Healthcare workers acquired COVID-19 disease from patients? An investigation by phylogenomics.

The increasing number of coronavirus disease 2019 (COVID-19) cases in the community has posed a significant epidemic pressure on healthcare settings. When healthcare workers (HCWs) acquire COVID-19, contact tracing and epidemiological investigation might not be adequate for determining the source of transmission. Here, we report a phylogenetic investigation involving two infected HCWs and nine patients to determine whether patient-to-HCW transmission had occurred in a hospital without a previous COVID-19 outbreak. This is the first study to apply phylogenomics to investigate suspected nosocomial transmission in a region with low prevalence of COVID-19. Our results do not support the occurrence of direct patient-to-HCW transmission.

Diagnostic stewardship programme for urine culture: impact on antimicrobial prescription in a multi-centre cohort.

BACKGROUND: Restricting urine culture to patients with genuine urinary tract infection (UTI) reduces excessive antimicrobial prescription for asymptomatic bacteriuria. AIM: To evaluate the impact of urine culture diagnostic stewardship on antimicrobial consumption. METHODS: This quasi-study involved two general hospitals and 10 community clinics. In the pre-intervention (control) phase (25th November 2018-2nd February 2019), microscopy and culture results of all urine specimens were reported. In the post-intervention (study) phase (25th November 2019-2nd February 2020), urine cultures were processed and reported only if at least one of the following criteria were met: presence of white blood cells or bacteria on microscopy; patient from obstetrics, urology, paediatrics, oncology or renal transplant ward; specimen labelled as 'pregnancy', 'urological procedure', 'renal transplant' or 'neutropenic'; and ureteric, nephrostomy or suprapubic urine. For urine samples that did not fulfil these criteria, the microscopy results and a rejection comment were reported. FINDINGS: In total, 12,282 urine specimens were included in the intervention phase. Of these, 4757 (38.7%) specimens did not fulfil the screening criteria, and the microscopy result and a rejection comment were reported. One hundred and sixty-three (3.4%) of these non-reported urine cultures yielded significant bacterial growth, and the majority were Escherichia coli (N=58, 35.6%). Diagnostic stewardship was independently associated with lower antimicrobial consumption [adjusted odds ratio 0.76, 95% confidence interval (CI) 0.70-0.83, P<0.001] on multi-variable logistic regression across all healthcare settings. Diagnostic stewardship had no effect on patient mortality (adjusted hazard ratio=0.95, 95% CI 0.89-1.01, P=0.08). No patients with unreported urine culture developed bacteraemia from untreated UTI. CONCLUSION: Diagnostic stewardship of urine culture safely reduced excessive antimicrobial prescription for asymptomatic bacteriuria.

Outcomes of adults hospitalised with severe influenza.

BACKGROUND: The aim of this study was to investigate factors affecting clinical outcomes of adults hospitalised with severe seasonal influenza. METHODS: A prospective, observational cohort study was conducted over 24 months (2007-2008) in two acute, general hospitals. Consecutive, hospitalised adult patients were recruited and followed once their laboratory diagnosis of influenza A/B was established (based on viral antigen detection and virus isolation from nasopharyngeal aspirates collected per protocol). Outcomes studied included in-hospital death, length of stay and duration of oxygen therapy. Factors affecting outcomes were analysed using multivariate Cox proportional hazards models. Sequencing analysis on the neuraminidase gene was performed for available H1N1 isolates. RESULTS: 754 patients were studied (influenza A, n=539; >75% H3N2). Their mean age was 70+/-18 years; co-morbidities and serious complications were common (61-77%). Supplemental oxygen and ventilatory support was required in 401 (53.2%) and 41 (5.4%) patients, respectively. 39 (5.2%) patients died; pneumonia, respiratory failure and sepsis were the causes. 395 (52%) patients received antiviral (oseltamivir) treatment. Omission of antiviral treatment was associated with delayed presentation or negative antigen detection results. The mortality rate was 4.56 and 7.42 per 1000 patient-days in the treated and untreated patients, respectively; among those with co-morbidities, it was 5.62 and 11.64 per 1000 patient-days, respectively. In multivariate analysis, antiviral use was associated with reduced risk of death (adjusted HR (aHR) 0.27 (95% CI 0.13 to 0.55); p<0.001). Improved survival was observed with treatment started within 4 days from onset. Earlier hospital discharge (aHR 1.28 (95% CI 1.04 to 1.57); p=0.019) and faster discontinuation of oxygen therapy (aHR 1.30 (95% CI 1.01 to 1.69); p=0.043) was associated with early treatment within 2 days. Few (n=15) H1N1 isolates in this cohort had the H275Y mutation. CONCLUSIONS: Antiviral treatment for severe influenza is associated with reduced mortality and improved clinical outcomes.

Enterobacteriaceae peritonitis complicating peritoneal dialysis: a review of 210 consecutive cases.

Enterobacteriaceae peritonitis is a serious complication in peritoneal dialysis (PD), but the clinical course of PD-related Enterobacteriaceae peritonitis remains unclear. We reviewed all Enterobacteriaceae peritonitis in our dialysis unit from 1995 to 2004. During this period, there were 1748 episodes of peritonitis recorded; 210 episodes (12.0%) in 123 patients were caused by Enterobacteriaceae. The most common species was Escherichia coli, accounting for 111 episodes. The primary response rate was 84.8% and complete cure rate was 58.1%. The presence of exit site infection was associated with a lower complete cure rate (43.2 versus 61.3%, P = 0.034). A total of 82 episodes (39.0%) did not respond to single antibiotic treatment despite sensitivity in vitro, and a second antibiotic was added. Patients treated with two antibiotics had a marginally lower risk of relapse and recurrence than those with one antibiotic (21.4 versus 36.1%, P = 0.051). The episodes that had recent antibiotic therapy had a marginally lower complete cure rate (49.3 versus 62.8%, P = 0.06). There was a gradual increase in the prevalence of resistance to several commonly used antibiotics over the years. Recent antibiotic therapy was associated with resistance to cefotaxime, ceftazidime, cefoperazone/sulbactam, and piperacillin/tazobactam. We conclude that Enterobacteriaceae peritonitis is a serious complication of PD. Recent antibiotic therapy is the major risk factor of antibiotic resistance. Exit site infection, and probably recent antibiotic therapy, is associated with poor therapeutic response. Contrary to the current recommendation, treatment with two antibiotics may reduce the risk of relapse and recurrence.

Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study.

BACKGROUND: We investigated the temporal progression of the clinical, radiological, and virological changes in a community outbreak of severe acute respiratory syndrome (SARS). METHODS: We followed up 75 patients for 3 weeks managed with a standard treatment protocol of ribavirin and corticosteroids, and assessed the pattern of clinical disease, viral load, risk factors for poor clinical outcome, and the usefulness of virological diagnostic methods. FINDINGS: Fever and pneumonia initially improved but 64 (85%) patients developed recurrent fever after a mean of 8.9 (SD 3.1) days, 55 (73%) had watery diarrhoea after 7.5 (2.3) days, 60 (80%) had radiological worsening after 7.4 (2.2) days, and respiratory symptoms worsened in 34 (45%) after 8.6 (3.0) days. In 34 (45%) patients, improvement of initial pulmonary lesions was associated with appearance of new radiological lesions at other sites. Nine (12%) patients developed spontaneous pneumomediastinum and 15 (20%) developed acute respiratory distress syndrome (ARDS) in week 3. Quantitative reverse-transcriptase (RT) PCR of nasopharyngeal aspirates in 14 patients (four with ARDS) showed peak viral load at day 10, and at day 15 a load lower than at admission. Age and chronic hepatitis B virus infection treated with lamivudine were independent significant risk factors for progression to ARDS (p=0.001). SARS-associated coronavirus in faeces was seen on RT-PCR in 65 (97%) of 67 patients at day 14. The mean time to seroconversion was 20 days. INTERPRETATION: The consistent clinical progression, shifting radiological infiltrates, and an inverted V viral-load profile suggest that worsening in week 2 is unrelated to uncontrolled viral replication but may be related to immunopathological damage.

Malassezia furfur fungaemia in a ventilator-dependent patient without known risk factors.

Malassezia furfur is the lipophilic yeast which causes tinea versicolor and is an uncommon cause of fungaemia. It usually occurs in the context of hyperalimentation with lipid emulsion, immunosuppression, or the presence of a central venous catheter. We report a case of a ventilator-dependent patient who developed Malassezia furfur fungaemia in the absence of these known risk factors. A likely risk factor in this patient was receipt of multiple courses of broad-spectrum antibiotics. This case highlights the importance of recognising Malassezia furfur as a cause of fungaemia, as well as the need for special culture techniques to aid identification.