Risk factors for fluoroquinolone- and macrolide-resistance among swine using multi-layered chain graphs.

resistant to fluoroquinolones and macrolides are serious public health threats. Studies aiming to identify risk factors for drug-resistant have narrowly focused on antimicrobial use at the farm level. Using chain graphs, we quantified risk factors for fluoroquinolones- and macrolide-resistance in isolated from two distinctive swine production systems, conventional and antibiotic-free (ABF).

Influence of Sequencing Technology on Pangenome-level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens.

Unlabelled: As sequencing costs decrease, short-read and long-read technologies are indispensable tools for uncovering the genetic drivers behind bacterial pathogen resistance. This study explores the differences between the use of short-read (Illumina) and long-read (Oxford Nanopore Technologies, ONT) sequencing in detecting antimicrobial resistance (AMR) genes in ESKAPE pathogens ( and ). Utilizing a dataset of 1,385 whole genome sequences and applying commonly used bioinformatic methods in bacterial genomics, we assessed the differences in genomic completeness, pangenome structure, and AMR gene and point mutation identification.

The contribution of community transmission to the burden of hospital-associated pathogens: A systematic scoping review of epidemiological models.

Healthcare-associated infections (HAI), particularly those involving multi-drug resistant organisms (MDRO), pose a significant public health threat. Understanding the transmission of these pathogens in short-term acute care hospitals (STACH) is crucial for effective control. Mathematical and computational models play a key role in studying transmission but often overlook the influence of long-term care facilities (LTCFs) and the broader community on transmission.

The effect of temporal resolution and contact duration on Real-Time location system-based contact networks for confined feedlot cattle.

Empirical data on livestock contact networks are scarce but digital technologies are increasingly used to characterize animal behavior and describe the dynamics of contact networks. The objective of this study was to use contact network analysis to quantify contacts within three pens of feedlot cattle across three consecutive years at varying temporal resolutions to better inform the construction of network-based disease transmission models for cattle within confined-housing systems. We also aimed to describe the influence of the variation in Real-Time Location System (RTLS) average tag read rates and the effect of increasing minimum contact duration (MCD) on the contact networks of feedlot cattle.

Quantifying trade-offs between therapeutic efficacy and resistance dissemination for enrofloxacin dose regimens in cattle.

The use of antimicrobial drugs in food-producing animals contributes to the selection pressure on pathogenic and commensal bacteria to become resistant. This study aims to evaluate the existence of trade-offs between treatment effectiveness, cost, and the dynamics of resistance in gut commensal bacteria. We developed a within-host ordinary differential equation model to track the dynamics of antimicrobial drug concentrations and bacterial populations in the site of infection (lung) and the gut.

Quantifying trade-offs between therapeutic efficacy and resistance dissemination for enrofloxacin dose regimens in cattle.

The use of antimicrobial drugs in food-producing animals increases the selection pressure on pathogenic and commensal bacteria to become resistant. This study aims to evaluate the existence of trade-offs between treatment effectiveness, cost, and the dissemination of resistance in gut commensal bacteria. We developed a within-host ordinary differential equation model to track the dynamics of antimicrobial drug concentrations and bacterial populations in the site of infection (lung) and the gut.

Modeling county level COVID-19 transmission in the greater St. Louis area: Challenges of uncertainty and identifiability when fitting mechanistic models to time-varying processes.

We use a compartmental model with a time-varying transmission parameter to describe county level COVID-19 transmission in the greater St. Louis area of Missouri and investigate the challenges in fitting such a model to time-varying processes. We fit this model to synthetic and real confirmed case and hospital discharge data from May to December 2020 and calculate uncertainties in the resulting parameter estimates.

Geographic disparities and predictors of COVID-19 vaccination in Missouri: a retrospective ecological study.

Background: Limited information is available on geographic disparities of COVID-19 vaccination in Missouri and yet this information is essential for guiding efforts to improve vaccination coverage. Therefore, the objectives of this study were to (a) investigate geographic disparities in the proportion of the population vaccinated against COVID-19 in Missouri and (b) identify socioeconomic and demographic predictors of the identified disparities.

Methods: The COVID-19 vaccination data for time period January 1 to December 31, 2021 were obtained from the Missouri Department of Health.

Modeling impact of vaccination on COVID-19 dynamics in St. Louis.

The region of St. Louis, Missouri, has displayed a high level of heterogeneity in COVID-19 cases, hospitalization, and vaccination coverage. We investigate how human mobility, vaccination, and time-varying transmission rates influenced SARS-CoV-2 transmission in five counties in the St.

Early evaluation of the Food and Drug Administration (FDA) guidance on antimicrobial use in food animals on antimicrobial resistance trends reported by the National Antimicrobial Resistance Monitoring System (2012-2019).

Antimicrobial resistance (AMR) is one of the biggest challenges to global public health. To address this issue in the US, governmental agencies have implemented system-wide guidance frameworks and recommendations aimed at reducing antimicrobial use. In particular, the Food and Drug Administration (FDA) prohibited the extra-label use of cephalosporins in food animals in 2012 and issued the guidance for industry (GFI) #213 about establishing a framework to phase out the use of all medically relevant drugs for growth promotion in 2012.

Early coronavirus disease 2019 (COVID-19) pandemic effects on individual-level risk for healthcare-associated infections in hospitalized patients.

Objective: We compared the individual-level risk of hospital-onset infections with multidrug-resistant organisms (MDROs) in hospitalized patients prior to and during the coronavirus disease 2019 (COVID-19) pandemic. We also quantified the effects of COVID-19 diagnoses and intrahospital COVID-19 burden on subsequent MDRO infection risk.

Design: Multicenter, retrospective, cohort study.

Impacts of the COVID-19 pandemic on antimicrobial use in companion animals in an academic veterinary hospital in North Carolina.

Antimicrobial resistance (AMR) in bacterial pathogens reduces the effectiveness of these drugs in both human and veterinary medicine, making judicious antimicrobial use (AMU) an important strategy for its control. The COVID-19 pandemic modified operations in both human and veterinary healthcare delivery, potentially impacting AMU. The goal of this research is to quantify how antimicrobial drug prescribing practices for companion animals in an academic veterinary hospital changed during the pandemic.

Extensions of mean-field approximations for environmentally-transmitted pathogen networks.

Many pathogens spread via environmental transmission, without requiring host-to-host direct contact. While models for environmental transmission exist, many are simply constructed intuitively with structures analogous to standard models for direct transmission. As model insights are generally sensitive to the underlying model assumptions, it is important that we are able understand the details and consequences of these assumptions.

Geographic disparities and determinants of COVID-19 incidence risk in the greater St. Louis Area, Missouri (United States).

Background: Evidence seems to suggest that the risk of Coronavirus Disease 2019 (COVID-19) might vary across communities due to differences in population characteristics and movement patterns. However, little is known about these differences in the greater St Louis Area of Missouri and yet this information is useful for targeting control efforts. Therefore, the objectives of this study were to investigate (a) geographic disparities of COVID-19 risk and (b) associations between COVID-19 risk and socioeconomic, demographic, movement and chronic disease factors in the Greater St.

Epidemiology of Plasmid Lineages Mediating the Spread of Extended-Spectrum Beta-Lactamases among Clinical Escherichia coli.

The prevalence of extended-spectrum beta-lactamases (ESBLs) among clinical isolates of Escherichia coli has been increasing, with this spread driven by ESBL-encoding plasmids. However, the epidemiology of ESBL-disseminating plasmids remains understudied, obscuring the roles of individual plasmid lineages in ESBL spread. To address this, we performed an in-depth genomic investigation of 149 clinical ESBL-like E.

Identifying patient-level risk factors associated with non-β-lactam resistance outcomes in invasive MRSA infections in the United States using chain graphs.

Background: MRSA is one of the most common causes of hospital- and community-acquired infections. MRSA is resistant to many antibiotics, including β-lactam antibiotics, fluoroquinolones, lincosamides, macrolides, aminoglycosides, tetracyclines and chloramphenicol.

Objectives: To identify patient-level characteristics that may be associated with phenotype variations and that may help improve prescribing practice and antimicrobial stewardship.

A review of epidemiological models of Clostridioides difficile transmission and control (2009-2021).

Clostridioides difficile is the leading cause of infectious diarrhea and one of the most common healthcare-acquired infections worldwide. We performed a systematic search and a bibliometric analysis of mathematical and computational models for Clostridioides difficile transmission. We identified 33 publications from 2009 to 2021.

Geographic disparities and predictors of COVID-19 hospitalization risks in the St. Louis Area, Missouri (USA).

Background: There is evidence of geographic disparities in COVID-19 hospitalization risks that, if identified, could guide control efforts. Therefore, the objective of this study was to investigate Zip Code Tabulation Area (ZCTA)-level geographic disparities and identify predictors of COVID-19 hospitalization risks in the St. Louis area.

Assessing the efficacy of interventions to control indoor SARS-Cov-2 transmission: An agent-based modeling approach.

Nonpharmaceutical interventions for minimizing indoor SARS-CoV-2 transmission continue to be critical tools for protecting susceptible individuals from infection, even as effective vaccines are produced and distributed globally. We developed a spatially-explicit agent-based model for simulating indoor respiratory pathogen transmission during discrete events taking place in a single room within a sub-day time frame, and used it to compare effects of four interventions on reducing secondary SARS-CoV-2 attack rates during a superspreading event by simulating a well-known case study. We found that preventing people from moving within the simulated room and efficacious mask usage appear to have the greatest effects on reducing infection risk, but multiple concurrent interventions are required to minimize the proportion of susceptible individuals infected.

Combining epidemiological and ecological methods to quantify social effects on transmission.

Enteric microparasites like use multiple transmission pathways to propagate within and between host populations. Characterizing the relative transmission risk attributable to host social relationships and direct physical contact between individuals is paramount for understanding how microparasites like spread within affected communities and estimating colonization rates. To measure these effects, we carried out commensal transmission experiments in two cattle () herds, wherein all individuals were equipped with real-time location tracking devices.

Modelling the role of mortality-based response triggers on the effectiveness of African swine fever control strategies.

African swine fever (ASF) is considered the most impactful transboundary swine disease. In the absence of effective vaccines, control strategies are heavily dependent on mass depopulation and shipment restrictions. Here, we developed a nested multiscale model for the transmission of ASF, combining a spatially explicit network model of animal shipments with a deterministic compartmental model for the dynamics of two ASF strains within 3 km × 3 km pixels in one Brazilian state.

Mathematically modeling the effect of touch frequency on the environmental transmission of Clostridioides difficile in healthcare settings.

Clostridioides difficile, formerly Clostridium difficile, is the leading cause of infectious diarrhea and one of the most common healthcare acquired infections in United States hospitals. C. difficile persists well in healthcare environments because it forms spores that can survive for long periods of time and can be transmitted to susceptible patients through contact with contaminated hands and fomites, objects or surfaces that can harbor infectious agents.

Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen.

Indirect (environmental) and direct (host-host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem that combines epidemiological information (temporal, spatial information) with pathogen whole-genome sequencing data to infer transmission trees of epidemics. However, factors such as differences in mutation and transmission rates between host and non-host environments may obscure phylogenetic inference from these methods.

When can we stop wearing masks? Agent-based modeling to identify when vaccine coverage makes nonpharmaceutical interventions for reducing SARS-CoV-2 infections redundant in indoor gatherings.

As vaccination efforts to combat the COVID-19 pandemic are ramping up worldwide, there are rising concerns that individuals will begin to eschew nonpharmaceutical interventions for preventing SARS-CoV-2 transmission and attempt to return to pre-pandemic normalcy before vaccine coverage levels effectively mitigate transmission risk. In the U.S.