There was a relatively high incidence of polymicrobial infection but the number of specimens with anaerobes was small, which may be because of the use of empiric metronidazole before surgical intervention. Most infections were community-acquired and responded well to a combination of surgical drainage and antibiotic therapy. The emergence of MRSA in this group of patients is, however, worrying.

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Multilocus sequence typing (MLST) systems have been reported previously for multiple food- and food animal-associated Campylobacter species (e.g., C. jejuni, C. coli, C. lari, and C. fetus) to both differentiate strains and identify clonal lineages. These MLST methods focused primarily on campylobacters of human clinical (e.g., C. jejuni) or veterinary (e.g., C. fetus) relevance. However, other, emerging, Campylobacter species have been isolated increasingly from environmental, food animal, or human clinical samples. We describe herein four MLST methods for five emerging Campylobacter species: C. hyointestinalis, C. lanienae, C. sputorum, C. concisus, and C. curvus. The concisus/curvus method uses the loci aspA, atpA, glnA, gltA, glyA, ilvD, and pgm, whereas the other methods use the seven loci defined for C. jejuni (i.e., aspA, atpA, glnA, gltA, glyA, pgm, and tkt). Multiple food animal and human clinical C. hyointestinalis (n = 48), C. lanienae (n = 34), and C. sputorum (n = 24) isolates were typed, along with 86 human clinical C. concisus and C. curvus isolates. A large number of sequence types were identified using all four MLST methods. Additionally, these methods speciated unequivocally isolates that had been typed ambiguously using other molecular-based speciation methods, such as 16S rDNA sequencing. Finally, the design of degenerate primer pairs for some methods permitted the typing of related species; for example, the C. hyointestinalis primer pairs could be used to type C. fetus strains. Therefore, these novel Campylobacter MLST methods will prove useful in differentiating strains of multiple, emerging Campylobacter species.

Objectives We characterized clinical isolates of Campylobacter using whole-genome sequencing (WGS) for detection of virulence genes, antimicrobial resistance markers and phylogenetic analysis in order to increase the knowledge on the molecular epidemiology of Campylobacter in Ireland, where there are significant gaps due to the widespread in the use of culture independent methods for the diagnosis of campylobacteriosis. Methods WGS was applied to 122 Campylobacter human isolates collected over a 10-years period, from diarrhoeal stool samples submitted for routine enteric screening. Results Genes associated with cytotoxin production such as cdtA , cdtB and cdtC were found in 88%, 89% and 89% isolates, respectively; adherence, colonization and invasion genes such as cadF , dnaJ , racR , iam , virB11 and ciaB were found in 99%, 99%, 98%, 99%, 1% and 80% isolates, respectively. Genetic markers associated with resistance to quinolones (C257T in gyrA ), beta-lactams ( bla oxa-61 ) and tetracycline ( tet (O)) were present in 43%, 71% and 25% isolates, respectively. The cmeABC operon was present in 94% of isolates. No macrolide or aminoglycoside resistance markers were detected. Phylogenetic analysis showed that 112 isolates were assigned to 29 sequence types grouped into 17 clonal complexes. Four clusters previously unidentified were detected. These results shown the similarity of Irish data compared to what has been described globally. Conclusions WGS has shown a high discriminatory power for cluster detection, demonstrating that its integration in routine laboratory surveillance could improve the detection and management of outbreaks. In addition we were able to demonstrate that virulence genes in clinical Campylobacter infections in Ireland were similar to those known previously. High prevalence of quinolone resistance markers has been found, which has implications for antimicrobial stewardship.

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In this institution all patients with clinically significant blood culture isolates are routinely reviewed by members of the clinical microbiology team. After clinical assessment, further investigations and management are advised in consultation with the primary care team responsible for the patient. This form of laboratory-ward liaison is a well established practice but has rarely been audited. The clinical impact of laboratory data has been questioned, particularly when broad spectrum empirical antimicrobial treatment is available. ' We undertook a prospective analysis of our blood culture reporting protocol with particular reference to our hospital antibiotic policy. This policy gives guidance on empiric antibiotic treatment in light of the probable source of infection. The policy is produced under the guidance of the consultant clinical microbiologist, with contributions on individual categories of infection from relevant clinicians. It is approved by each clinical consultant before distribution to all non-consultant hospital doctors. Educational follow up is given at induction days for new interns and at medical and surgical grand rounds. This study was undertaken just before the biannual update of the policy.Methods Data was gathered prospectively on patients with clinically significant isolates recovered from blood over a nine month period. Blood cultures were processed using the Bactec NR-730 system (Becton-Dickinson Microbiology Systems, Sparks, Maryland, USA) and identified by standard microbiological techniques. Patients were reviewed by members of the clinical microbiology team. In addition to demographic and microbiological data, the source of bacteraemia was noted together with any significant underlying illness. Choice of agent(s), dose, frequency, and route of administration of empiric treatment was noted. The appropriateness of this treatment was assessed in relation to the organism(s) isolated, the underlying source, and the recommendations of the hospital antibiotic policy. Details were also recorded of changes in treatment recommended on the basis of Gram stain result and further changes made on the basis of culture and sensitivity results. Data were analysed using the Student's t test.

A total of 122 human and animal Salmonella Typhimurium DT104 isolates and 6 epidemiologically related DT104b isolates from human and animal products were analysed by pulsed-field gel electrophoresis (PFGE). Genomic DNA was subjected to macrorestriction with three enzymes, SpeI, SfiI and XbaI. A total of 14 restriction fragment length polymorphism (RFLP) profiles were identified when the PFGE patterns from the three enzymes were combined. The majority of isolates (81.2%) exhibited the same RFLP profile. Six animal DT104 isolates, susceptible to enrofloxacin and resistant to naladixic acid, were identified from the antibiotic susceptibility test. Four of these isolates had a different PFGE profile from the common RFLP. In addition, 4 of the 6 isolates were geographically clustered in one region. It was concluded that there was one predominant strain of S. Typhimurium DT104 in Ireland and that the potential and selection pressures for emergence of fluoroquinolone-resistant isolates were present.

The first documented British outbreak of Shiga toxin-producing Escherichia coli (STEC) O55:H7 began in the county of Dorset, England, in July 2014. Since then, there have been a total of 31 cases of which 13 presented with haemolytic uraemic syndrome (HUS). The outbreak strain had Shiga toxin (Stx) subtype 2a associated with an elevated risk of HUS. This strain had not previously been isolated from humans or animals in England. The only epidemiological link was living in or having close links to two areas in Dorset. Extensive investigations included testing of animals and household pets. Control measures included extended screening, iterative interviewing and exclusion of cases and high risk contacts. Whole genome sequencing (WGS) confirmed that all the cases were infected with similar strains. A specific source could not be identified. The combination of epidemiological investigation and WGS indicated, however, that this outbreak was possibly caused by recurrent introductions from a local endemic zoonotic source, that a highly similar endemic reservoir appears to exist in the Republic of Ireland but has not been identified elsewhere, and that a subset of cases was associated with human-to-human transmission in a nursery.