Autocycler: long-read consensus assembly for bacterial genomes.

Motivation: Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using Trycycler can improve accuracy, but its lack of automation limits scalability. There is a need for an automated method to generate high-quality consensus bacterial genome assemblies from long-read data.

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Typhi.

Background: Typhoid fever results from systemic infection with serovar Typhi (Typhi) and causes 10 million illnesses annually. Disease control relies on prevention (water, sanitation, and hygiene interventions or vaccination) and effective antimicrobial treatment. Antimicrobial resistant (AMR) Typhi lineages have emerged and become established in many parts of the world.

Regulation of airway fumarate by host and pathogen promotes Staphylococcus aureus pneumonia.

Staphylococcus aureus is a leading cause of healthcare-associated pneumonia, contributing significantly to morbidity and mortality worldwide. As a ubiquitous colonizer of the upper respiratory tract, S. aureus must undergo substantial metabolic adaptation to achieve persistent infection in the distinctive microenvironment of the lung.

Genetic Correlates of Synergy Mechanisms of Daptomycin Plus Fosfomycin in Daptomycin-Susceptible and -Resistant Methicillin-Resistant (MRSA).

This study elucidates potential genetic determinants and mechanisms involved in the synergistic effects of daptomycin (DAP) + fosfomycin (FOF) combination therapy. Among 33 clinically derived DAP-susceptible (S)/DAP-resistant (R) isogenic strain pairs, mutations in the gene occurred in 30/33 DAP-R strains, including polymorphisms of L826F (33%) or T345A/L/I (15%). Strain variants of DAP-S CB1483 serially passaged in vitro for 10 days in DAP +/- FOF identified a key non-synonymous mutation in (L826F) only in the DAP monotherapy arm.

Global diversity and evolution of Salmonella enterica serovar Panama: a genomic epidemiology study.

Background: Non-typhoidal Salmonella is a globally important bacterial pathogen, typically associated with foodborne gastrointestinal infection. Some non-typhoidal Salmonella serovars can also colonise typically sterile sites in people to cause invasive non-typhoidal Salmonella disease. Salmonella enterica serovar Panama is responsible for a substantial number of cases of human bloodstream infection, but despite its global dissemination, numerous outbreaks, and a reported association with invasive non-typhoidal Salmonella disease, S enterica serovar Panama (S Panama) is understudied.

Global analysis of the genomic diversity, antimicrobial resistance and potential vaccine candidates carried by the major global bovine pathogen .

is a leading cause of bovine mastitis, resulting in large economic losses and welfare issues for affected cows. However, relatively little is known about the global distribution and emergence of bovine mastitis-causing lineages and dissemination of antimicrobial resistance or virulence genes in the species. Here, we present a global framework for based on whole-genome sequencing data from isolates across four continents (=1,070).

Selecting candidate Neisseria gonorrhoeae strains for oropharyngeal gonorrhoea human challenge: a genomics-based analysis of clinical isolates.

Background: Neisseria gonorrhoeae is a human pathogen of major public health importance due to its increasing global prevalence and antimicrobial resistance (AMR). Evidence suggests that oropharyngeal infection plays a key role in N gonorrhoeae transmission and AMR; however, our understanding of oropharyngeal gonorrhoea pathogenesis is poor. A controlled human infection model (CHIM) for oropharyngeal gonorrhoea will improve understanding of infection and accelerate urgently needed novel gonorrhoea prevention and therapeutic strategies.

Human leptospirosis in the central division of Fiji: a retrospective epidemiological study.

Background: Leptospirosis is a major cause of human disease in Fiji. However, the epidemiology is poorly defined. This study was conducted to determine the epidemiology of human leptospirosis in the Central Division and to characterize the largest urban outbreak in Fiji.

The impact of integrated genomic surveillance on non-typhoidal infection in Australia: an ecological study.

Background: Whole Genome Sequencing (WGS) is a powerful technology for monitoring and detecting outbreaks of infectious pathogens, including non-typhoidal (NTS). Despite its higher cost than traditional typing methods, WGS offers numerous advantages, including higher resolution and potentially quicker turnaround time. However, evidence regarding its effectiveness in NTS surveillance has predominantly stemmed from micro-simulations or small-scale data.

Distinct adaptation and epidemiological success of different genotypes within serovar Dublin.

Dublin is a host-adapted, invasive nontyphoidal (iNTS) serovar that causes bloodstream infections in humans and demonstrates increasing prevalence of antimicrobial resistance (AMR). Using a global dataset of 1303 genomes, coupled with in vitro assays, we examined the evolutionary, resistance, and virulence characteristics of . Dublin.

Genomics to understand the global landscape of linezolid resistance in and .

Linezolid is an oxazolidinone antibiotic and is a last-line agent for treating infections caused by vancomycin-resistant (VRE). Limited work has been done to study the genomic epidemiology and population structure of linezolid-resistant (LRE) spp. in Victoria, Australia, and globally.

Transposon-directed insertion-site sequencing (TraDIS) analysis of using nanopore sequencing and a WebAssembly analysis platform.

Vancomycin-resistant (VREfm) are healthcare-associated opportunistic pathogens of global significance. Genetic tools are needed to understand the molecular basis for VREfm clinically relevant phenotypes, such as persistence within the human gut or antimicrobial resistance. Here, we present a transposon-directed insertion-site sequencing (TraDIS) platform optimized for .

A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections.

Bacterial genomics is increasingly used for infectious diseases surveillance, outbreak detection and prediction of antibiotic resistance. With expanding availability of rapid whole-genome sequencing, bacterial genomics data could become a valuable tool for clinicians managing bacterial infections, driving precision medicine strategies. Here, we present a clinician-driven bacterial genomics framework that applies within-patient evolutionary analysis to identify in real-time microbial genetic changes that have an impact on treatment outcomes of severe Staphylococcus aureus infections, a strategy that is increasingly used in cancer genomics.

Effects of Decentralized Sequencing on National Listeria monocytogenes Genomic Surveillance, Australia, 2016-2023.

We assessed turnaround times in the national Listeria monocytogenes genomic surveillance system in Australia before and after decentralized sequencing. Using 1,204 samples collected during 2016-2023, we observed statistically significant reductions in median time from sample collection to issuance of national genomic surveillance report to 26 days, despite sample numbers doubling in 2022 and 2023. During 2016-2018, all jurisdictions referred samples to the National Listeria Reference Laboratory for sequencing and analysis, but as jurisdictional sequencing capacity increased, 4 jurisdictions transitioned to sequencing their own samples and referring sequence data to the national laboratory.

Molecular Epidemiology of SARS-CoV-2 in Bangladesh.

Mutation is one of the most important drivers of viral evolution and genome variability, allowing viruses to potentially evade host immune responses and develop drug resistance. In the context of COVID-19, local genomic surveillance of circulating virus populations is therefore critical. The goals of this study were to describe the distribution of different SARS-CoV-2 lineages, assess their genomic differences, and infer virus importation events in Bangladesh.

Extended spectrum beta-lactamase producing Escherichia coli and antimicrobial resistance gene sharing at the interface of human, poultry and environment: results of ESBL tricycle surveillance in Kathmandu, Nepal.

Background: The spread of antimicrobial resistant pathogens, including extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae is a global health threat and can be addressed only through a One Health approach. We aimed to characterize ESBL producing Escherichia coli isolates from World Health Organization Tricycle surveillance using data from whole genome sequencing (WGS) to decipher the potential dynamics of their circulation at the human, poultry and environment interface.

Methods: WGS was performed on 100 non-duplicate representative ESBL E.

Genomics for antimicrobial resistance-progress and future directions.

Antimicrobial resistance (AMR) is a critical global public health threat, with bacterial pathogens of primary concern. Pathogen genomics has revolutionized the study of bacterial pathogens and provided deep insights into the mechanisms and dissemination of AMR, with the precision of whole-genome sequencing informing better control strategies. However, generating actionable data from genomic surveillance and diagnostic efforts requires integration at the public health and clinical interface that goes beyond academic efforts to identify resistance mechanisms, undertake analyses of outbreaks, and share data after research publications.

Salmonella pathogenicity islands in the genomic era.

Serovars of Salmonella are significant bacterial pathogens and are leading contributors to the global burden of diarrhoeal disease. Salmonella pathogenicity islands (SPIs) are essential for the survival and success of this genus, enabling colonisation, invasion, and survival in hostile environments. While genomics has transformed efforts to understand the evolution, dissemination, and antimicrobial resistance of members, its use to explore virulence determinants that contribute to the pathogenicity of specific organisms and severity of infection remains varied.

Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study.

Background: Defining the temporal dynamics of invasive Streptococcus pyogenes (group A Streptococcus) and differences between hyperendemic and lower-incidence regions provides crucial insights into pathogen evolution and, in turn, informs preventive measures. We aimed to examine the clinical and temporal lineage dynamics of S pyogenes across different disease settings in Australia to improve understanding of drivers of pathogen diversity.

Methods: In this retrospective, multicentre, clinical and genomic epidemiology study, we identified cases of invasive S pyogenes infection from normally sterile sites between Jan 1, 2011, and Feb 28, 2023.

Rapid, reference-free identification of bacterial pathogen transmission using optimized split -mer analysis.

Infections caused by multidrug-resistant organisms (MDROs) are difficult to treat and often life threatening and place a burden on the healthcare system. Minimizing the transmission of MDROs in hospitals is a global priority with genomics proving to be a powerful tool for identifying the transmission of MDROs. To optimize the utility of genomics for prospective infection control surveillance, results must be available in real time, reproducible and simple to communicate to clinicians.

Establishing carbapenem resistant organism surveillance, prevention, and control in a middle-income country: implementation of a hospital-based program in Fiji.

Antimicrobial resistance (AMR) is a major public health threat with the highest burden being estimated to be in low- and middle-income countries. Fiji is an upper-middle-income country in Oceania. Recent studies from Fiji highlighted the increasing burden of carbapenem resistant organisms (CRO) such as Acinetobacter baumannii, Pseudomonas aeruginosa and Escherichia coli.

Genomic interrogation of invasive group A (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective study.

Background: Invasive group A (iGAS) cases have increased globally in 2022-2023, raising concerns within the medical and public health communities, including in Australia, while this impact is polyclonal in nature the worldwide spread and dominance of M1 has been particularly concerning.

Methods: To investigate these changes and prepare to implement routine genomic surveillance of iGAS for public health purposes, we performed whole genome sequencing (WGS) on iGAS isolates from Victoria, Australia between 2017 and 2022. Genomic analyses were conducted to determine the epidemiology, genetic diversity, and population dynamics of iGAS.

High-throughput method characterizes hundreds of previously unknown antibiotic resistance mutations.

A fundamental obstacle to tackling the antimicrobial resistance crisis is identifying mutations that lead to resistance in a given genomic background and environment. We present a high-throughput technique - Quantitative Mutational Scan sequencing (QMS-seq) - that enables quantitative comparison of which genes are under antibiotic selection and captures how genetic background influences resistance evolution. We compare four E.