Predicting sepsis mortality into an era of pandrug-resistant E. coli through modeling.

Background: Infections caused by antibiotic-resistant bacteria are increasingly frequent, burdening healthcare systems worldwide. As pathogens acquire resistance to all known antibiotics - i.e.

Pediatric urinary tract infections caused by poultry-associated .

is the leading cause of urinary tract infections (UTIs) in children and adults. The gastrointestinal tract is the primary reservoir of uropathogenic , which can be acquired from a variety of environmental exposures, including retail meat. In the current study, we used a novel statistical-genomic approach to estimate the proportion of pediatric UTIs caused by foodborne zoonotic strains.

Assessing the difference in contamination of retail meat with multidrug-resistant bacteria using for-consumer package label claims that indicate on-farm antibiotic use practices- United States, 2016-2019.

Background: Antibiotic use in food-producing animals can select for antibiotic resistance in bacteria that can be transmitted to people through contamination of food products during meat processing. Contamination resulting in foodborne illness contributes to adverse health outcomes. Some livestock producers have implemented antibiotic use reduction strategies marketed to consumers on regulated retail meat packaging labels ("label claims").

Distance and destination of retail meat alter multidrug resistant contamination in the United States food system.

Antibiotic-resistant infections are a global concern, especially those caused by multidrug-resistant (MDR) bacteria, defined as those resistant to more than three drug classes. The animal agriculture industry contributes to the antimicrobial resistant foodborne illness burden via contaminated retail meat. In the United States, retail meat is shipped across the country.

Impact of California's Senate Bill 27 on Antimicrobial-Resistant Escherichia coli Urinary Tract Infection in Humans: Protocol for a Study of Methods and Baseline Data.

Background: Overuse of antibiotics contributes to antimicrobial resistance (AMR) and is a growing threat to human health worldwide. Previous work suggests a link between antimicrobial use in poultry and human AMR extraintestinal pathogenic Escherichia coli (E coli) urinary tract infections (UTIs). However, few US-based studies exist, and none have comprehensively assessed both foodborne and environmental pathways using advanced molecular and spatial epidemiologic methods in a quasi-experimental design.

Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome.

Dolosigranulum pigrum-a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D.

Impact of a Statewide Livestock Antibiotic Use Policy on Resistance in Human Urine Isolates: A Synthetic Control Analysis.

Background: On 1 January 2018, California implemented Senate Bill 27 (SB27), banning, for the first time in the United States, routine preventive use of antibiotics in food-animal production and any antibiotic use without a veterinarian's prescription.

Objectives: Our objective was to assess whether SB27 was associated with decreased antimicrobial resistance among isolated from human urine.

Methods: We used U.

Policy reforms for antibiotic use claims in livestock.

Antibiotics detected in "raised without antibiotics" cattle underscore the need to ensure the integrity of labeling claims.

Integrating sample similarities into latent class analysis: a tree-structured shrinkage approach.

This paper is concerned with using multivariate binary observations to estimate the probabilities of unobserved classes with scientific meanings. We focus on the setting where additional information about sample similarities is available and represented by a rooted weighted tree. Every leaf in the given tree contains multiple samples.

Contamination of Retail Meat Samples with Multidrug-Resistant Organisms in Relation to Organic and Conventional Production and Processing: A Cross-Sectional Analysis of Data from the United States National Antimicrobial Resistance Monitoring System, 2012-2017.

Background: During food animal production, animals are exposed to, colonized by, and sometimes infected with bacteria that may contaminate animal products with susceptible and multidrug-resistant organisms (MDRO). The United States' Organic Foods Production Act resulted in decreased antibiotic use in some animal production operations. Some studies have reported that decreased antibiotic use is associated with reduced MDRO on meat.

Getting ahead of antibiotic-resistant Staphylococcus aureus in U.S. hogs.

Antibiotic-resistant strains of Staphylococcus aureus, an opportunistic bacterial pathogen, have emerged in industrial livestock operations and agricultural settings. In the United States, there is limited access to industrial livestock operations and farm-level antibiotic use data. As a result, studies often rely on retail meat as a proxy for direct animal sampling.

Transmission of Antimicrobial-Resistant Staphylococcus aureus Clonal Complex 9 between Pigs and Humans, United States.

Transmission of livestock-associated Staphylococcus aureus clonal complex 9 (LA-SA CC9) between pigs raised on industrial hog operations (IHOs) and humans in the United States is poorly understood. We analyzed whole-genome sequences from 32 international S. aureus CC9 isolates and 49 LA-SA CC9 isolates from IHO pigs and humans who work on or live near IHOs in 10 pig-producing counties in North Carolina, USA.

Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics.

Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE-host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR-Cas systems and their corresponding iMGEs.

Phage-Mediated Immune Evasion and Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus in Humans.

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) can acquire phage-encoded immune modulators, such as the immune evasion cluster (IEC), which protects bacteria from components of the human innate immune system, and the enzyme TarP, which protects against antibody-mediated immune recognition. We used whole-genome sequencing and epidemiologic investigations to study the effects of IEC- and tarP-harboring phages on household transmission of LA-MRSA in North Denmark Region during 2004-2011. We reviewed information about all patients throughout Denmark who experienced LA-MRSA infection during 2007-2018 to determine whether IEC is associated with increased spread into the general population.

mcr-Positive Escherichia coli ST131-H22 from Poultry in Brazil.

Escherichia coli sequence type (ST) 131 is of concern because it can acquire antimicrobial resistance and cause extraintestinal infections. E. coli ST131-H22 sublineage appears capable of being transmitted to humans through poultry.

Effects of concentrated poultry operations and cropland manure application on antibiotic resistant Escherichia coli and nutrient pollution in Chesapeake Bay watersheds.

Manure from poultry operations is typically applied to nearby cropland and may affect nutrient loading and the spread of antibiotic resistance (ABR). We analyzed the concentrations of nitrogen and phosphorus and the occurrence of ABR in Escherichia coli (E. coli) and extra-intestinal pathogenic E.

Emergence of Enteroaggregative Escherichia coli within the ST131 Lineage as a Cause of Extraintestinal Infections.

sequence type 131 (ST131) is a major cause of urinary and bloodstream infections. Its association with extended-spectrum β-lactamases (ESBLs) significantly complicates treatment. Its best-described component is the rapidly expanding 30Rx clade, containing allele 30 of the type 1 fimbrial adhesin gene This lineage appears to have emerged in the United States and spread around the world in part due to the acquisition of the ESBL-encoding gene and resistance to fluoroquinolones.

Draft Whole-Genome Sequences of Ciprofloxacin-Resistant Derivatives of a Bacillus anthracis ΔANR Strain Lacking pXO1 and pXO2 Plasmids.

Mutants of an attenuated (ΔANR) strain conferring increasing levels of ciprofloxacin resistance have been described. Here, we report the draft genome sequences of the parent strain (ΔANR pXO1, pXO2) and its derivatives conferring low (step 1; 0.5 μg/ml), medium (step 2; 8 to 16 μg/ml), and high (step 3; 32 to 64 μg/ml) levels of ciprofloxacin resistance.

External Societal Costs of Antimicrobial Resistance in Humans Attributable to Antimicrobial Use in Livestock.

Antimicrobial use (AMU) in animal agriculture contributes to antimicrobial resistance (AMR) in humans, which imposes significant health and economic costs on society. Economists call these costs negative externalities, societal costs that are not properly reflected in market prices. We review the relevant literature and develop a model to quantify the external costs of AMU in animal agriculture on AMR in humans.

The Effect of Antiretroviral Therapy Initiation on the Vaginal Microbiome in HIV-Infected Women.

Background: The impact of antiretroviral therapy (ART) initiation on the vaginal microbiome is unknown. This is of particular importance among women living in sub-Saharan Africa. Understanding this relationship could help elucidate if and how the host immune system interacts with the vaginal microbiome.

Author Correction: Comparison of livestock-associated and community-associated Staphylococcus aureus pathogenicity in a mouse model of skin and soft tissue infection.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.