel, only two had been to regions deemed to be ‘high risk’. Therefore, those seven cases that travelled to perceived ‘low-risk’ regions would have been excluded from testing for this reason. This summary highlights the need for significant improvements to the selection criteria for Giardia testing. Laboratories should be encouraged towards the testing of all routinely submitted stools for this neglected pathogen to ensure cases that are acquired locally are properly identified and treated effectively.

The type identity of strains of Pseudomonas aeruginosa from primary and recurrent blood stream infection (BSI) has not been widely studied. Twenty-eight patients were identified retrospectively from 2008 to 2013 from five different laboratories; available epidemiological, clinical and microbiological data were obtained for each patient. Isolates were genotyped by iPLEX MassARRAY MALDI-TOF MS and rep-PCR. This showed that recurrent P. aeruginosa BSI was more commonly due to the same genotypically related strain as that from the primary episode. Relapse due to a genotypically related strain occurred earlier in time than a relapsing infection from an unrelated strain (median time: 26 vs. 91 days, respectively). Line related infections were the most common source of suspected BSI and almost half of all BSI episodes were associated with neutropenia, possibly indicating translocation of the organism from the patient's gut in this setting. Development of meropenem resistance occurred in two relapse isolates, which may suggest that prior antibiotic therapy for the primary BSI was a driver for the subsequent development of resistance in the recurrent isolate.

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.

Fifteen confirmed cases and 15 possible cases of Shiga toxin-producing Escherichia coli (STEC) O157 phage type 21/28 were linked to direct contact with lambs at a ‘Lambing Live’ event in the North West of England between 29 March and 21 April 2014. Twenty-one (70%) of the cases were female, 23 (77%) were children aged <16 years, of whom 14 (46%) were in the 0–5 years age group. Five children developed haemolytic uraemic syndrome. Multilocus variable number tandem repeat analysis (MLVA) profiles on 14 human cases were indistinguishable, and 6/10 animal isolates had a MLVA profile identical to the outbreak profile. Whole-genome sequencing analysis revealed that all isolates, both human and animal, fell within a 5-single nucleotide polymorphism cluster indicating the isolates belonged to the same point source. On inspection of the premises, extensive and uncontrolled physical contact between visitors and animals was occuring within the animal pens and during bottle-feeding. Public areas were visibly contaminated with animal faeces. Information to visitors, and the infection control awareness demonstrated by staff, was inadequate. Managing the risk to visitors of STEC O157 infection at animal petting events and open farms requires implementation of stringent control measures by the operator, as outlined in the industry code of practice. Enforcement action is sometimes required to prevent high-risk activities taking place at both permanent and temporary attractions.

Five cases of STEC O157 phage type (PT) 21/28 reported consumption of raw cows' drinking milk (RDM) produced at a dairy farm in the South West of England. STEC O157 PT21/28 was isolated from faecal specimens from milking cows on the implicated farm. Whole genome sequencing (WGS) showed that human and cattle isolates were the same strain. Further analysis of WGS data confirmed that sequences of isolates from an additional four cases (who did not report consumption of RDM when first questioned) fell within the same five single nucleotide polymorphism cluster as the initial five cases epidemiologically linked to the consumption of RDM. These four additional cases identified by WGS were investigated further and were, ultimately, associated with the implicated farm. The RDM outbreak strain encoded stx2a, which is associated with increased pathogenicity and severity of symptoms. Further epidemiological analysis showed that 70% of isolates within a wider cluster containing the outbreak strain were from cases residing in, or linked to, the same geographical region of England. During this RDM outbreak, use of WGS improved case ascertainment and provided insights into the evolution of a highly pathogenic clade of STEC O157 PT21/28 stx2a associated with the South West of England.

For influenza surveillance and diagnosis typical clinical symptoms are traditionally used to discriminate influenza virus infections from infections by other pathogens. During the 2013 influenza season we performed a multiplex assay for 16 different viruses in 665 swabs from patients with acute respiratory infections (ARIs) to display the variety of different pathogens causing ARI and to test the diagnostic value of both the commonly used case definitions [ARI, and influenza like illness (ILI)] as well as the clinical judgement of physicians, respectively, to achieve a laboratory-confirmed influenza diagnosis. Fourteen different viruses were identified as causing ARI/ILI. Influenza diagnosis based on clinical signs overestimated the number of laboratory-confirmed influenza cases and misclassified cases. Furthermore, ILI case definition and physicians agreed in only 287/651 (44%) cases with laboratory confirmation. Influenza case management has to be supported by laboratory confirmation to allow evidence-based decisions. Epidemiological syndromic surveillance data should be supported by laboratory confirmation for reasonable interpretation.

Salmonella enterica subsp. enterica serovar Dublin is an uncommon cause of human salmonellosis; however, a relatively high proportion of cases are associated with invasive disease. The serotype is associated with cattle. A geographically diffuse outbreak of S. Dublin involving nine patients occurred in Ireland in 2013. The source of infection was not identified. Typing of outbreak associated isolates by pulsed-field gel electrophoresis (PFGE) was of limited value because PFGE has limited discriminatory power for S. Dublin. Whole genome sequencing (WGS) showed conclusively that the isolates were closely related to each other, to an apparently unrelated isolate from 2011 and distinct from other isolates that were not readily distinguishable by PFGE.

Many serogroups of Shiga toxin-producing Escherichia coli (STEC) other than serogroup O157 (non-O157 STEC), for example STEC O26:H11, are highly pathogenic and capable of causing haemolytic uraemic syndrome. A recent increase in non-O157 STEC cases identified in England, resulting from a change in the testing paradigm, prompted a review of the current methods available for detection and typing of non-O157 STEC for surveillance and outbreak investigations. Nineteen STEC O26:H11 strains, including four from a nursery outbreak were selected to assess typing methods. Serotyping and multilocus sequence typing were not able to discriminate between the stx-producing strains in the dataset. However, genome sequencing provided rapid and robust confirmation that isolates of STEC O26:H11 associated with a nursery outbreak were linked at the molecular level, had a common source and were distinct from the other strains analysed. Virulence gene profiling of DNA extracted from a polymerase chain reaction (PCR)-positive/culture-negative faecal specimen from a case that was epidemiologically linked to the STEC O26:H11 nursery outbreak, provided evidence at the molecular level to support that link. During this study, we describe the utility of PCR and the genome sequencing approach in facilitating surveillance and enhancing the response to outbreaks of non-O157 STEC.

The food court at a shopping mall is a potential transfer point for pathogenic microbes, but to date, this environment has not been the subject of detailed molecular microbiological study. We used a combination of culture-based and culture-independent approaches to investigate the types and numbers of bacteria present on food court tables, and on a food court cleaning cloth. Bacteria were found at 102–105 c.f.u./m2 on food court tables and 1010 c.f.u./m2 on the cleaning cloth. Tag-pyrosequencing of amplified 16S rRNA genes revealed that the dominant bacterial types on the cleaning cloth were genera known to include pathogenic species (Stenotrophomonas, Aeromonas), and that these genera were also evident at lower levels on table surfaces, suggesting possible cross-contamination. The evidence suggests a public health threat is posed by bacteria in the food court, and that this may be due to cross-contamination between cleaning equipment and table surfaces.

Space–time clustering of people who fall acutely ill with jaundice, then slip into coma and death, is an alarming phenomenon, more markedly so when the victims are mostly or exclusively pregnant. Documentation of the peculiar, fatal predisposition of pregnant women during outbreaks of jaundice identifies hepatitis E and enables construction of its epidemic history. Between the last decade of the 18th century and the early decades of the 20th century, hepatitis E-like outbreaks were reported mainly from Western Europe and several of its colonies. During the latter half of the 20th century, reports of these epidemics, including those that became serologically confirmed as hepatitis E, emanated from, first, the eastern and southern Mediterranean littoral and, thereafter, Southern and Central Asia, Eastern Europe, and the rest of Africa. The dispersal has been accompanied by a trend towards more frequent and larger-scale occurrences. Epidemic and endemic hepatitis E still beset people inhabiting Asia and Africa, especially pregnant women and their fetuses and infants. Their relief necessitates not only accelerated access to potable water and sanitation but also vaccination against hepatitis E.

Isolation rates in Canada of Salmonella enterica serovar Typhi increased from 0·29 to 0·55 isolations/100 000 population during 2000–2006. Although no ciprofloxacin resistance was detected, nalidixic acid resistance increased from 41% to 80%. Multidrug-resistant S. Typhi represented 18% of the strains tested. Pulsed-field gel electrophoresis (PFGE) analysis of 222 isolates resulted in 91 distinct patterns clustering into four major genetic similarity groups. The five most frequently occurring PFGE patterns accounted for 46% of the isolates. Drug-resistant isolates predominantly occurred in one PFGE similarity group. There were 39 phage types identified in 826 isolates analysed with 60% described by five phage types; 134 were untypable. The phage types associated with multidrug resistance were phage types 53, B1, D1, E1, E9, G3 and M1. Improved integration of epidemiological and laboratory case data will facilitate the protection of public health in Canada during an era of increasing travel and globalization.

Campylobacter jejuni is a leading cause of human bacterial gastroenteritis throughout the industrialized world. We investigated whether or not differences in gene complement at the lipooligosaccharide (LOS) biosynthesis locus can identify epidemiologically useful binary genomotypes in 87 C. jejuni isolates from poultry-associated multilocus sequence types (STs) collected during the course of a sentinel surveillance study. Using a PCR-based approach, we correlated assignment of both isolate LOS locus class and binary genomotype with ST. We found that isolates within STs 45, 190, 354 and 474 displayed mosaicism in gene complement at the intra-ST level. For example, based upon their binary genomotypes, we assigned individual ST-45 isolates from human clinical cases as probably originating from either a poultry or wild-bird source. However, intra-ST mosaicism in gene complement was observed alongside broader patterns of congruence in LOS locus class and gene complement that distinguished between isolates from different STs.

Antimicrobial resistance (AMR) in Neisseria gonorrhoeae compromises patient treatment and disease control. Epidemiologically based surveillance of AMR in gonococci is needed to optimize standard treatment regimens. Validation of AMR surveillance data depends on external quality assurance schemes (EQAS). AMR surveillance data quality in India during 2001–2007 was assessed by participants testing panels of reference strains and repeated re-challenge with identical controls, accompanied by educative feedback. Overall, correct results were obtained for 944 (82%) of 1030 tests performed for five ‘core’ antibiotics. Aggregated error rates decreased from 33% (123 tests) in 2001 to 4·4% (180 tests) in 2007 with improvements in individual laboratory performance. Cephalosporin test results produced high error rates without improvement. Reference centre and network laboratory collaboration produced marked improvements in test performance through annual EQAS integrating proficiency testing and participant education. More frequent EQAS cycles would assist this process. These experiences may be applicable in similar settings elsewhere.

In the Dutch national vaccination campaign for behavioural risk groups, anti-HBcore is used as the primary HBV screening test. Samples with positive results undergo testing for active infection (HBsAg) but are otherwise accepted as indicating past infection, thereby assuming immunity. This study evaluated evidence for immunity in the target population screened on the basis of this algorithm, by re-analysing 1000 anti-HBcore-positive blood samples equally divided among risk groups: 14·7% of confirmed anti-HBcore lacked anti-HBs (‘isolated’ anti-HBcore). Independent risk factors for isolated anti-HBcore were risk group, HCV infection in hard-drug users (DU) and origin from Sub-Saharan Africa. After extrapolation, the proportion of participants who were said to be immune but lacked any additional evidence of immunity amounted to 9·6% (ranging from 12·5% in DU to 6·5% in men who have sex with men). It is recommended that as a minimum anti-HBs screening is included in testing algorithms used to determine vaccination programmes for risk groups, in particular in DU.