Complete Genome Sequences of African Salmonella enterica Serovar Enteritidis Clinical Isolates Associated with Bloodstream Infection.

We report the complete genome sequencing and annotation of four Salmonella enterica serovar Enteritidis isolates, two that are representative of the Central/Eastern African clade (CP255 and D7795) and two of the Global Epidemic clade (A1636 and P125109).

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.

An epidemiological paradox surrounds Salmonella enterica serovar Enteritidis. In high-income settings, it has been responsible for an epidemic of poultry-associated, self-limiting enterocolitis, whereas in sub-Saharan Africa it is a major cause of invasive nontyphoidal Salmonella disease, associated with high case fatality. By whole-genome sequence analysis of 675 isolates of S. Enteritidis from 45 countries, we show the existence of a global epidemic clade and two new clades of S. Enteritidis that are geographically restricted to distinct regions of Africa. The African isolates display genomic degradation, a novel prophage repertoire, and an expanded multidrug resistance plasmid. S. Enteritidis is a further example of a Salmonella serotype that displays niche plasticity, with distinct clades that enable it to become a prominent cause of gastroenteritis in association with the industrial production of eggs and of multidrug-resistant, bloodstream-invasive infection in Africa.

Determination of Giardia duodenalis assemblages and multi-locus genotypes in patients with sporadic giardiasis from England.

BACKGROUND: The protozoan Giardia duodenalis is a common but highly diverse human parasite that comprises a complex of seven morphologically identical genetic assemblages, further divided into sub-assemblages. There is very little information available on the diversity of Giardia sub-assemblages and multi-locus genotypes infecting people in the United Kingdom. In this study we studied the molecular epidemiology of Giardia in symptomatic patients from North West England. METHODS: Whole faecal DNA was extracted from the faecal samples of 406 Giardia cases and the parasites assemblage, sub-assemblage and multi-locus genotype were determined using PCR amplification, DNA sequencing and phylogenetic analysis of the beta-giardin, glutamate dehydrogenase, triose-phosphate isomerase and small-subunit ribosomal RNA genes. Information about age, gender and self-reported clinical outcomes was also collected from the patients to check for differences associated with the infecting Giardia assemblage. RESULTS: Our results showed a difference in the age prevalence of the two assemblages, with assemblage A being more common in older cases. Cases infected with assemblage B more often reported vomiting and a longer illness than cases infected with assemblage A. The majority of infections (64%) were caused by assemblage B followed by assemblage A (33%), while mixed-assemblage infections were rare (3%). Assemblage A isolates mostly belonged to the sub-assemblage AII and showed completed identity with previously described isolates. The level of genetic sub-structuring was significantly higher in assemblage B isolates, since a higher proportion of novel assemblage B sequences was detected compared to assemblage A. A high number of assemblage B sequences showed heterogeneous nucleotide positions that prevented the unambiguous assignment to a specific sub-assemblage. Both previously described and novel multi-locus genotypes were described in both assemblages, and up to 17 different assemblage B multi-locus genotypes were found. CONCLUSIONS: We have produced the first data on the parasite multi-locus genotypes in the UK and have demonstrated that the molecular diversity of Giardia is similar to other developed countries. Furthermore, we showed that the parasite assemblages infecting humans may be associated with patients of different ages and with different clinical outcomes.

Case-Control Study of Risk Factors for Sporadic Giardiasis and Parasite Assemblages in North West England.

Giardia duodenalis is a major cause of infectious gastroenteritis worldwide, and it is diversified into eight genetic assemblages (A to H), which are distinguishable only by molecular typing. There is some evidence that the assemblages infecting humans (assemblages A and B) may have different transmission routes, but systematically acquired data, combining epidemiological and molecular findings, are required. We undertook a case-control study with Giardia genotyping in North West England, to determine general and parasite assemblage-specific risk factors. For people without a history of foreign travel, swimming in swimming pools and changing diapers were the most important risk factors for the disease. People infected with assemblage B reported a greater number of symptoms and higher frequencies of vomiting, abdominal pain, swollen stomach, and loss of appetite, compared with people infected with assemblage A. More importantly, keeping a dog was associated only with assemblage A infections, suggesting the presence of a potential zoonotic reservoir for this assemblage. This is the first case-control study to combine epidemiological data with Giardia genotyping, and it shows the importance of integrating these two levels of information for better understanding of the epidemiology of this pathogen.

Detection of IgG antibodies in sera from patients with Cryptosporidium parvum and Cryptosporidium hominis.

OBJECTIVES: Detection of anti-Cryptosporidium immunoglobulin G (IgG) antibodies in human sera has been used to demonstrate population exposure to this gastro-intestinal protozoan parasite. We characterised the dynamics of IgG antibody responses to two Cryptosporidium parvum (IOWA isolate) sporozoite antigens (15/17 kDa and 27 kDa) using longitudinal sera taken from laboratory-confirmed cryptosporidiosis cases in England and Wales. The effect of the infecting Cryptosporidium species was also investigated. METHODS: A mini-gel Western blot was used to test sera from ten Cryptosporidium stool-positive diarrhoea patients, taken soon after diagnosis and at 3 month intervals. RESULTS: Overall responses to the 15/17 kDa antigen complex were stronger and over a greater range than those to the 27 kDa antigen, but declined between 181 and 240 days and were barely detectable thereafter. Responses to the 27 kDa antigen were much weaker but remained detectable for a greater length of time. No differences were detected in either antibody response to infection with C. hominis or C. parvum. CONCLUSIONS: The assay appears to be applicable for the study of recent exposure to C. parvum or C. hominis in the United Kingdom population, with strong responses to the 15/17 kDa antigen occurring within 6 months of infection.

High metabolic potential may contribute to the success of ST131 uropathogenic Escherichia coli.

Uropathogenic Escherichia coli (UPEC) is the predominant cause of urinary tract infection in both hospital and community settings. The recent emergence of multidrug-resistant clones like the O25b:H4-ST131 lineage represents a significant threat to health, and numerous studies have explored the virulence potential of these organisms. Members of the ST131 clone have been described as having variable carriage of key virulence factors, and it has been suggested that additional unidentified factors contribute to virulence. Here we demonstrated that ST131 isolates have high metabolic potential and biochemical profiles that distinguish them from isolates of many other sequence types (STs). A collection of 300 UPEC isolates recovered in 2007 and 2009 in the Northwest region of England were subjected to metabolic profiling using the Vitek2 Advanced Expert System (AES). Of the 47 tests carried out, 30 gave a positive result with at least one of the 300 isolates examined. ST131 isolates demonstrated significant association with eight tests, including those for peptidase, decarboxylase, and alkalinization activity. Metabolic activity also correlated with antibiotic susceptibility profiles, with resistant organisms displaying the highest metabolic potential. This is the first comprehensive study of metabolic potential in the ST131 lineage, and we suggest that high metabolic potential may have contributed to the fitness of members of the ST131 clone, which are able to exploit the available nutrients in both the intestinal and urinary tract environments.

Estimating incidence rates using exact or interval-censored data with an application to hospital-acquired infections.

Health-care providers in the UK and elsewhere are required to maintain records of incidents relating to patient safety, including the date and time of each incident. However, for reporting and analysis, the resulting data are typically grouped into discrete time intervals, for example, weekly or monthly counts. The grouping represents a potential loss of information for estimating variations in incidence over time. We use a Poisson point process model to quantify this loss of information. We also suggest some diagnostic procedures for checking the goodness of fit of the Poisson model. Finally, we apply the model to the data on hospital-acquired methicillin-resistant Staphylococcus aureus infections in two hospitals in the north of England. We find that, in one of the hospitals, the estimated incidence decreased by a factor of approximately 2.3 over a 7-year period from 0.323 to 0.097 cases per day per 1000 beds, whereas in the other, the estimated incidence showed only a small and nonsignificant decrease over the same period from 0.137 to 0.131.

Observational study of need for thrombolytic therapy and incidence of bacteremia using taurolidine-citrate-heparin, taurolidine-citrate and heparin catheter locks in patients treated with hemodialysis.

Catheter-related blood stream infections may be reduced by interdialytic locking with Taurolidine, a nontoxic antimicrobial agent. A formulation of 1.35% Taurolidine in 4% citrate (TC) is associated with a greater need for thrombolysis to maintain catheter patency than 5000 U/ml heparin. Our aim was to determine whether addition of 500 Units/ml of heparin to TC reduces the need for thrombolysis. TCH (1.35% taurolidine, 4% citrate and 500 U/ml heparin) was compared to TC and Heparin 5000 U/ml using retrospective data. Hundred and six adult hemodialysis patients with internal jugular tunnelled intravascular catheters using TCH were compared with 34 patients using TC and 34 patients using heparin 5000 U/ml respectively. Outcomes were time to first use of thrombolysis and bacteremia rates.TCH reduced the need for thrombolysis compared to TC (hazard ratio, 0.2; 95%CI: 0.06, 0.5; p < 0.001) and was not significantly different from heparin 5000 U/ml (hazard ratio, 1.4; 95%CI: 0.5, 3.9; p = 0.5). The bacteremia rates from all causes were 1.33, 1.22 and 3.25 per 1000 catheter- days (p < 0.001) in the TCH, TC and heparin groups respectively. Addition of 500 U/ml heparin to TC reduces the need for thrombolysis without increasing bacteremia and may achieve patency comparable to heparin 5000 U/ml.

Population structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli from Northwest England.

OBJECTIVES: Multilocus sequence typing (MLST) has been used to characterize diverse pathogens, including uropathogenic Escherichia coli (UPEC). There has been significant interest in the contribution of the O25b:H4-ST131 lineage to UPEC disease, as these isolates are often highly virulent and exhibit multidrug resistance. To reveal the wider impact of sequence type (ST) 131, we have examined its contribution to the overall population structure of UPEC isolates that were not selected on the basis of virulence or antibiotic resistance. METHODS: Three hundred UPEC isolates were recovered from community and hospital urine samples examined by clinical microbiology laboratories in the Northwest region of England in June 2007 and June 2009. They were characterized by susceptibility profiling, MLST and virulence gene PCR. PFGE was used to examine isolates from key clones. RESULTS: The most common lineage was ST73 (16.6%) followed by ST131 (13.3%), ST69 (9%), ST95 (6.3%), ST10 (4.3%) and ST127 (3.6%). ST131 isolates were significantly more likely to exhibit high levels of antibiotic resistance (35% being CTX-M-15 PCR positive) and those of ST127 were the most widely susceptible but carried the highest number of virulence genes. Only when the CTX-M-15-O25b-positive strains were examined was a high level of virulence observed for ST131 isolates. PFGE indicated ongoing local evolution in ST131. CONCLUSIONS: ST131 isolates are well established in the wider UPEC population. This clone is still evolving and we further support suggestions that it represents a real threat to health. We suggest that ST127 is a recently emerged, community-associated, virulent clone that warrants further study.

A randomized double-blind controlled trial of taurolidine-citrate catheter locks for the prevention of bacteremia in patients treated with hemodialysis.

BACKGROUND: Bacteremia is a major cause of morbidity in patients using intravascular catheters. Interdialytic locking with antibiotics decreases the incidence of bacteremia, but risks antibiotic resistance. Taurolidine is a nontoxic broad-spectrum antimicrobial agent that has not been associated with resistance. Preliminary evidence suggests that taurolidine-citrate locks decrease bacteremia, but cause flow problems in established catheters. STUDY DESIGN: Double-blind randomized controlled trial. INTERVENTION: Interdialytic locking with taurolidine and citrate (1.35% taurolidine and 4% citrate) compared with heparin (5,000 U/mL) started at catheter insertion. SETTING & PARTICIPANTS: 110 adult hemodialysis patients with tunneled cuffed intravascular catheters inserted at 3 centers in Northwest England. OUTCOMES & MEASUREMENTS: Primary end points were time to first bacteremia episode from any cause and time to first use of thrombolytic therapy. RESULTS: There were 11 bacteremic episodes in the taurolidine-citrate group and 23 in the heparin group (1.4 and 2.4 episodes/1,000 patient-days, respectively; P = 0.1). There was no significant benefit of taurolidine-citrate versus heparin for time to first bacteremia (hazard ratio, 0.66; 95% CI, 0.2-1.6: P = 0.4). Taurolidine-citrate was associated with fewer infections caused by Gram-negative organisms than heparin (0.2 vs 1.1 infections/1,000 patient-days; P = 0.02); however, there was no difference for Gram-positive organisms (1.1 vs 1.2 infections/1,000 patient-days; P = 0.8). There was a greater need for thrombolytic therapy in the taurolidine-citrate versus heparin group (hazard ratio, 2.5; 95% CI, 1.3-5.2; P = 0.008). LIMITATIONS: Small sample size. The study included bacteremia from all causes and was not specific for catheter-related bacteremia. CONCLUSIONS: Taurolidine-citrate use did not decrease all-cause bacteremia and was associated with a greater need for thrombolytic treatment. There was a decrease in infections caused by Gram-negative organisms and a trend to a lower frequency of bacteremia, which warrants further study.

Multi-resistant Escherichia coli and mycotic aneurysm: two case reports.

INTRODUCTION: Mycotic aneurysms account for a small proportion of all aneurysms. Escherichia coli a gram-negative organism, is recognised as a rare cause of aortic aneurysm. We report two cases of mycotic aneurysm caused by the same strain of multi-resistant Escherichia coli. The purpose of this case report is to highlight the possibility that this strain may be associated with an increased risk of endovascular infection especially in extra-aortic sites. These aneurysms can be difficult to detect and can have serious consequences. CASE PRESENTATION: In case one, the patient presented with symptoms and signs of septicaemia secondary to a urinary tract infection. Despite adequate treatment the patient continued with pyrexia and raised inflammatory markers, therefore a series of CT scans of the abdomen and thorax were performed, which revealed two intra-thoracic pseudo-aneurysms with associated haematomas. In case two, the patient also developed Escherichia coli septicaemia. On day 44 he developed a swelling on the right side of his neck. An ultrasound scan showed a pseudoaneurysm of the right common carotid artery. CONCLUSIONS: Whilst a case report cannot prove that a heightened risk exists, we suggest that it is an area worthy of further surveillance. We recommend when older patients with atheromatosis develop prolonged Escherichia coli septicaemia, the possibility of an infected aneurysm should be borne in mind.

Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni.

Responsible for the majority of bacterial gastroenteritis in the developed world, Campylobacter jejuni is a pervasive pathogen of humans and animals, but its evolution is obscure. In this paper, we exploit contemporary genetic diversity and empirical evidence to piece together the evolutionary history of C. jejuni and quantify its evolutionary potential. Our combined population genetics-phylogenetics approach reveals a surprising picture. Campylobacter jejuni is a rapidly evolving species, subject to intense purifying selection that purges 60% of novel variation, but possessing a massive evolutionary potential. The low mutation rate is offset by a large effective population size so that a mutation at any site can occur somewhere in the population within the space of a week. Recombination has a fundamental role, generating diversity at twice the rate of de novo mutation, and facilitating gene flow between C. jejuni and its sister species Campylobacter coli. We attempt to calibrate the rate of molecular evolution in C. jejuni based solely on within-species variation. The rates we obtain are up to 1,000 times faster than conventional estimates, placing the C. jejuni-C. coli split at the time of the Neolithic revolution. We weigh the plausibility of such recent bacterial evolution against alternative explanations and discuss the evidence required to settle the issue.

Tracing the source of campylobacteriosis.

Campylobacter jejuni is the leading cause of bacterial gastro-enteritis in the developed world. It is thought to infect 2-3 million people a year in the US alone, at a cost to the economy in excess of US $4 billion. C. jejuni is a widespread zoonotic pathogen that is carried by animals farmed for meat and poultry. A connection with contaminated food is recognized, but C. jejuni is also commonly found in wild animals and water sources. Phylogenetic studies have suggested that genotypes pathogenic to humans bear greatest resemblance to non-livestock isolates. Moreover, seasonal variation in campylobacteriosis bears the hallmarks of water-borne disease, and certain outbreaks have been attributed to contamination of drinking water. As a result, the relative importance of these reservoirs to human disease is controversial. We use multilocus sequence typing to genotype 1,231 cases of C. jejuni isolated from patients in Lancashire, England. By modeling the DNA sequence evolution and zoonotic transmission of C. jejuni between host species and the environment, we assign human cases probabilistically to source populations. Our novel population genetics approach reveals that the vast majority (97%) of sporadic disease can be attributed to animals farmed for meat and poultry. Chicken and cattle are the principal sources of C. jejuni pathogenic to humans, whereas wild animal and environmental sources are responsible for just 3% of disease. Our results imply that the primary transmission route is through the food chain, and suggest that incidence could be dramatically reduced by enhanced on-farm biosecurity or preventing food-borne transmission.

UK epidemic Escherichia coli strains A-E, with CTX-M-15 beta-lactamase, all belong to the international O25:H4-ST131 clone.

OBJECTIVES: Uropathogenic and invasive Escherichia coli O25:H4-ST131 isolates producing CTX-M-15 extended-spectrum beta-lactamase (ESBL) enzymes have recently been shown to be disseminated across the globe. In the UK, many CTX-M-15 ESBL-producing E. coli strains have been previously defined as belonging to the epidemic strains A-E, as determined by PFGE. The present study was carried out to define the relationship between these two groups of pathogenic E. coli. METHODS: Multilocus sequence typing and PFGE were used for molecular characterization of a collection of 61 ESBL-producing E. coli isolates from across the UK. RESULTS: Strains A to E all belonged to the ST131 clone, further underscoring the epidemiological importance of this lineage. CONCLUSIONS: The future spread of the ST131 clone, and its UK variants, should be monitored closely and the pathogenic mechanisms explaining their success should be investigated.

Major uropathogenic Escherichia coli strain isolated in the northwest of England identified by multilocus sequence typing.

A total of 88 uropathogenic Escherichia coli isolates, including 68 isolates from urine and 20 isolates from blood, were characterized by multilocus sequence typing (MLST). MLST has identified an important genetic lineage of E. coli, designated sequence type 131 (ST-131), represented by 52 of these isolates, 51 of which were resistant to extended-spectrum cephalosporins. ST-131 appears to be a drug-resistant uropathogenic strain of E. coli responsible for causing urinary tract infections and bacteremia and is widely disseminated among both community and hospital patients from different geographical areas in the northwest of England. Application of MLST has helped to define the population biology which may underpin the epidemiology of pathogenic E. coli strains. The portability of MLST allows the accurate monitoring of this antibiotic-resistant uropathogenic strain of E. coli and will enhance surveillance for this important group of organisms.