Progression from new methicillin-resistant Staphylococcus aureus colonisation to infection: an observational study in a hospital cohort.

BACKGROUND: Patients newly colonised with methicillin-resistant Staphylococcus aureus (MRSA) are at higher risk of clinical MRSA infection. At present, there are limited data on the duration or magnitude of this risk in a hospital population with a known time of MRSA acquisition. METHODS: A retrospective cohort study of 909 adult patients known to have newly identified MRSA colonisation during admission to National University Hospital, Singapore between 1 July 2007 and 30 June 2011 was undertaken. Patients were excluded if they had history of previous MRSA colonisation or infection, or if they had been a hospital inpatient in the preceding 12 months. Data were collected on the development of MRSA infection requiring hospitalisation up to 30 June 2012. RESULTS: Of 840 patients newly colonised with MRSA as identified on active surveillance and not clinical specimens, 546 were men (65.0%) and the median age was 65 years (range 18-103 years). Median follow up was 24 months (range 0 -64 months, 85.1% followed >6 months). Clinical infection occurred in 121 patients (14.4%) with median time to infection of 22 days (95% CI 14-31). Overall 71.9% (87/121) of infected patients developed infection within 60 days of the date MRSA colonisation was detected. However, 17/121 patients (14.0%) developed clinical infection more than six months after documented MRSA acquisition. The most common sites of clinical infection were skin and soft tissue (49/121, 40.5%, 95% CI 31.7-49.8), respiratory tract (37/121, 30.6%, 95% CI 22.5-39.6) and bone and joint infections (14/121, 11.6%, 95% CI 6.5-18.7). Thirteen patients (13/121, 10.7%, 95% CI 5.8-17.7) had bacteraemias, of which six (5.0% 95% CI 1.8-10.5) were primary and seven (5.7%, 95% CI 2.3-11.6) were secondary to infection at other sites. Crude mortality at 30 days and six months was higher in patients with MRSA infection than colonisation alone (aOR 5.49, 95% CI 2.75-10.95, p<0.001 and aOR 2.94, 95% CI 1.78-4.85, p<0.001 respectively). CONCLUSION: Risk of clinical infection is highest soon after MRSA acquisition. Prevention of MRSA acquisition in hospital will have significant impact on morbidity and mortality for patients.

OXA-181-producing Klebsiella pneumoniae establishing in Singapore.

BACKGROUND: Carbapenemase producing Enterobacteriaceae are becoming a major public health concern globally, however, relatively little is known about the molecular and clinical epidemiology of these organisms in many parts of the world. METHODS: As part of a laboratory surveillance programme, 96 carbapenem non-susceptible Enterobacteriaceae isolates from clinical samples from patients in seven hospitals were referred for investigation for carbapenemases. Using polymerase chain reaction (PCR) to screen for a collection of genes encoding carbapenemases, 33 of 96 (34.5%) isolates were confirmed as carbapenemase producers. NDM-1 producers were the most prevalent at 64% (21/33) whilst OXA-181 was the second most common carbapenemase constituting 24.5% (8/33) of the carbapenemase producing isolates. Seven of these eight OXA-181 positive isolates underwent further characterisation with screening for other transmissible antimicrobial resistance determinants using PCR. Clonal relatedness was explored using Multilocus sequence typing (MLST) and Pulsed Field Gel Electrophoresis (PFGE). Plasmid characterisation was performed including restriction analysis and transfer by conjugation or transformation. RESULTS: In addition to the OXA-181 gene, all contained other transmissible resistance determinants including extended spectrum ß-lactamases, oxacillinases or 16S rRNA methylase genes, but none contained metallo-ß-lactamases or serine carbapenemases. All isolates had a multidrug resistant phenotype with two isolates being resistant to every antibiotic tested including colistin. Multilocus sequence typing confirmed five isolates belonged to ST17 and two to ST14, with those belonging to the same sequence type having identical PFGE profiles. The OXA-181 gene was typically carried on large plasmids which were mostly non-conjugative. CONCLUSIONS: OXA-181 carbapenemase appears to be an important and probably under-recognised cause of carbapenem resistance in Enterobacteriaceae in Singapore. Further coordinated research into clinical and molecular epidemiology of carbapenemases is urgently required in Singapore and throughout Asia.

Molecular characterization of newly emerged blaKPC-2-producing Klebsiella pneumoniae in Singapore.

In Asia, bla(KPC) detection has been limited to East Asia and not yet seen in Southeast Asia. We report four bla(KPC-2)-containing Klebsiella pneumoniae isolates from two different hospitals in Singapore. All isolates belonged to strain type 11 (ST11) and were indistinguishable by pulsed-field gel electrophoresis (PFGE). bla(KPC-2) was located on nonconjugative plasmids and flanked by mobile genetic structures composed of a partial Tn4401 transposon and a Tn3-based transposon which previously have been described only in Chinese isolates.

A diagnostic polymerase chain reaction assay for Zika virus.

Zika virus (ZIKV) is a mosquito-borne flavivirus. Infection results in a dengue-like illness with fever, headache, malaise, and a maculopapular rash. Nearly all cases are mild and self-limiting but in 2007, a large outbreak of ZIKV was reported from the island of Yap (in Micronesia, northwest of Indonesia). Singapore is already endemic for dengue, and its impact on public health and economic burden is significant. Other dengue-like infections (e.g., Chikungunya virus) are present. Yet only 10% of reported dengue cases have laboratory confirmation. The identification and control of other dengue-like, mosquito-transmitted infections is thus important for the health of Singapore's population, as well as its economy. Given that ZIKV shares the same Aedes mosquito vector with both dengue and Chikungunya, it is possible that this virus is present in Singapore and causing some of the mild dengue-like illness. A specific and sensitive one-step, reverse transcription polymerase chain reaction (RT-PCR) with an internal control (IC) was designed and tested on 88 archived samples of dengue-negative, Chikungunya-negative sera from patients presenting to our hospital with a dengue-like illness, to determine the presence of ZIKV in Singapore. The assay was specific for detection of ZIKV and displayed a lower limit of detection (LoD) of 140 copies viral RNA/reaction when tested on synthetic RNA standards prepared using pooled negative patient plasma. Of the 88 samples tested, none were positive for ZIKV RNA, however, the vast majority of these were from patients admitted to hospital and further study may be warranted in community-based environments.

Effect of Blood Culture Contamination on Antibiotic Use in an Institution With Rapid Laboratory Methods and Phone-Based Clinical Follow-up of Blood Culture Results.

In a multivariate analysis of 30 574 blood culture (BC) results, BC contamination was associated with only a small increase in antibiotic length of therapy compared to no-growth BCs (difference, 0.36 days [95% confidence interval, .05-.67]; P = .02). Stewardship processes at our institution appear to be effective in reducing the impact of BC contamination.

The design, validation and clinical verification of an in-house qualitative PCR to detect Yersinia enterocolitica and Yersinia pseudotuberculosis in faeces.

Yersiniosis is a zoonotic foodborne infection of public health significance. The aim of this study was to design and validate a simple, accurate and cost-effective polymerase chain reaction (PCR) to detect pathogenic Yersinia spp. in faecal samples. An intercalating dye (EvaGreen)-based real-time multiplex PCR assay was designed to detect yadA, ystB and inv by melt curve analysis, allowing undifferentiated detection of all Yersinia enterocolitica biotypes, including biotype 1A, and Yersinia pseudotuberculosis. The assay was validated using cultured bacteria and clinical samples. A total of 107 positive and 51 negative samples were tested. The sensitivity and specificity was 98% and 100%. The limit of detection was 104-105 CFU/g faeces. A total of 605 samples (9 positive) were tested in the clinical verification with an accuracy and negative predictive value of 99% [95% confidence interval (CI) 97.9-99.6%] and 99.8% (95% CI 97.9-99.6%), respectively. This is an accurate, simple and cost-effective assay for the detection of pathogenic Yersinia spp.

The burden of Legionnaires' disease in New Zealand (LegiNZ): a national surveillance study.

BACKGROUND: Legionnaires' disease is under-diagnosed because of inconsistent use of diagnostic tests and uncertainty about whom to test. We assessed the increase in case detection following large-scale introduction of routine PCR testing of respiratory specimens in New Zealand. METHODS: LegiNZ was a national surveillance study done over 1-year in which active case-finding was used to maximise the identification of cases of Legionnaires' disease in hospitals. Respiratory specimens from patients of any age with pneumonia, who could provide an eligible lower respiratory specimen, admitted to one of 20 participating hospitals, covering a catchment area of 96% of New Zealand's population, were routinely tested for legionella by PCR. Additional cases of Legionnaires' disease in hospital were identified through mandatory notification. FINDINGS: Between May 21, 2015, and May 20, 2016, 5622 eligible specimens from 4862 patients were tested by PCR. From these, 197 cases of Legionnaires' disease were detected. An additional 41 cases were identified from notification data, giving 238 cases requiring hospitalisation. The overall incidence of Legionnaires' disease cases in hospital in the study area was 5·4 per 100 000 people per year, and Legionella longbeachae was the predominant cause, found in 150 (63%) of 238 cases. INTERPRETATION: The rate of notified disease during the study period was three-times the average over the preceding 3 years. Active case-finding through systematic PCR testing better clarified the regional epidemiology of Legionnaires' disease and uncovered an otherwise hidden burden of disease. These data inform local Legionnaires' disease testing strategies, allow targeted antibiotic therapy, and help identify outbreaks and effective prevention strategies. The same approach might have similar benefits if applied elsewhere in the world. FUNDING: Health Research Council of New Zealand.

Streptococcus gallinaceus bacteraemia in an abattoir worker presenting with a febrile illness.

Streptococcus gallinaceus is a newly described species of viridans streptococci, previously only identified as causing disease in broiler chickens. This organism was recovered in pure culture from blood taken from a New Zealand abattoir worker presenting with a febrile illness. This first report of bacteraemia caused by S. gallinaceus in a human may help the understanding of the ecology of this recently described organism.

Molecular testing for viral and bacterial enteric pathogens: gold standard for viruses, but don't let culture go just yet?

Contemporary diagnostic microbiology is increasingly adopting molecular methods as front line tests for a variety of samples. This trend holds true for detection of enteric pathogens (EP), where nucleic acid amplification tests (NAAT) for viruses are well established as the gold standard, and an increasing number of commercial multi-target assays are now available for bacteria and parasites. NAAT have significant sensitivity and turnaround time advantages over traditional methods, potentially returning same-day results. Multiplex panels offer an attractive 'one-stop shop' that may provide workflow and cost advantages to laboratories processing large sample volumes. However, there are a number of issues which need consideration. Reflex culture is required for antibiotic susceptibility testing and strain typing when needed for food safety and other epidemiological investigations. Surveillance systems will need to allow for differences in disease incidence due to the enhanced sensitivity of NAAT. Laboratories should be mindful of local epidemiology when selecting which pathogens to include in multiplex panels, and be thoughtful regarding which pathogens will not be detected. Multiplex panels may not be appropriate in certain situations, such as hospital-onset diarrhoea, where Clostridium difficile testing might be all that is required, and laboratories may wish to retain the flexibility to run single tests in such situations. The clinical impact of rapid results is also likely to be relatively minor, as infective diarrhoea is a self-limiting illness in the majority of cases. Laboratories will require strategies to assist users in the interpretation of the results produced by NAAT, particularly where pathogens are detected at low levels with uncertain clinical significance. These caveats aside, faecal NAAT are increasingly being used and introduce a new era of diagnosis of gastrointestinal infection.