HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data.

Existing tools for phylogeographic and epidemiological visualisation primarily provide a macro-geographic view of epidemic and pandemic transmission events but offer little support for detailed investigation of outbreaks in healthcare settings. Here, we present HAIviz, an interactive web-based application designed for integrating and visualising genomic epidemiological information to improve the tracking of healthcare-associated infections (HAIs). HAIviz displays and links the outbreak timeline, building map, phylogenetic tree, patient bed movements, and transmission network on a single interactive dashboard. HAIviz has been developed for bacterial outbreak investigations but can be utilised for general epidemiological investigations focused on built environments for which visualisation to customised maps is required. This paper describes and demonstrates the application of HAIviz for HAI outbreak investigations.

Melioidosis Queensland: An analysis of clinical outcomes and genomic factors.

BACKGROUND: The clinical and genomic epidemiology of melioidosis varies across regions. AIM: To describe the clinical and genetic diversity of B. pseudomallei across Queensland, Australia. METHODS: Whole genome sequencing of clinical isolates stored at the melioidosis reference lab from 1996-2020 was performed and analysed in conjunction with available clinical data. RESULTS: Isolates from 292 patients were analysed. Bacteraemia was present in 71% and pneumonia in 65%. The case-fatality rate was 25%. Novel sequence types (ST) accounted for 51% of all isolates. No association was identified between the variable virulence factors assessed and patient outcome. Over time, the proportion of First Nation's patients declined from 59% to 26%, and the proportion of patients aged >70 years rose from 13% to 38%. CONCLUSION: This study describes a genomically diverse and comparatively distinct collection of B. pseudomallei clinical isolates from across Queensland, Australia. An increasing incidence of melioidosis in elderly patients may be an important factor in the persistently high case-fatality in this region and warrants further investigation and directed intervention.

Characterization of antibiotic resistance genes and mobile elements in extended-spectrum ß-lactamase-producing Escherichia coli strains isolated from hospitalized patients in Guangdong, China.

AIM: This study aimed to investigate the high-resolution phenotypic and genotypic characterization of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli strains isolated from hospitalized patients to explore the resistance genes and mobile genetic elements (MGEs) involved in horizontal dissemination. METHODS: Between May and September 2021, a total of 216 ESBL-producing E. coli isolates were recovered from multiple departments. The identification of strains was performed using MALDI-TOF mass spectrometry and PCR, while antibiotic susceptibility testing was carried out using the Vitek 2 COMPACT system to determine resistance patterns, while PCR was used to detect different resistance genes and MGEs. In addition, a conjugation assay was performed to investigate the horizontal gene transfer of resistance genes. Selected isolates underwent whole-genome sequencing (WGS) using the Illumina MiSeq platform. RESULTS: A total of 216 out of 409 E. coli isolates recovered from a tertiary hospital were observed to be ESBL-producing, giving a carriage rate of 52.8%, as determined by phenotypic screening. The most frequent sources of ESBL-producing E. coli isolates were urine (129/216, 59.72%) and blood (50/216, 23.14%). The most prevalent ESBL genes identified were blaCTX-M (60.18%), blaTEM (40.27%), and blaSHV (18.05%). Three E. coli isolates were found to carry the genes blaNDM, mcr-1, and fosA3 genes. The most prevalent MGEs were IS26 (95.37%), Int (87.03%), and IncFIB (76.85%). WGS analysis of eight MDR E. coli strains revealed that these isolates belonged to eight different sequence types (STs) and serotypes and were found to harbor multiple plasmid replicons and virulence factors. CONCLUSION: This study highlights a high incidence of antibiotic resistance genes and MGEs associated with the dissemination of ESBLs and other resistance genes.

Using Genomics To Investigate an Outbreak of Vancomycin-Resistant Enterococcus faecium ST78 at a Large Tertiary Hospital in Queensland.

To investigate an outbreak of vancomycin-resistant Enterococcus faecium (VREfm) sequence type 78 (ST78) in a large tertiary Australian hospital. A collection of 63 VREfm ST78 isolates, identified during a routine genomic surveillance program, were subjected to genomic epidemiological analysis based on whole-genome sequencing (WGS) data. The population structure was reconstructed using phylogenetic analysis, and a collection of publicly available VREfm ST78 genomes were used to provide global context. Core genome single nucleotide polymorphism (SNP) distances and available clinical metadata were used to characterize outbreak clusters and reconstruct transmission events. In silico genotyping confirmed that all study isolates were vanB-type VREfm carrying virulence characteristics of the hospital-associated E. faecium. Phylogenetic analysis identified two distinct phylogenetic clades, only one of which was responsible for a hospital outbreak. Four outbreak subtypes could be defined with examples of recent transmissions. Inference on transmission trees suggested complex transmission routes with unknown environmental reservoirs mediating the outbreak. WGS-based cluster analysis with publicly available genomes identified closely related Australian ST78 and ST203 isolates, highlighting the capacity for WGS to resolve complex clonal relationships between the VREfm lineages. Whole genome-based analysis has provided a high-resolution description of an outbreak of vanB-type VREfm ST78 in a Queensland hospital. Combined routine genomic surveillance and epidemiological analysis have facilitated better understanding of the local epidemiology of this endemic strain, providing valuable insight for better targeted control of VREfm. IMPORTANCE Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of health care-associated infections (HAIs) globally. In Australia, the spread of hospital-adapted VREfm is largely driven by a single clonal group (clonal complex [CC]), CC17, to which the lineage ST78 belongs. While implementing a genomic surveillance program in Queensland, we observed increased incidence of ST78 colonizations and infections among patients. Here, we demonstrate the use of real-time genomic surveillance as a tool to support and enhance infection control (IC) practices. Our results show that real-time whole-genome sequencing (WGS) can efficiently disrupt outbreaks by identifying transmission routes that in turn can be targeted using resource-limited interventions. Additionally, we demonstrate that by placing local outbreaks in a global context, high-risk clones can be identified and targeted prior to them becoming established within clinical environments. Finally, the persistence of these organism within the hospital highlights the need for routine genomic surveillance as a management tool to control VRE transmission.

GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach.

BACKGROUND: Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration. RESULTS: GraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes. The functionality of GraphSNP is demonstrated using examples from recent multi-drug resistant bacterial outbreaks in healthcare settings. CONCLUSIONS: GraphSNP is freely available at https://github.com/nalarbp/graphsnp . An online version of GraphSNP, including demonstration datasets, input templates, and quick start guide is available for use at https://graphsnp.fordelab.com .

Eco-Friendly Tannin-Based Non-Isocyanate Polyurethane Resins for the Modification of Ramie (Boehmeria nivea L.) Fibers.

This study aimed to develop tannin-based non-isocyanate polyurethane (tannin-Bio-NIPU) and tannin-based polyurethane (tannin-Bio-PU) resins for the impregnation of ramie fibers (Boehmeria nivea L.) and investigate their mechanical and thermal properties. The reaction between the tannin extract, dimethyl carbonate, and hexamethylene diamine produced the tannin-Bio-NIPU resin, while the tannin-Bio-PU was made with polymeric diphenylmethane diisocyanate (pMDI). Two types of ramie fiber were used: natural ramie without pre-treatment (RN) and with pre-treatment (RH). They were impregnated in a vacuum chamber with tannin-based Bio-PU resins for 60 min at 25 °C under 50 kPa. The yield of the tannin extract produced was 26.43 ± 1.36%. Fourier-transform infrared (FTIR) spectroscopy showed that both resin types produced urethane (-NCO) groups. The viscosity and cohesion strength of tannin-Bio-NIPU (20.35 mPa·s and 5.08 Pa) were lower than those of tannin-Bio-PU (42.70 mPa·s and 10.67 Pa). The RN fiber type (18.9% residue) was more thermally stable than RH (7.3% residue). The impregnation process with both resins could improve the ramie fibers' thermal stability and mechanical strength. The highest thermal stability was found in RN impregnated with the tannin-Bio-PU resin (30.5% residue). The highest tensile strength was determined in the tannin-Bio-NIPU RN of 451.3 MPa. The tannin-Bio-PU resin gave the highest MOE for both fiber types (RN of 13.5 GPa and RH of 11.7 GPa) compared to the tannin-Bio-NIPU resin.

Coexistence of bla NDM-5 and tet(X4) in international high-risk Escherichia coli clone ST648 of human origin in China.

The emergence of pathogens is conferring resistance to last-resort therapies such as tigecycline, colistin, and carbapenems, limiting the therapeutic options, and raising concerns about the emergence of new "superbugs." This study reports the first incident of a bla NDM-5 and tet(X4) co-harboring Escherichia coli with resistance to carbapenem and tigecycline recovered as the causative agent of a urinary tract infection in a 94-year-old patient. The E. coli strain ECCL209 carries multiple resistance genes [i.e., bla TEM-1B , bla NDM-5, bla CMY-2, aadA22, florR, erm(B), mph(A), erm(42), lnuG, qnrS1, and sul2] and exhibits resistance to almost all clinically used antibiotics. MLST analysis found that the strain belongs to ST648, considered a worldwide high-risk pandemic clone. Moreover, multiple plasmid incompatibility types were detected, i.e., IncHI1A, IncHI1B, IncFII, IncFIA, IncFIB, IncQ1, Col, and IncX4. Genetic analysis revealed that bla NDM-5 and tet(X4) genes were localized on two hybrid plasmids with multiple replicons. Continuous monitoring studies are suggested to quantify the antimicrobial resistance and assess the dissemination of such superbugs into a human healthcare setting.

CATHAI: cluster analysis tool for healthcare-associated infections.

Motivation: Whole genome sequencing (WGS) is revolutionizing disease surveillance where it facilitates high-resolution clustering of related organism and outbreak detection. However, visualizing and efficiently communicating genomic data back to clinical staff is crucial for the successful deployment of a targeted infection control response. Results: CATHAI (cluster analysis tool for healthcare-associated infections) is an interactive web-based visualization platform that couples WGS informed clustering with associated metadata, thereby converting sequencing data into informative and accessible clinical information for the management of healthcare-associated infections (HAI) and nosocomial outbreaks. Availability and implementation: All code associated with this application are free available from https://github.com/FordeGenomics/cathai. A demonstration version of CATHAI is available online at https://cathai.fordelab.com.

Enhancing Thermal and Mechanical Properties of Ramie Fiber via Impregnation by Lignin-Based Polyurethane Resin.

In this study, lignin isolated and fractionated from black liquor was used as a pre-polymer to prepare bio-polyurethane (Bio-PU) resin, and the resin was impregnated into ramie fiber (Boehmeria nivea (L.) Gaudich) to improve its thermal and mechanical properties. The isolated lignin was fractionated by one-step fractionation using two different solvents, i.e., methanol (MeOH) and acetone (Ac). Each fractionated lignin was dissolved in NaOH and then reacted with a polymeric 4,4-methane diphenyl diisocyanate (pMDI) polymer at an NCO/OH mole ratio of 0.3. The resulting Bio-PU was then used in the impregnation of ramie fiber. The characterization of lignin, Bio-PU, and ramie fiber was carried out using several techniques, i.e., Fourier-transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), pyrolysis-gas-chromatography-mass-spectroscopy (Py-GCMS), Micro Confocal Raman spectroscopy, and an evaluation of fiber mechanical properties (modulus of elasticity and tensile strength). Impregnation of Bio-PU into ramie fiber resulted in weight gain ranging from 6% to 15%, and the values increased when extending the impregnation time. The reaction between the NCO group on Bio-PU and the OH group on ramie fiber forms a C=O group of urethane as confirmed by FTIR and Micro Confocal Raman spectroscopies at a wavenumber of 1600 cm-1. Based on the TGA analysis, ramie fiber with lignin-based Bio-PU had better thermal properties than ramie fiber before impregnation with a greater weight residue of 21.7%. The mechanical properties of ramie fiber also increased after impregnation with lignin-based Bio-PU, resulting in a modulus of elasticity of 31 GPa for ramie-L-isolated and a tensile strength of 577 MPa for ramie-L-Ac. The enhanced thermal and mechanical properties of impregnated ramie fiber with lignin-based Bio-PU resins could increase the added value of ramie fiber and enhance its more comprehensive industrial application as a functional material.

Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care.

Background. Infections caused by carbapenem-resistant Acinetobacter baumannii (CR-Ab) have become increasingly prevalent in clinical settings and often result in significant morbidity and mortality due to their multidrug resistance (MDR). Here we present an integrated whole-genome sequencing (WGS) response to a persistent CR-Ab outbreak in a Brisbane hospital between 2016-2018.Methods. A. baumannii, Klebsiella pneumoniae, Serratia marcescens and Pseudomonas aeruginosa isolates were sequenced using the Illumina platform primarily to establish isolate relationships based on core-genome SNPs, MLST and antimicrobial resistance gene profiles. Representative isolates were selected for PacBio sequencing. Environmental metagenomic sequencing with Illumina was used to detect persistence of the outbreak strain in the hospital.Results. In response to a suspected polymicrobial outbreak between May to August of 2016, 28 CR-Ab (and 21 other MDR Gram-negative bacilli) were collected from Intensive Care Unit and Burns Unit patients and sent for WGS with a 7 day turn-around time in clinical reporting. All CR-Ab were sequence type (ST)1050 (Pasteur ST2) and within 10 SNPs apart, indicative of an ongoing outbreak, and distinct from historical CR-Ab isolates from the same hospital. Possible transmission routes between patients were identified on the basis of CR-Ab and K. pneumoniae SNP profiles. Continued WGS surveillance between 2016 to 2018 enabled suspected outbreak cases to be refuted, but a resurgence of the outbreak CR-Ab mid-2018 in the Burns Unit prompted additional screening. Environmental metagenomic sequencing identified the hospital plumbing as a potential source. Replacement of the plumbing and routine drain maintenance resulted in rapid resolution of the secondary outbreak and significant risk reduction with no discernable transmission in the Burns Unit since.Conclusion. We implemented a comprehensive WGS and metagenomics investigation that resolved a persistent CR-Ab outbreak in a critical care setting.