Epidemiological analysis of the first 1000 cases of SARS-CoV-2 lineage BA.1 (B.1.1.529, Omicron) compared with co-circulating Delta in Wales, UK.

BACKGROUND: The Omicron (lineage B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wales, UK, on 3 December 2021. The aim of the study was to describe the first 1000 cases of the Omicron variant by demographic, vaccination status, travel and severe outcome status and compare this to contemporaneous cases of the Delta variant. METHODS: Testing, typing and contact tracing data were collected by Public Health Wales and analysis undertaken by the Communicable Disease Surveillance Centre (CDSC). Risk ratios for demographic factors and symptoms were calculated comparing Omicron cases to Delta cases identified over the same time period. RESULTS: By 14 December 2021, 1000 cases of the Omicron variant had been identified in Wales. Of the first 1000, just 3% of cases had a prior history of travel revealing rapid community transmission. A higher proportion of Omicron cases were identified in individuals aged 20-39, and most cases were double vaccinated (65.9%) or boosted (15.7%). Age-adjusted analysis also revealed that Omicron cases were less likely to be hospitalised (0.4%) or report symptoms (60.8%). Specifically a significant reduction was observed in the proportion of Omicron cases reporting anosmia (8.9%). CONCLUSION: Key findings include a lower risk of anosmia and a reduced risk of hospitalisation in the first 1000 Omicron cases compared with co-circulating Delta cases. We also identify that existing measures for travel restrictions to control importations of new variants identified outside the United Kingdom did not prevent the rapid ingress of Omicron within Wales.

Comparative incidence of early and late bloodstream and respiratory tract co-infection in patients admitted to ICU with COVID-19 pneumonia versus Influenza A or B pneumonia versus no viral pneumonia: wales multicentre ICU cohort study.

OBJECTIVE: The aim is to characterise early and late respiratory and bloodstream co-infection in patients admitted to intensive care units (ICUs) with SARS-CoV-2-related acute hypoxemic respiratory failure (AHRF) needing respiratory support in seven ICUs within Wales, during the first wave of the COVID-19 pandemic. We compare the rate of positivity of different secondary pathogens and their antimicrobial sensitivity in three different patient groups: patients admitted to ICU with COVID-19 pneumonia, Influenza A or B pneumonia, and patients without viral pneumonia. DESIGN: Multicentre, retrospective, observational cohort study with rapid microbiology data from Public Health Wales, sharing of clinical and demographic data from seven participating ICUs. SETTING: Seven Welsh ICUs participated between 10 March and 31 July 2020. Clinical and demographic data for COVID-19 disease were shared by each participating centres, and microbiology data were extracted from a data repository within Public Health Wales. Comparative data were taken from a cohort of patients without viral pneumonia admitted to ICU during the same period as the COVID-19 cohort (referred to as no viral pneumonia or 'no viral' group), and to a retrospective non-matched cohort of consecutive patients with Influenza A or B admitted to ICUs from 20 November 2017. The comparative data for Influenza pneumonia and no viral pneumonia were taken from one of the seven participating ICUs. PARTICIPANTS: A total of 299 consecutive patients admitted to ICUs with COVID-19 pneumonia were compared with 173 and 48 patients admitted with no viral pneumonia or Influenza A or B pneumonia, respectively. MAIN OUTCOME MEASURES: Primary outcome was to calculate comparative incidence of early and late co-infection in patients admitted to ICU with COVID-19, Influenza A or B pneumonia and no viral pneumonia. Secondary outcome was to calculate the individual group of early and late co-infection rate on a per-patient and per-sample basis, with their antimicrobial susceptibility and thirdly to ascertain any statistical correlation between clinical and demographic variables with rate of acquiring co-infection following ICU admission. RESULTS: A total of 299 adults (median age 57, M/F 2:1) were included in the COVID-19 ICU cohort. The incidence of respiratory and bloodstream co-infection was 40.5% and 15.1%, respectively. Staphylococcus aureus was the predominant bacterial pathogen within the first 48 h. Gram-negative organisms from Enterobacterales group were predominantly seen after 48 h in COVID-19 cohort. Comparative no viral pneumonia cohort had lower rates of respiratory tract infection and bloodstream infection. The influenza cohort had similar rates respiratory tract infection and bloodstream infection. Mortality in all three groups was similar, and no clinical or demographic variables were found to increase the rate of co-infection and ICU mortality. CONCLUSIONS: Higher incidence of bacterial co-infection was found in COVID-19 cohort as compared to the no viral pneumonia cohort admitted to ICUs for respiratory support.

Genome-Wide Identification of Myxobacterial Predation Genes and Demonstration of Formaldehyde Secretion as a Potentially Predation-Resistant Trait of Pseudomonas aeruginosa.

Despite widespread use in human biology, genome-wide association studies (GWAS) of bacteria are few and have, to date, focused primarily on pathogens. Myxobacteria are predatory microbes with large patchwork genomes, with individual strains secreting unique cocktails of predatory proteins and metabolites. We investigated whether a GWAS strategy could be applied to myxobacteria to identify genes associated with predation. Deduced proteomes from 29 myxobacterial genomes (including eight Myxococcus genomes sequenced for this study), were clustered into orthologous groups, and the presence/absence of orthologues assessed in superior and inferior predators of ten prey organisms. 139 'predation genes' were identified as being associated significantly with predation, including some whose annotation suggested a testable predatory mechanism. Formaldehyde dismutase (fdm) was associated with superior predation of Pseudomonas aeruginosa, and predatory activity of a strain lacking fdm could be increased by the exogenous addition of a formaldehyde detoxifying enzyme, suggesting that production of formaldehyde by P. aeruginosa acts as an anti-predation behaviour. This study establishes the utility of bacterial GWAS to investigate microbial processes beyond pathogenesis, giving plausible and verifiable associations between gene presence/absence and predatory phenotype. We propose that the slow growth rate of myxobacteria, coupled with their predatory mechanism of constitutive secretion, has rendered them relatively resistant to genome streamlining. The resultant genome expansion made possible their observed accumulation of prey-specific predatory genes, without requiring them to be selected for by frequent or recent predation on diverse prey, potentially explaining both the large pan-genome and broad prey range of myxobacteria.