Biology subjects

Pitt, M.

Publications and source records attributed to Pitt, M..

9 recordsLinked to original sources

bioRxiv2026

The Sustained Alteration Of Brain Waves In Cynomolgus Macaques Following Aerosol Infection With Venezuelan Equine Encephalitis Virus Subtype IAB

Venezuelan equine encephalitis virus subtype IAB (VEEV-IAB) is a mosquito-borne virus that can cause fatal encephalitis in humans and equids. During the 20th century, sporadic but widespread outbreaks occurred throughout the Americas. In addition, VEEV-IAB was investigated as a potential biological warfare agent during the Cold War. Currently, no countermeasures are available to treat or prevent human infection. A critical impediment to understanding VEEV-IAB pathogenesis and developing countermeasures is the lack of a detailed disease course in a susceptible animal model. This study evaluated VEEV-IAB disease progression in cynomolgus macaques using advanced telemetry technology to continuously monitor physiological parameters, including temperature, respiration, activity, heart rate, blood pressure, electrocardiography (ECG), and electroencephalography (EEG), following an aerosol challenge of 6.0 log10 PFU. Following infection, all parameters were altered relative to baseline; temperature (+3.1 to +4.0{degrees}C), respiration rate (+45 to +91%), activity [daytime (-29 to -55%) and nighttime (+14 to +34%)], heart rate (-27 to +191%), systolic (+11 to +39%) and diastolic blood pressure (+7 to +39%). Cardiac abnormalities included increases in QTc (Bazett), PR interval, and QRS duration. All EEG frequency bands were rapidly altered (-250% to +4,800%) and did not return to baseline during the 28-day post-infection period. Despite these profound physiological changes, brain tissues collected at 28 dpi showed minimal evidence of viral persistence or pathology. These data demonstrate that VEEV-IAB aerosol infection rapidly and markedly alters physiological parameters regulated by the autonomic nervous system, as well as provides new insights into VEEV-IAB pathogenesis and countermeasure development.

microbiology↗

bioRxiv2026

Sublethal exposure to the insecticide chlorantraniliprole does not alter antipredator behaviour in wild field crickets

Pesticide exposure has been proposed as a major driver of global insect declines. Sublethal effects occur when non-fatal pesticide exposure disrupts behaviour or physiology in ways that may reduce survival or reproductive success. However, most evidence for sublethal effects comes from laboratory studies under controlled conditions. We tested whether exposure to a sublethal dose of chlorantraniliprole, a widely used diamide insecticide known for its long environmental persistence, affects antipredator escape behaviours in wild field crickets (Gryllus campestris). Adult crickets were treated with either pesticide or a sham control. They then underwent behavioural tests in the wild. Following a simulated predator attack, we measured two key behaviours: escape speed and subsequent latency to re-emerge from their burrow. We found no consistent effects of pesticide exposure on either behaviour. Re-emergence latency increased over successive days across both groups, while escape speed did not change. Re-emergence latency showed greater individual variability than escape speed. This likely reflects its role as a risk-assessment behaviour, which is more context-dependent than escape speed. Our findings challenge the assumption, largely derived from laboratory assays, that sublethal pesticide exposure universally impairs insect behaviour. Overall, our results underscore the need to integrate environmental context when evaluating pesticide impacts on insect behaviour.

animal behavior and cognition↗

bioRxiv2025

Co-isolation of genetically distinct Burkholderia pseudomallei strains from a single patient in North Queensland

While investigating colony morphology variation (CMV) within clinical isolates of Burkholderia pseudomallei (Bp) isolated from a single infection, we identified two distinct strains (based on their multi-locus sequence type) from Bp TSV292. Simultaneous co-infection is rare, previously reported in only 2 of 133 cases. Here, we present the first comprehensive multi-omics characterization of co-infecting Bp strains isolated from a single infection at a hospital in Townsville, Australia in 2018. This finding impacts the design of future diagnosis and treatment of Bp. ImportanceMelioidosis, a severe disease caused by the bacterium Burkholderia pseudomallei, is rarely caused by more than one strain at the same time. In this study, we examined two bacterial strains isolated at once from a patient treated for melioidosis at a hospital in northern Queensland (Australia). By comparing their genomes, proteins, and physical traits, we found important strain differences that may affect how they adapt and survive during infection. Considering strain diversity when studying how this pathogen causes disease is essential, as it directly impacts future diagnosis and treatment.

microbiology↗

bioRxiv2025

An Asgard archaeon from a modern analog of ancient microbial mats

It has been proposed that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea. Here we describe a highly enriched culture of a novel Asgard archaeon, Nerearchaeum marumarumayae, with a bacterium Stromatodesulfovibrio nilemahensis from a stromatolite-associated microbial mat. The N. marumarumayae genome indicates it produces H2, acetate, formate, and sulfite, while S. nilemahensis synthesizes amino acids and vitamins, which can be exchanged in a syntrophic partnership. Electron cryotomography revealed N. marumarumayae cells produce chains of budded envelope vesicles attached to the coccoid cell body by extracellular fibers, and intracellular tube- and cage-like structures. Furthermore, the two species were observed interacting via intercellular nanotubes assembled by the bacterium. These characteristics and interactions may reflect an early step in the symbiotic evolution of eukaryotic cells.

microbiology↗

bioRxiv2022

Genomic neighbor typing for bacterial outbreaksurveillance

Genomic neighbor typing enables heuristic inference of bacterial lineages and phenotypes from nanopore sequencing data. However, small reference databases may not be sufficiently representative of the diversity of lineages and genotypes present in a collection of isolates. In this study, we explore the use of genomic neighbor typing for surveillance of community-associated Staphylococcus aureus outbreaks in Papua New Guinea (PNG) and Far North Queensland, Australia (FNQ). We developed Sketchy, an implementation of genomic neighbor typing that queries exhaustive whole genome reference databases using MinHash. Evaluations were conducted using nanopore read simulations and six species-wide reference sketches (4832 - 47616 genomes), as well as two S. aureus outbreak data sets sequenced at low depth using a sequential multiplex library protocol on the MinION (n = 160, with matching Illumina data). Heuristic inference of lineages and antimicrobial resistance profiles allowed us to conduct multiplex genotyping in situ at the Papua New Guinea Institute of Medical Research in Goroka, on low-throughput Flongle adapters and using multiple successive libraries on the same MinION flow cell (n = 24 - 48). Comparison to phylogenetically informed genomic neighbor typing with RASE on the dominant outbreak sequence type suggests slightly better performance at predicting lineage-scale genotypes using large sketch sizes, but inferior performance in resolving clade-specific genotypes (methicillin resistance). Sketchy can be used for large-scale bacterial outbreak surveillance and in challenging sequencing scenarios, but improvements to clade-specific genotype inference are needed for diagnostic applications. Sketchy is available open-source at: https://github.com/esteinig/sketchy

bioinformatics↗

bioRxiv2020

Direct RNA sequencing and early evolution of SARS-CoV-2

Fundamental aspects of SARS-CoV-2 biology remain to be described, having the potential to provide insight to the response effort for this high-priority pathogen. Here we describe the first native RNA sequence of SARS-CoV-2, detailing the coronaviral transcriptome and epitranscriptome, and share these data publicly. A data-driven inference of viral genetic features and evolutionary rate is also made. The rapid sharing of sequence information throughout the SARS-CoV-2 pandemic represents an inflection point for public health and genomic epidemiology, providing early insights into the biology and evolution of this emerging pathogen.

microbiology↗

bioRxiv2018

Evaluating the Genome and Resistome of Extensively Drug-Resistant Klebsiella pneumoniae using Native DNA and RNA Nanopore Sequencing

Klebsiella pneumoniae frequently harbour multidrug resistance and current methodologies are struggling to rapidly discern feasible antibiotics to treat these infections. While rapid DNA sequencing has been proposed for prediction of resistance profile; the role of rapid RNA sequencing has yet to be fully explored. The MinION sequencer can sequence native DNA and RNA in real-time, providing an opportunity to contrast the utility of DNA and RNA for prediction of drug susceptibility. This study interrogated the genome and transcriptome of four extensively drug-resistant (XDR) K. pneumoniae clinical isolates. The majority of acquired resistance ([≥]75%) resided on plasmids including several megaplasmids ([≥]100 kbp). DNA sequencing identified most resistance genes ([≥]70%) within 2 hours of sequencing. Direct RNA sequencing (with a [~]6x slower pore translocation) was able to identify [≥]35% of resistance genes, including aminoglycoside, {beta}-lactam, trimethoprim and sulphonamide and also quinolone, rifampicin, fosfomycin and phenicol in some isolates, within 10 hours of sequencing. Polymyxin-resistant isolates showed a heightened transcription of phoPQ ([≥]2-fold) and the pmrHFIJKLM operon ([≥]8-fold). Expression levels estimated from direct RNA sequencing displayed strong correlation (Pearson: 0.86) compared to qRT-PCR across 11 resistance genes. Overall, MinION sequencing rapidly detected the XDR K. pneumoniae resistome and direct RNA sequencing revealed differential expression of these genes.

genomics↗

bioRxiv2018

Octapeptin C4 Induces Less Resistance and Novel Mutations in an Epidemic Carbapenemase-producing Klebsiella pneumoniae ST258 Clinical Isolate Compared to Polymyxins

Polymyxin B and E (colistin) have been pivotal in the treatment of extensively drug-resistant (XDR) Gram-negative bacterial infections, with increasing use over the past decade. Unfortunately, resistance to these antibiotics is rapidly emerging. The structurally-related octapeptin C4 (OctC4) has shown significant potency against XDR bacteria, including against polymyxin-resistant (Pmx-R) strains, but its mode of action remains undefined. We sought to compare and contrast the acquisition of XDR Klebsiella pneumoniae (ST258) resistance in vitro with all three lipopeptides to help elucidate the mode of action of the drugs and potential mechanisms of resistance evolution. Strikingly, 20 days of exposure to the polymyxins resulted in a dramatic (1000-fold) increase in the minimum inhibitory concentration (MIC) for the polymyxins, reflecting the evolution of resistance seen in clinical isolates, whereas for OctC4 only a 4-fold increase was witnessed. There was no cross-resistance observed between the polymyxin - and octapeptin-induced resistant strains. Sequencing revealed previously known gene alterations for polymyxin resistance, including crrB, mgrB, pmrB, phoPQ and yciM, and novel mutations in qseC. In contrast, mutations in mlaDF and pqiB, 1genes related to phospholipid transport, were found in octapeptin-resistant isolates. Mutation effects were validated via complementation assays. These genetic variations were reflected in phenotypic changes to lipid A. Pmx-R isolates increased 4-amino-4-deoxy-arabinose fortification to phosphate groups of lipid A, whereas OctC4 induced strains harbored a higher abundance of hydroxymyristate and palmitoylate. The results reveal a differing mode of action compared to polymyxins which provides hope for future therapeutics to combat the increasingly threat of XDR bacteria.

microbiology↗

bioRxiv2017

Multifactorial Chromosomal Variants Regulate Polymyxin Resistance In Extensively Drug-Resistant Klebsiella pneumoniae

Extensively drug-resistant Klebsiella pneumoniae (XDR-KP) infections cause high mortality and are disseminating globally. Identifying the genetic basis underpinning resistance allows for rapid diagnosis and treatment. XDR isolates sourced from Greece and Brazil, including nineteen polymyxin-resistant and five polymyxin-susceptible strains, underwent whole genome sequencing. Approximately 90% of polymyxin resistance was enabled by alterations upstream or within mgrB. The most common mutation identified was an insertion at nucleotide position 75 in mgrB via an ISKpn26-like element in the ST258 lineage and ISKpn13 in one ST11 isolate. Three strains acquired an IS1 element upstream of mgrB and another strain had an ISKpn25 insertion at 133 bp. Other isolates had truncations (C28STOP, Q30STOP) or a missense mutation (D31E) affecting mgrB. Complementation assays revealed all mgrB perturbations contributed to resistance. Missense mutations in phoQ (T281M, G385C) were also found to facilitate resistance. Several variants in phoPQ co-segregating with the ISKpn26-like insertion were identified as potential partial suppressor mutations. Three ST258 samples were found to contain subpopulations with different resistance conferring mutations, including the ISKpn26-like insertion colonising with a novel mutation in pmrB (P158R), both confirmed via complementation assays. We also characterized a new multi-drug resistant Klebsiella quasipneumoniae strain ST2401 which was susceptible to polymyxins. These findings highlight the broad spectrum of chromosomal modifications which can facilitate and regulate resistance against polymyxins in K. pneumoniae.\n\nDATA SUMMARYO_LIWhole genome sequencing of the 24 clinical isolates has been deposited under BioProject PRJNA307517 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA307517).\nC_LI\n\nIMPACT STATEMENTKlebsiella pneumoniae contributes to a high abundance of nosocomial infections and the rapid emergence of antimicrobial resistance hinders treatment. Polymyxins are predominantly utilized to treat multidrug-resistant infections, however, resistance to the polymyxins is arising. This increasing prevalence in polymyxin resistance is evident especially in Greece and Brazil. Identifying the genomic variations conferring resistance in clinical isolates from these regions assists with potentially detecting novel alterations and tracing the spread of particular strains. This study commonly found mutations in the gene mgrB, the negative regulator of PhoPQ, known to cause resistance in KP. In the remaining isolates, missense mutations in phoQ were accountable for resistance. Multiple novel mutations were detected to be segregating with mgrB perturbations. This was either due to a mixed heterogeneous sample of two polymyxin-resistant strains, or because of multiple mutations within the same strain. Of interest was the validation of novel mutations inphoPQ segregating with a previously known ISKpn26-like element in disrupted mgrB isolates. Complementation of these phoPQ mutations revealed a reduction in minimum inhibitory concentrations and suggests the first evidence of partial suppressor mutations in KP. This research builds upon our current understanding of heteroresistance, lineage specific mutations and regulatory variations relating to polymyxin resistance.

microbiology↗