A laboratory framework for ongoing optimization of amplification-based genomic surveillance programs.

IMPORTANCE: This study provides a laboratory framework to ensure ongoing relevance and performance of amplification-based whole genome sequencing to strengthen public health surveillance during extended outbreaks or pandemics. The framework integrates regular reviews of the performance of a genomic surveillance system and highlights the importance of ongoing monitoring and the identification and implementation of improvements to whole genome sequencing methods to enhance public health responses to pathogen outbreaks.

Genome entropy and network centrality contrast exploration and exploitation in evolution of foodborne pathogens.

Modelling evolution of foodborne pathogens is crucial for mitigation and prevention of outbreaks. We apply network-theoretic and information-theoretic methods to trace evolutionary pathways ofSalmonellaTyphimurium in New South Wales, Australia, by studying whole genome sequencing surveillance data over a five-year period which included several outbreaks. The study derives both undirected and directed genotype networks based on genetic proximity, and relates the network's structural property (centrality) to its functional property (prevalence). The centrality-prevalence space derived for the undirected network reveals a salient exploration-exploitation distinction across the pathogens, further quantified by the normalised Shannon entropy and the Fisher information of the corresponding shell genome. This distinction is also analysed by tracing the probability density along evolutionary paths in the centrality-prevalence space. We quantify the evolutionary pathways, and show that pathogens exploring the evolutionary search-space during the considered period begin to exploit their environment (their prevalence increases resulting in outbreaks), but eventually encounter a bottleneck formed by epidemic containment measures.

Pangenome Analysis of a Salmonella Enteritidis Population Links a Major Outbreak to a Gifsy-1-Like Prophage Containing Anti-Inflammatory Gene gogB.

A major outbreak of the globally significant Salmonella Enteritidis foodborne pathogen was identified within a large clinical data set by a program of routine WGS of clinical presentations of salmonellosis in New South Wales, Australia. Pangenome analysis helped to quantify and isolate prophage content within the accessory partition of the pangenome. A prophage similar to Gifsy-1 (henceforth GF-1L) was found to occur in all isolates of the outbreak core SNP cluster, and in three other isolates. Further analysis revealed that the GF-1L prophage carried the gogB virulence factor. These observations suggest that GF-1L may be an important marker of virulence for S. Enteritidis population screening and, that anti-inflammatory, gogB-mediated virulence currently associated with Salmonella Typhimurium may also be displayed by S. Enteritidis. IMPORTANCE We examined 5 years of genomic and epidemiological data for the significant global foodborne pathogen, Salmonella enterica. Although Salmonella enterica subspecies enterica serovar Enteritidis (S. Enteritidis) is the leading cause of salmonellosis in the USA and Europe, prior to 2018 it was not endemic in the southern states of Australia. However, in 2018 a large outbreak led to the endemicity of S. Enteritidis in New South Wales, Australia, and a unique opportunity to study this phenomenon. Using pangenome analysis we uncovered that this clone contained a Gifsy-1-like prophage harboring the known virulence factor gogB. The prophage reported has not previously been described in S. Enteritidis isolates.

Guiding the design of SARS-CoV-2 genomic surveillance by estimating the resolution of outbreak detection.

Genomic surveillance of SARS-CoV-2 has been essential to inform public health response to outbreaks. The high incidence of infection has resulted in a smaller proportion of cases undergoing whole genome sequencing due to finite resources. We present a framework for estimating the impact of reduced depths of genomic surveillance on the resolution of outbreaks, based on a clustering approach using pairwise genetic and temporal distances. We apply the framework to simulated outbreak data to show that outbreaks are detected less frequently when fewer cases are subjected to whole genome sequencing. The impact of sequencing fewer cases depends on the size of the outbreaks, and on the genetic and temporal similarity of the index cases of the outbreaks. We also apply the framework to an outbreak of the SARS-CoV-2 Delta variant in New South Wales, Australia. We find that the detection of clusters in the outbreak would have been delayed if fewer cases had been sequenced. Existing recommendations for genomic surveillance estimate the minimum number of cases to sequence in order to detect and monitor new virus variants, assuming representative sampling of cases. Our method instead measures the resolution of clustering, which is important for genomic epidemiology, and accommodates sampling biases.

Identifying factors associated with intravenous fluid administration in patients with sepsis presenting to the emergency department: a retrospective cohort study.

BACKGROUND: Appropriate and timely administration of intravenous fluids to patients with sepsis-induced hypotension is one of the mainstays of sepsis management in the emergency department (ED), however, fluid resuscitation remains an ongoing challenge in ED. Our study has been undertaken with two specific aims: firstly, for patients with sepsis, to identify factors associated with receiving intravenous fluids while in the ED; and, secondly to identify determinants associated with the actual time to fluid administration. METHODS: We conducted a retrospective multicentre cohort study of adult ED presentations between October 2018 and May 2019 in four metropolitan hospitals in Western Sydney, Australia. Patients meeting pre-specified criteria for sepsis and septic shock and treated with antibiotics within the first 24 h of presentation were included. Multivariable models were used to identify factors associated with fluid administration in sepsis. RESULTS: Four thousand one hundred forty-six patients met the inclusion criteria, among these 2,300 (55.5%) patients with sepsis received intravenous fluids in ED. The median time to fluid administration from the time of diagnosis of sepsis was 1.6 h (Interquartile Range (IQR) 0.5 to 3.8), and the median volume of fluids administered was 1,100 mL (IQR 750 to 2058). Factors associated with patients receiving fluids were younger age (Odds Ratio (OR) 1.05, 95% Confidence Interval (CI (1.03 to 1.07), p < 0.001); lower systolic blood pressure (OR 1.11, 95% CI (1.08 to 1.13), p < 0.001); presenting to smaller hospital (OR 1.48, 95% CI (1.25 to 1.75, p < 0.001) and a Clinical Rapid Response alert activated (OR 1.64, 95% CI (1.28 to 2.11), p < 0.001). Patients with Triage Category 1 received fluids 101.22 min earlier (95% CI (59.3 to131.2), p < 0.001) and those with Category 2 received fluids 43.58 min earlier (95% CI (9.6 to 63.1), p < 0.001) compared to patients with Triage Category 3-5. Other factors associated with receiving fluids earlier included septic shock (-49.37 min (95% CI (-86.4 to -12.4), p < 0.001)); each mmol/L increase in serum lactate levels (-9.0 min, 95% CI (-15.7 to -2.3), p < 0.001) and presenting to smaller hospitals (-74.61 min, 95% CI (-94.0 to -55.3), p < 0.001). CONCLUSIONS: Younger age, greater severity of sepsis, and presenting to a smaller hospital increased the probability of receiving fluids and receiving it earlier. Recognition of these factors may assist in effective implementation of sepsis management guidelines which should translate into better patient outcomes. Future studies are needed to identify other associated factors that we have not explored.