Biology subjects

O'Connor, A.

Publications and source records attributed to O'Connor, A..

16 recordsLinked to original sources

bioRxiv2026

Over-the-counter fiber supplementation associates with metabolic and microbial shifts in rectal mucosa

Fiber supplements are the first line of treatment for all patients with benign anorectal disease. In addition, fiber has been found to support gut microbiota and reduce inflammation; however, their integrated effect on the colonic mucosal environment is incompletely defined. We evaluated how mixed-fiber formulations may collectively shape the rectal mucosal environment through coordinated effects on microbiota composition, short-chain fatty acid (SCFA) handling, and host transcription. We evaluated multi-compartment responses to a 28-day mixed-fiber intervention in 37 participants with benign anorectal disease (~15 g/day; 7.5g psyllium husk, 8g wheat dextrin) and assessed the microbiota (16S rRNA), the metabolome (GC-MS and LC-MS), and transcriptome (subset n=10) before (PRE) and after (POST) supplementation. Changes in KEGG pathways were tested with gene set enrichment analysis (GSEA). Associations were tested by Spearman correlation, and microbiota-based prediction of SCFA responses by random-forest regression. Microbiota diversity was stable after the fiber intervention, however, 10 mucosal ASVs were differentially abundant including Parabacteroides and Lachnospiraceae NK4A136 group while SCFAs, propionate and isobutyrate, both decreased in rectal tissue and butyrate decreased in serum. To understand these shifts in the metabolome, we proceeded with the transcriptome where we identified 130 differentially expressed genes and enrichment of metabolic and SCFA-related pathways. Random forest regression captured a modest signal for serum butyrate. Taken together, short-term mixed-fiber supplementation produced selective rectal mucosal taxonomic shifts and enriched mucosal metabolic and SCFA-metabolism program despite reduced SCFA pools, suggesting that even brief over-the-counter fiber supplementation may reshape the mucosal metabolic environment.

microbiology↗

bioRxiv2026

Incubation of craving for alcohol-associated cues is reduced by running-wheel exercise.

Craving - the powerful urge to seek and consume alcohol in response to alcohol-associated cues does not diminish after drinking cessation but rather is magnified throughout abstinence. This phenomenon, termed "incubation of craving", contributes to the relapsing nature of alcohol use disorder. Despite its occurrence in human populations and being well-studied in rodent models of psychostimulant drug relapse, the underlying neural mechanisms and potential treatments remain largely unexplored for alcohol-related incubation of craving. Our research seeks to meet this gap, and this particular study investigated the neural correlates of the incubation of craving for alcohol-associated cues and assessed whether exercise could prevent increased relapse propensity in rats. Male Long Evans rats were trained to lever press for an alcohol reward delivered with simultaneous presentation of a discrete cue. This response was then extinguished and reinstated by presenting the discrete cue alone when rats pressed the lever. Cue-induced reinstatement occurred either on day 1 following extinction (No Abstinence) or on day 29 (Abstinence). A third group was tested on day 29 and had 4-hour daily voluntary running wheel access throughout this abstinence period (Exercise). All rats were perfused 90 minutes following test, and relative activation across the brain was estimated by quantifying c-Fos protein immunoreactivity. The brain-wide coordination of neural activity was also mapped. We found a robust incubation of craving effect for alcohol-associated cues, which was mitigated by exercise. Immunohistochemistry revealed that the Abstinence group demonstrated higher c-Fos immunoreactivity compared to the No Abstinence group in multiple reinstatement-related brain regions. This effect was reversed in the Exercise group. Brain-wide neural mapping demonstrated that the Abstinence group had decreased modularity (groups of coordinating brain regions) compared to the no-abstinence group. Although network connectivity profile in the exercise group was different from no abstinence, we found that overall neural activation returned to a similar modularity profile of clustered regions as this condition, indicating that exercise does not attenuate the incubation of craving effect by reversing all the neural effects of abstinence. Rather, exercise may be acting upon select brain regions or pathways to exert relapse protective effects by restoring widespread interconnectivity. This is the first study to investigate neural activation in incubated alcohol-seeking, and provides supporting evidence for promoting voluntary exercise as an adjunctive treatment for relapse prevention in alcohol-use disorder.

neuroscience↗

bioRxiv2025

Aging Alters Hair Cell Physiological Properties in Mice with Late-Onset Age-Related Hearing Loss.

Cochlear hair cells convert sound stimuli into electrical signals. Age-related hearing loss (ARHL) is characterized by the progressive reduction of these hair cells and their synapses, but the underlying mechanisms remain poorly understood. In this study, we tested the hypothesis that hair cell function declines with age in CBA/CaJ mice, a strain known for its very slow ARHL progression. We found that hair cell size began to decrease from 10 months of age, before hearing loss was detectable. This structural change was associated with a significant decrease in the total current response and a distinct reduction in the expression of large conductance calcium-activated potassium (BK) channel currents (IK,f). However, the magnitude of the mechanoelectrical transducer (MET) currents at the hair cell stereociliary bundles remained unaffected. This observation challenges the common conception that stereocilia are the most fragile component of sensory cells in aging. Our results provide clear evidence of an early decline in hair cell function with age, which precedes measurable hearing loss, suggesting that these cellular deficits define a distinct pathological route to ARHL in the CBA/CaJ mouse model.

physiology↗

bioRxiv2025

Plasmidome, resistome, and virulence-associated genes characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting.

Evidence shows persistence of non-spore-forming Acinetobacter johnsonii in high-stakes controlled and nutrient-limited environments. This study aims to explore the mechanisms underpinning such adaptability through a comprehensive genomic analysis of 22 isolates of A. johnsonii from NASAs Payload Hazardous Servicing Facility (PHSF) and one carbapenem-resistant strain (E154408A) from patient colonization in Ireland. Core-genome phylogeny revealed clustering of PHSF-originating isolates in a monophyletic clade divergent from the main species lineage. Species-wide virulence-associated genes and metabolic profiling indicated the unique presence in PHSF-originating isolates of two complete efflux pumps and of a conserved allantoin racemase, suggesting adaptability for multiple environmental stresses. Observed ubiquity of blaOXA in investigated genomes (n=112) and phenotypically-validated multidrug-resistant profile of E154408A strain highlight A. johnsoniis potential as antimicrobial resistance (AMR) reservoir. Plasmidome analysis suggested gain/loss events across the monophyletic population and potential AMR acquisition pathways. Genome-to-metagenome mapping identified genomic signatures of A. johnsonii in PHSF >10 years post initial isolation. ImportanceAcinetobacter johnsonii is increasingly recognized as an emerging human pathogen, with growing evidence of its ability to persist in controlled, high-stakes environments, posing risks as both persisting environmental contaminant and antimicrobial resistance (AMR) reservoir. Yet, gaps remain in our understanding of its AMR profile and the mechanisms that enable its enhanced environmental adaptability. This knowledge is necessary in contexts where biological cleanliness is a priority such as clinical settings and spacecraft assembly facilities cleanrooms, where contamination of hardware with terrestrial microorganisms is concerning. In this study, we aim to address some of key knowledge gaps by providing genomic insights into a rare multi-drug resistant clinical isolate and 22 NASA cleanroom isolates that persisted for over a decade in extremely clean conditions. Our findings will help evaluate the contamination risk of A. johnsonii in high-stakes environments and ultimately strengthen our ability to manage this microbial contaminant across terrestrial and extraterrestrial settings. HighlightsO_LICleanrooms-derived A. johnsonii genomes show favorable traits for increased adaptability C_LIO_LIGenomic signatures of A. johnsonii persisted in the cleanrooms for >10 years C_LIO_LIblaOXA is ubiquitously found in the genome of all A. johnsonii C_LIO_LIE154408A is the first patient colonization by carbapenem-resistant A. johnsonii in Europe C_LI

genomics↗

bioRxiv2024

Heterozygous Eif4nif1 Stop Gain Mice Replicate the Primary Ovarian Insufficiency Phenotype in Women

We created the c.1286C>G stop-gain mutation found in a family with primary ovarian insufficiency (POI) at age 30 years. The Eif4enif1 C57/Bl6 transgenic mouse model contained a floxed exon 10-19 cassette with a conditional knock-in cassette containing the c.1286C>G stop-gain mutation in exon 10. The hybrid offspring of CMV-Cre mice with Eif4enif1WT/flx mice were designated Eif4enif1WT/{Delta} for simplicity. A subset of female heterozygotes (Eif4enif1WT/{Delta}) had no litters. In those with litters, the final litter was earlier (5.4{+/-}2.6 vs. 10.5{+/-}0.7 months; p=0.02). Heterozygous breeding pair (Eif4enif1WT/{Delta} x Eif4enif1WT/{Delta}) litter size was 60% of WT litter size (3.9{+/-}2.0 vs. 6.5{+/-}3.0 pups/litter; p<0.001). The genotypes were 35% Eif4enif1WT/flx and 65% Eif4enif1WT/{Delta}, with no homozygotes. Homozygote embryos did not develop beyond the 4-8 cell stage. The number of follicles in ovaries from Eif4enif1WT/{Delta} mice was lower starting at the primordial (499{+/-}290 vs. 1445{+/-}381) and primary follicle stage (1069{+/-}346 vs. 1450{+/-}193) on day 10 (p<0.05). The preantral follicle number was lower starting on day 21 (213{+/-}86 vs. 522{+/-}227; p<0.01). Examination of ribosome protected mRNAs (RPR) demonstrated altered mRNA expression. The Eif4enif1 stop-gain mice replicate the POI phenotype in women. The unique mouse model provides a platform to study regulation of protein translation across oocyte and embryo development in mammals.

developmental biology↗

bioRxiv2023

Fertility is compromised after oocyte-specific deletion of Katanin A-subunit, Katna1, but not Katnal1

Katanins are microtubule severing enzymes that play roles in shaping diverse microtubule-based structures during all cell cycle stages. To address the role of katanin A-subunits in mammalian oocytes, we have used the Zp3-CreLox approach to specifically delete katanin A1 (Katna1) and katanin A-like 1 (Katnal1) from the start of oocyte growth in mice. Here, we show that Katnal1 is not required for normal female fertility, but that deletion of Katna1 causes a 50% decrease in fertility. Further investigation in Katna1-/- oocytes revealed no effect on MI spindle morphology but a significant effect on the morphology of MII spindles. This was accompanied by a decreased rate of fertilisation. Resultant Katna1+/- heterozygous embryos that reached the 2-cell stage developed at normal rates to the blastocyst stage. Diploid homozygous parthenotes derived from Katna1-/- oocytes revealed a reduced rate of blastocyst formation, decreased cell number and increased nuclear size. The ability of the paternal allele to rescue preimplantation development suggests the origin of the decrease in the fertility of conditional Katna1-/- mice lies in abnormalities arising in the egg to embryo transition prior to embryonic genome activation.

developmental biology↗

bioRxiv2022

Replication stress tolerance and management differs between naive and primed pluripotent cells

Replication stress is an endemic threat to genome stability. For reasons unknown, replication stress response factors become essential during peri-implantation development. This coincides with a stem cell potency switch from the naive to the primed state. Using genetically matched, chimera-derived mouse naive embryonic (mESC) and primed epiblast stem cells (mEpiSC) we found that replication stress management differs between potency states. Primed mEpiSCs rely on Atr activity to prevent replication catastrophe, minimize genomic damage, avoid apoptosis, and re-enter the cell cycle. Conversely, under replications stress, mESCs readily activate Atm regardless of Atr activity, undergo replication catastrophe, and induce apoptosis. Primed pluripotent cells therefore engage Atr to counteract replication difficulties and maintain viability, whereas cells in the naive state are more readily cleared under the same conditions. We anticipate these divergent strategies enable pluripotent cells of different potency states to meet associated proliferative or developmental demands during early development.

developmental biology↗

bioRxiv2022

Heavy metal pollution impacts soil bacterial community structure and antimicrobial resistance at the Birmingham 35th Avenue Superfund Site

Heavy metals (HMs) are known to modify bacterial communities both in the laboratory and in situ. As a consequence, soils in HM contaminated sites like the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that metal tolerant bacteria are often also resistant to antimicrobial agents (AMR), and therefore HM contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility soil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund site) and in six public areas in a neighboring reference zip code (35214). Sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated concentrations of HMs As, Mn, Pb, and Zn reduced microbial diversity and altered community structure within each zip code. While there was no difference between zip codes in the proportion of total culturable microbes that survived antimicrobial or metal exposure, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUST2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human bacterial disease.

microbiology↗

bioRxiv2021

Developmental regulation and functional prediction of microRNAs in an expanded Fasciola hepatica miRNome

1The liver fluke, Fasciola hepatica, is a global burden on the wellbeing and productivity of farmed ruminants, and a zoonotic threat to human health. Despite the clear need for accelerated discovery of new drug and vaccine treatments for this pathogen, we still have a relatively limited understanding of liver fluke biology and host interactions. Noncoding RNAs, including micro (mi)RNAs, are key to transcriptional regulation in all eukaryotes, such that an understanding of miRNA biology can shed light on organismal function at a systems level. Four previous publications have reported up to 89 mature miRNA sequences from F. hepatica, but our data show that this does not represent a full account of this species miRNome. We have expanded on previous studies by sequencing, for the first time, miRNAs from multiple life stages (adult, newly excysted juvenile (NEJ), metacercariae and adult-derived extracellular vesicles (EVs)). These experiments detected an additional 61 high-confidence miRNAs, most of which have not been described in any other species, expanding the F. hepatica miRNome to 150 mature sequences. We used quantitative (q)PCR assays to provide the first developmental profile of miRNA expression across metacercariae, NEJ, adult and adult-derived Evs. The majority of miRNAs were expressed most highly in metacercariae, with at least six distinct expression clusters apparent across life stages. Intracellular miRNAs were functionally analysed to identify target mRNAs with inversely correlated expression in F. hepatica tissue transcriptomes, highlighting regulatory interactions with key virulence transcripts including cathepsin proteases, and neuromuscular genes that control parasite growth, development and motility. We also linked 28 adult-derived EV miRNAs with downregulation of 397 host genes in F. hepatica-infected transcriptomes from ruminant lymph node, peripheral blood mononuclear cell (PBMC) and liver tissue transcriptomes. These included genes involved in signal transduction, immune and metabolic pathways, adding to the evidence for miRNA-based immunosuppression during fasciolosis. These data expand our understanding of the F. hepatica miRNome, provide the first data on developmental miRNA regulation in this species, and provide a set of testable hypotheses for functional genomics interrogations of liver fluke miRNA biology. CONTRIBUTION TO THE FIELDPrevious studies identified 89 micro (mi)RNAs (non-coding RNAs responsible for regulating gene expression) in the trematode parasite, Fasciola hepatica, and attached functional annotations to the miRNAs that are secreted by liver fluke in vitro. This study expands the known miRNA complement of F. hepatica by 40%, adding an additional 61 miRNAs, many of which appear Fasciola-specific. We used this expanded dataset to perform the first analysis of developmental miRNA expression across intra-mammalian parasites, showing clear developmentally regulated expression profiles across infectious metacercariae, juvenile and adult parasites, and extracellular vesicles secreted by adult parasites. We performed rigorous functional annotation of cellular miRNAs, correlating their expression with mRNA transcriptomes to identify potential roles for specific miRNAs in regulating expression of important proteases and nerve/muscle transcripts, all of which are important for parasite virulence. We also functionally analysed miRNAs secreted by adult parasites in terms of interactions with host transcripts; for the first time this analysis was supported by host transcriptome data, linking secreted miRNAs with mRNAs that are downregulated by fluke infection in sheep and cattle. This work contributes new data, insights and analyses to the field, providing a rich source of hypotheses for future experimental validation.

molecular biology↗

bioRxiv2021

Plasma amyloid beta ratios in autosomal dominant Alzheimers disease: the influence of genotype

In-vitro studies of autosomal dominant Alzheimers disease (ADAD) implicate longer A{beta} peptides in pathogenesis, however less is known about the behaviour of ADAD mutations in-vivo. In this cross-sectional cohort study, we used liquid chromatography-tandem mass spectrometry to analyse 66 plasma samples from ADAD family members who were at-risk of inheriting a mutation or were already symptomatic. We tested for differences in plasma A{beta}42:38, 38:40 and 42:40 ratios between Presenilin1 (PSEN1) and Amyloid Precursor Protein (APP) carriers. We examined the relationship between plasma and in-vitro models of A{beta} processing and, among PSEN1 carriers, tested for associations with parental age at onset (AAO). 39 participants were mutation carriers (28 PSEN1 and 11 APP). Age- and sex-adjusted models showed marked differences in plasma A{beta} between APP and PSEN1: higher A{beta}42:38 in PSEN1 versus APP (p<0.001) and non-carriers (p<0.001); higher A{beta}38:40 in APP versus PSEN1 (p<0.001) and non-carriers (p<0.001), while A{beta}42:40 was higher in APP and PSEN1 compared to non-carriers (both p<0.001). A{beta} profiles were reasonably consistent in plasma and cell lines. Within PSEN1, sex-adjusted models demonstrated negative associations between (i)A{beta}42:40 (ii)A{beta}42:38 and parental AAO. In-vivo differences in A{beta} processing between APP and PSEN1 provide insights into ADAD pathophysiology which can inform therapy development.

neuroscience↗

bioRxiv2020

Distinct VIP interneurons in the cingulate cortex encode anxiogenic and social stimuli

A hallmark of higher-order cortical regions is their functional heterogeneity, but it is not well understood how these areas encode such diverse information. The anterior cingulate cortex (ACC), for example, is important in both emotional regulation and social cognition. Previous work shows activation of the ACC to anxiety-related and social stimuli, but it is unknown how subpopulations or microcircuits within the ACC simultaneously encode these distinct stimuli. One type of inhibitory interneuron, which is positive for vasoactive intestinal peptide (VIP), is known to alter the activity of many cells in local cortical microcircuits, but it is unknown whether the activity of VIP cells in the ACC (VIPACC) encodes anxiety-related or social information. Using in vivo calcium imaging and miniscopes in freely behaving mice to monitor VIPACC activity, we identified distinct, non-overlapping subpopulations of VIPACC that preferentially activated to either anxiogenic, anxiolytic, social, or non-social stimuli. We determined that stimulus-selective cells encode the animals behavioral states and VIP interneuron clusters may co-activate, improving this encoding. Finally, we used trans-synaptic tracing to show that VIPACC receive widespread inputs from regions implicated in emotional regulation and social cognition. These findings demonstrate not only that the ACC is not homogeneous in its function, but also that there is marked functional heterogeneity even within disinhibitory interneuron populations. This work contributes to our understanding of how the cortex encodes information across diverse contexts and provides insight into the complexity of neural processes involved in anxiety and social behavior.

neuroscience↗

bioRxiv2020

A Universal Stress Protein upregulated by hypoxia may contribute to chronic lung colonisation and intramacrophage survival in cystic fibrosis.

Universal stress proteins (USPs) are ubiquitously expressed in bacteria, plants and eukaryotes and play a lead role in adaptation to environmental conditions. In Gram negative bacteria they enable adaption of bacterial pathogens to the conditions encountered in the human niche, including hypoxia, oxidative stress, osmotic stress, nutrient deficiency or acid stress, thereby facilitating colonisation. We previously reported that all six USP proteins encoded within a low-oxygen responsive locus in Burkholderia cenocepacia showed increased abundance during chronic colonisation of the CF lung. However, the role of USPs in chronic infection is not known. Using mutants derived from B. cenocepacia strain, K56-2, we show that USP76 is required for growth and survival in many conditions associated with the CF lung including, hypoxia, acidic conditions, oxidative stress. Moreover, it is involved in attachment to host epithelial cells, but not virulence. It also has a role in survival in macrophages isolated from people with CF. In contrast, another USP encoded in the same locus, USP92 had no effect on host cell attachment or oxidative stress, but was responsible for a 3-fold increase in virulence. Overall this shows that these USPs, both upregulated during chronic infection, have distinct roles in Burkholderia pathogenesis and may support the survival of B. cenocepacia in the CF lung. Specifically, USP76 is involved in its survival within CF macrophages, a hallmark of Burkholderia infection.

microbiology↗

bioRxiv2020

LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications

We present LipidFinder 2.0, incorporating four new modules that apply artefact filters, remove lipid and contaminant stacks, in-source fragments and salt clusters, and a new isotope deletion method which is significantly more sensitive than available open-access alternatives. We also incorporate a novel false discovery rate (FDR) method, utilizing a target-decoy strategy, which allows users to assess data quality. A renewed lipid profiling method is introduced which searches three different databases from LIPID MAPS and returns bulk lipid structures only, and a lipid category scatter plot with color blind friendly pallet. An API interface with XCMS Online is made available on LipidFinders online version. We show using real data that LipidFinder 2.0 provides a significant improvement over non-lipid metabolite filtering and lipid profiling, compared to available tools. AvailabilityLipidFinder 2.0 is freely available at https://github.com/ODonnell-Lipidomics/LipidFinder and http://lipidmaps.org/resources/tools/lipidfinder. Contactlipidfinder@cardiff.ac.uk Supplementary informationSupplementary data are available at Bioinformatics online.

biochemistry↗

bioRxiv2019

Metabolic dysregulation of the lysophospholipid/autotaxin axis in the chromosome 9p21 gene SNP rs10757274

AimsCommon chromosome 9p21 SNPs increase coronary heart disease (CHD) risk, independent of \"traditional lipid risk factors\". However, lipids comprise large numbers of structurally-related molecules not measured in traditional risk measurements, and many have inflammatory bioactivities. Here we applied lipidomic and genomic approaches to three model systems, to characterize lipid metabolic changes in common Chr9p21 SNPs which confer [~]30% elevated CHD risk associated with altered expression of ANRIL, a long ncRNA.\n\nMethods and ResultsUntargeted and targeted lipidomics was applied to plasma samples from Northwick Park Heart Study II (NPHSII) homozygotes for AA or GG in rs10757274. Elevated risk GG correlated with reduced lysophosphospholipids (lysoPLs), lysophosphatidic acids (lysoPA) and autotaxin (ATX). Five other risk SNPs did not show this phenotype. Correlation and network analysis showed that lysoPL-lysoPA interconversion was uncoupled from ATX in GG, indicating metabolic dysregulation. To identify candidate genes, transcriptomic data from shRNA downregulation of ANRIL in HEK293 cells was mined. Significantly-altered expression of several lysoPL/lysoPA metabolising enzymes was found (MBOAT2, PLA2G4C, LPCAT2, ACSL6, PNPLA2, PLBD1, PLPP1, PLPP2 and PLPPR2). Next, vascular smooth muscle cells differentiated from iPSCs of individuals homozygous for Chr9p21 risk SNPs were examined. Here, the presence of risk alleles was associated with altered expression of several lysoPL/lysoPA enzymes. Importantly, for several, deletion of the risk locus fully or partially reversed their expression to non-risk haplotype levels: ACSL3, DGKA, PLA2G2A, LPCAT2, LPL, PLA2G3, PNPLA3, PLA2G12A LIPC, LCAT, PLA2G6, ACSL1, MBOAT2.\n\nConclusionA Chr9p21 risk SNP associates with complex alterations in immune-bioactive phospholipids and their enzymatic metabolism. Lipid metabolites and genomic pathways associated with CHD pathogenesis in Chr9p21 and ANRIL-associated disease are demonstrated.\n\nOne sentence summaryInflammatory phospholipid metabolism defines a cardiovascular disease SNP

physiology↗

bioRxiv2019

A method of back-calculating the log odds ratio and standard error of the log odds ratio from the reported group-level risk of disease

In clinical trials and observational studies, the effect of an intervention or exposure can be reported as an absolute or relative comparative measure such as risk difference, odds ratio or risk ratio, or at the group level with the estimated risk of disease in each group. For meta-analysis of results with covariate adjustment, the log of the odds ratio (log odds ratio), with its standard error, is a commonly used measure of effect. However, extracting the adjusted log odds ratio from the reported estimates of disease risk in each group is not straightforward. Here, we propose a method to transform the adjusted probability of the event in each group to the log of the odds ratio and obtain the appropriate (approximate) standard error, which can then use used in a meta-analysis. We also use example data to compare our method with two other methods and show that our method is superior in calculating the standard error of the log odds ratio.

bioengineering↗

bioRxiv2019

A hierarchical Bayesian latent class mixture model with censorship for detection of linear temporal changes in antibiotic resistance

Identifying and controlling the emergence of antimicrobial resistance (AMR) is a high priority for researchers and public health officials. One critical component of this control effort is timely detection of emerging or increasing resistance using surveillance programs. Currently, detection of temporal changes in AMR relies mainly on analysis of the proportion of resistant isolates based on the dichotomization of minimum inhibitory concentration (MIC) values. In our work, we developed a hierarchical Bayesian latent class mixture model that incorporates a linear trend for the mean log2MIC of the non-resistant population. By introducing latent variables, our model addressed the challenges associated with the AMR MIC values, compensating for the censored nature of the MIC observations as well as the mixed components indicated by the censored MIC distributions. Inclusion of linear regression with time as a covariate in the hierarchical structure allowed modelling of the linear creep of the mean log2MIC in the non-resistant population. The hierarchical Bayesian model was accurate and robust as assessed in simulation studies. The proposed approach was illustrated using Salmonella enterica I,4,[5],12:i:- treated with chloramphenicol and ceftiofur in human and veterinary samples, revealing some significant linearly increasing patterns from the applications. Implementation of our approach to the analysis of an AMR MIC dataset would provide surveillance programs with a more complete picture of the changes in AMR over years by exploring the patterns of the mean resistance level in the non-resistant population. Our model could therefore serve as a timely indicator of a need for antibiotic intervention before an outbreak of resistance, highlighting the relevance of this work for public health. Currently, however, due to extreme right censoring on the MIC data, this approach has limited utility for tracking changes in the resistant population.

microbiology↗