Evaluating the dynamics of hospital COVID-19 contacts and subsequent conversion to SARS-CoV-2 infection: a multi-centre retrospective cohort study.

We investigated the dynamics of COVID-19 contacts subsequent conversion to SARS-CoV-2 infection in an inpatient setting across three National Health Service (NHS) Trusts. 9.2% (476/5,156) COVID-19 contacts met inclusion criteria, were typable and tested positive for COVID-19. There was no significant difference between Omicron and non-Omicron contacts overall conversion proportions. Omicron contacts converted faster than non-Omicron contacts (median 3 days vs 4 days, P=0.03), and had significantly greater proportions of early conversions at day 3, 5, and 7 timepoints.

National action plans for antimicrobial resistance and variations in surveillance data platforms.

Objective: To assess how national antimicrobial susceptibility data used to inform national action plans vary across surveillance platforms. Methods: We identified available open-access, supranational, interactive surveillance platforms and cross-checked their data in accordance with the World Health Organization's (WHO's) Data Quality Assurance: module 1. We compared platform usability and completeness of time-matched data on the antimicrobial susceptibilities of four blood isolate species: Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus and Streptococcus pneumoniae from WHO's Global Antimicrobial Resistance and Use Surveillance System, European Centre for Disease Control's (ECDC's) network and Pfizer's Antimicrobial Testing Leadership and Surveillance database. Using Bland-Altman analysis, paired t-tests, and Wilcoxon signed-rank tests, we assessed susceptibility data and number of isolate concordances between platforms. Findings: Of 71 countries actively submitting data to WHO, 28 also submit to Pfizer's database; 19 to ECDC; and 16 to all three platforms. Limits of agreement between WHO's and Pfizer's platforms for organism-country susceptibility data ranged from -26% to 35%. While mean susceptibilities of WHO's and ECDC's platforms did not differ (bias: 0%, 95% confidence interval: -2 to 2), concordance between organism-country susceptibility was low (limits of agreement -18% to 18%). Significant differences exist in isolate numbers reported between WHO-Pfizer (mean of difference: 674, P-value: < 0.001, and WHO-ECDC (mean of difference: 192, P-value: 0.04) platforms. Conclusion: The considerable heterogeneity of nationally submitted data to commonly used antimicrobial resistance surveillance platforms compromises their validity, thus undermining local and global antimicrobial resistance strategies. Hence, we need to understand and address surveillance platform variability and its underlying mechanisms.

Retrospective review of the epidemiology, microbiology, management and outcomes of intra-cranial abscesses at a neurosurgical tertiary referral centre, 2018-2020.

BACKGROUND: Intracranial abscesses are rare but serious, and are associated with significant morbidity and mortality. Due to both the rarity and severity of these infections, well-controlled trials have not been reported in the literature, and optimal management is a matter for expert opinion. Advances in surgical management have improved outcomes and increased rates of microbiological diagnosis. However, the approach to antimicrobial chemotherapy varies considerably, including the choice of antibiotic, the duration of treatment, and the timing of oral switch. METHODS: We conducted a retrospective review of 43 cases of intracranial abscesses from a large, tertiary neurosurgical centre in London, UK, between 2018 and 2020, including 29 primary intra-parenchymal abscesses, 11 subdural abscesses and 3 extradural abscesses. RESULTS: The majority of cases had surgical intervention; 6/43 (14%) required repeat intervention (all intra-parenchymal abscesses). A microbiological diagnosis was made in 83% of cases. Intravenous antibiotics were given for a median of 33 days (IQR 23-44 days), with a variable duration of oral follow-on antibiotics. Total duration of antibiotic treatment ranged from 0 to 467 days. Only three patients from our cohort are known to have died. CONCLUSION: Shorter courses of intravenous antibiotics for brain abscesses were not associated with increased mortality. In the absence of well-controlled trials, a national registry of intracranial abscesses would provide invaluable data to inform optimal treatment.

Prolonged QT predicts prognosis in COVID-19.

BACKGROUND: Coronavirus disease-2019 (COVID-19) causes severe illness and multi-organ dysfunction. An abnormal electrocardiogram is associated with poor outcome, and QT prolongation during the illness has been linked to pharmacological effects. This study sought to investigate the effects of the COVID-19 illness on the corrected QT interval (QTc). METHOD: For 293 consecutive patients admitted to our hospital via the emergency department for COVID-19 between 01/03/20 -18/05/20, demographic data, laboratory findings, admission electrocardiograph and clinical observations were compared in those who survived and those who died within 6 weeks. Hospital records were reviewed for prior electrocardiograms for comparison with those recorded on presentation with COVID-19. RESULTS: Patients who died were older than survivors (82 vs 69.8 years, p < 0.001), more likely to have cancer (22.3% vs 13.1%, p = 0.034), dementia (25.6% vs 10.7%, p = 0.034) and ischemic heart disease (27.8% vs 10.7%, p < 0.001). Deceased patients exhibited higher levels of C-reactive protein (244.6 mg/L vs 146.5 mg/L, p < 0.01), troponin (1982.4 ng/L vs 413.4 ng/L, p = 0.017), with a significantly longer QTc interval (461.1 ms vs 449.3 ms, p = 0.007). Pre-COVID electrocardiograms were located for 172 patients; the QTc recorded on presentation with COVID-19 was longer than the prior measurement in both groups, but was more prolonged in the deceased group (448.4 ms vs 472.9 ms, pre-COVID vs COVID, p < 0.01). Multivariate Cox-regression analysis revealed age, C-reactive protein and prolonged QTc of >455 ms (males) and >465 ms (females) (p = 0.028, HR 1.49 [1.04-2.13]), as predictors of mortality. QTc prolongation beyond these dichotomy limits was associated with increased mortality risk (p = 0.0027, HR 1.78 [1.2-2.6]). CONCLUSION: QTc prolongation occurs in COVID-19 illness and is associated with poor outcome.

Trends in paediatric nosocomial bacteraemia in a London tertiary hospital.

AIM: To describe the incidence and microbiological characteristics of nosocomial bloodstream infections in childhood over a 9-year period at a South London tertiary hospital. METHODS: Analysis of prospective data collected for clinically significant nosocomial bloodstream infections in children aged <16 years during 2001-2009. RESULTS: During the study period, although the absolute number of nosocomial bloodstream infections were similar for the neonatal unit (n = 254) and paediatric wards (n = 224), rates were 11.6-fold (95% CI, 9.8-13.9) higher for the former (5.8 vs. 0.50/100 discharges, respectively). Analysis of trends revealed a significant reduction in rates for both the neonatal unit (7.8-2.5 episodes/100 discharges; p < 0.001) and paediatric wards (1.2-0.4 episodes/100 discharges; p < 0.001), mainly due a decline in catheter-associated staphylococcal bacteraemia, which accounted for 115 (45%) and 164 (73%) episodes in the paediatric wards and neonatal units, respectively. Gram-positive cocci were the most frequent pathogens recovered, accounting for 200 (79%) and 185 (83%) cases in the neonatal unit and paediatric wards, respectively. Overall, antimicrobial resistance rates were low compared with other industrialized countries. CONCLUSION: Nosocomial bloodstream infections rates declined significantly in our hospital over the past decade, likely driven by local introduction of national infection-control bundles particularly focussing on insertion and maintenance of intravascular catheters.

Detection of mobile-genetic-element variation between colonizing and infecting hospital-associated methicillin-resistant Staphylococcus aureus isolates.

Whole-genome analysis by 62-strain microarray showed variation in resistance and virulence genes on mobile genetic elements (MGEs) between 40 isolates of methicillin-resistant Staphylococcus aureus (MRSA) strain CC22-SCCmecIV but also showed (i) detection of two previously unrecognized MRSA transmission events and (ii) that 7/8 patients were infected with a variant of their own colonizing isolate.

Are nasal carriers of Staphylococcus aureus more likely to become colonized or infected with methicillin-resistant Staphylococcus aureus on admission to a hospital?

Of 840 patients at hospital admission, 2.7% were positive for methicillin-resistant Staphylococcus aureus (MRSA) and 22.3% were positive for methicillin-susceptible S. aureus (MSSA). During the next 8 months, 4.8% of the MSSA-positive patients acquired MRSA with no lineage association. A total of 5.2% of noncarriers acquired MRSA. We find no evidence that colonized hosts are more susceptible to acquiring MRSA.

Risk factors for late onset gram-negative infections: a case-control study.

OBJECTIVES: To determine the incidence, mortality and risk factors for neonatal late onset gram-negative sepsis and meningitis (LOGNS). DESIGN: Retrospective case-control study. SETTING: Tertiary neonatal unit in London. PATIENTS: Consecutive inborn infants with late onset (>48 h of life) invasive gram-negative infections diagnosed between 1999 and 2005. Controls were healthy infants matched for gestation and time of admission to the neonatal unit. MAIN OUTCOME MEASURES: Clinical and risk factor data. RESULTS: 73 cases of LOGNS were identified of which 48 were inborn and included in the study (incidence 1.85/1000 live births). Enterobacter spp. (28%), Escherichia coli (27%) and Klebsiella spp. (21%) were the most common pathogens. The majority of infants were of very low birthweight (VLBW; 79%), and cases and controls were well matched (median gestation 26 weeks). Overall case death was 27% in cases versus 13.5% in controls (p=0.08). There was no significant difference between cases and controls regarding maternal risk factors. Mechanical ventilation, total parenteral nutrition (TPN) and its duration, presence of a central venous line and its duration, use of specific antibiotics and the occurrence of necrotising enterocolitis at or before the first positive culture were all significantly associated with case status in univariate analysis. In multivariate logistic regression analysis, only duration of TPN at or before first positive blood culture remained independently associated with LOGNS (p<0.001). CONCLUSIONS: LOGNS occurs predominantly in VLBW infants. When the influence of gestational age is accounted for, the only independent risk factor found for late onset gram-negative neonatal infections is the duration of TPN.

Diagnosis of Clostridium difficile infection by toxin detection kits: a systematic review.

Clostridium difficile can be a fatal hospital-acquired infection and its prevalence has increased. Accurate diagnosis of C difficile is essential for patient management, infection control, and for defining its epidemiology. We did a systematic review of commonly used commercial assays for detection of C difficile toxin (CDT) A and B in stool samples. By comparison of detection of CDT in cell culture with or without selective culture for C difficile, the median sensitivities and specificities (IQR) were as follows: Meridian Premier 0.95 (0.86-0.97) and 0.97 (0.95-0.98), TechLab Tox A/B II 0.83 (0.82-0.85) and 0.99 (0.98-1.00), TechLab Tox A/B Quik Chek 0.84 (0.81-0.87) and 1.00 (0.99-1.00), Remel Xpect 0.82 (0.75-0.89) and 0.96 (0.95-0.98), Meridian Immunocard 0.90 (0.84-0.92) and 0.99 (0.98-1.00), and BioMérieux VIDAS 0.76 and 0.93. If the prevalence of CDT A and B in stool samples is relatively low (<10%), the positive predictive value of these assays is unacceptably low (eg, <50% in some circumstances) and will vary depending on the assay and number of samples tested. This low positive predictive value impinges on clinical management, outbreaks, and makes epidemiological data unreliable. To improve diagnosis, we suggest a two-stage testing strategy for C difficile toxin with an initial highly sensitive rapid screening test to identify positive samples that are then confirmed by a reference method.

Prevalence of nasopharyngeal carriage of pneumococcus in preschool children attending day care in London.

OBJECTIVE: To estimate the prevalence of nasopharyngeal (NP) carriage of pneumococcus (Streptococcus pneumoniae) and describe the antibiotic resistance patterns and serotypes in young children attending group day care in London. DESIGN AND SUBJECTS: Cross-sectional survey of attendees at a sample of registered child day care centres (CDCCs) in a London borough. SETTING: Urban setting with a socially and culturally diverse population. METHODS AND OUTCOMES: 19 CDCCs (13% of total) participated between March and November 2003. A single NP swab was required from each child, and parents completed a questionnaire about their child's health and attendance at day care. WHO methodology for pneumococcal carriage studies was followed. RESULTS: 30% of parents consented. 234 swabs were collected from children aged 6 months to 5 years. 53% were boys and 81% were white. 120 children (51%, 95% CI 45% to 58%) carried pneumococci in their nasopharynx. None of the isolates were resistant to penicillin (upper CL 3%). 21 isolates were resistant to erythromycin (17.5%, 95% CI 11% to 25.5%). 68 isolates (57%) were serotypes included in the 7-valent conjugate vaccine. Non-white children had a lower prevalence of carriage (27% vs 58%). CONCLUSION: The prevalence of pneumococcal NP carriage was high. The penicillin resistance rate is lower than in many other countries and may reflect a decrease in community antibiotic prescribing in the UK. Monitoring circulating serotypes is important in the context of recent changes to the vaccination policy. Further study is required to explore the association with ethnicity and risk factors for antibiotic resistance.

Helicobacter pylori antibiotic-resistance patterns and risk factors in adult dyspeptic patients from ethnically diverse populations in central and south London during 2000.

Surveillance of Helicobacter pylori antibiotic susceptibility from patients in London, the largest metropolitan area in the UK, is limited, despite resistance being a key factor in treatment failure. A two-centre survey was performed over 12 months (1999-2000) to determine antibiotic-resistance rates of isolates from dyspeptic patients attending endoscopy clinics serving two ethnically diverse central and south London communities. The in vitro antibiotic susceptibilities were determined from disc diffusion and epsilometer (E) tests on 101 H. pylori isolates. Overall resistance rates were 59% for metronidazole and 11% for clarithromycin, with 8 % resistance to both antibiotics. Corresponding primary resistance rates were 50% and 7%, respectively. High-level-resistance was a feature of 82% of the metronidazole (MIC > or = 256 mg l(-1)) -resistant and 55% of the clarithromycin (MIC > or = 32 mg l(-1)) -resistant strains. All isolates were susceptible to amoxycillin and tetracycline. No associations between resistance and either the gender or the age of the patients were detected. The main risk for resistance to metronidazole was non-UK birth as comparative rates were 68% for non-UK vs. 40% for UK-born individuals. Resistant isolates were genotypically diverse with respect to cagA/vacA type. Four 23S rDNA nucleotide polymorphisms were associated with clarithromycin resistance, mostly (9/11) at A2143G. In conclusion, the high overall metronidazole-resistance rate of 59% for H. pylori from inner London was twice the rate found in other UK-based studies and was attributed to the higher risk of resistant strains infecting individuals born outside the UK. The need for continued resistance surveillance is indicated to monitor the effects of the 'test and treat' strategy for H. pylori eradication, particularly of isolates from at-risk individuals.

Isolation of cholesterol-dependent Candida glabrata from clinical specimens.

In the past few years, we have detected in the United Kingdom and in the United States several isolates of Candida glabrata that grew poorly unless bile was available. Cholesterol, a component of bile, stimulated equivalent growth of the bile-dependent isolates. The bile-dependent C. glabrata isolates appeared resistant to amphotericin B, but their resistance to fluconazole was unclear. These results demonstrate that occasional isolates of C. glabrata require cholesterol to grow, they may not be detected in specimens set up on standard primary plating media, and they may be difficult to eradicate in patients with antifungal agents directed against ergosterol and its synthetic pathway.