Microdiversity of Kentucky During Long-Term Colonization of a Dairy Herd.

subsp. serovar Kentucky was repeatedly isolated from a commercial dairy herd that was enrolled in a longitudinal study where feces of asymptomatic dairy cattle were sampled intensively over an 8-year period. The genomes of 5 Kentucky isolates recovered from the farm 2 years before the onset of the long-term colonization event and 13 isolates collected during the period of endemicity were sequenced.

Genome-Wide Analysis of Isolated from Dairy Animals Identifies Virulence Factors and Genes Enriched in Multidrug-Resistant Strains.

The gastrointestinal tracts of dairy calves and cows are reservoirs of antimicrobial-resistant bacteria (ARB), which are present regardless of previous antimicrobial therapy. Young calves harbor a greater abundance of resistant bacteria than older cows, but the factors driving this high abundance are unknown. Here, we aimed to fully characterize the genomes of multidrug-resistant (MDR) and antimicrobial-susceptible strains isolated from pre-weaned calves, post-weaned calves, dry cows, and lactating cows and to identify the accessory genes that are associated with the MDR genotype to discover genetic targets that can be exploited to mitigate antimicrobial resistance in dairy farms.

Characterization of Antimicrobial Resistance Genes and Virulence Factors in the Genomes of ST69 Isolates from Preweaned Dairy Calves and Their Phylogenetic Relationship with Poultry and Human Clinical Strains.

sequence type 69 (ST69) are common causative agents of extraintestinal infections occurring in the bloodstream, cerebrospinal fluid, surgical sites, and, most frequently, the urinary tract. The objective of this study was to analyze the genomic characteristics of 45 antimicrobial-resistant ST69 strains that were isolated from 28 calves on eight dairy farms in Pennsylvania, USA. The genomes were sequenced and the antimicrobial resistance genes (ARGs), virulence factors (VFs), and plasmid replicons were identified .

Genomic diversity of antimicrobial-resistant and Shiga toxin gene-harboring non-O157 Escherichia coli from dairy calves.

Objectives: Shiga toxin-producing Escherichia coli (STEC) are globally significant foodborne pathogens. Dairy calves are a known reservoir of both O157 and non-O157 STEC. The objective of this study was to comprehensively evaluate the genomic attributes, diversity, virulence factors, and antimicrobial resistance gene (ARG) profiles of the STEC from preweaned and postweaned dairy calves in commercial dairy herds.

Differences between the global transcriptomes of Salmonella enterica serovars Dublin and Cerro infecting bovine epithelial cells.

Background: The impact of S. enterica colonization in cattle is highly variable and often serovar-dependent. The aim of this study was to compare the global transcriptomes of highly pathogenic bovine-adapted S.

Genome and virulome characterization of Escherichia coli encoding multiple antimicrobial resistance genes isolated from commercial dairy operations.

Objectives: The aim of this study was to describe the genome sequences of 12 Escherichia coli isolates that encode antimicrobial resistance genes (ARGs) and were isolated from composite dairy animal faecal samples.

Methods: The isolates were recovered between 2013 and 2014 from a larger study evaluating the presence of resistance on dairy operations in Pennsylvania, USA. The draft genomes were sequenced on an Illumina NextSeq 500 platform and were assembled using SPAdes.

Draft Genome Sequence of Escherichia coli ARS-CC7049, a Sequence Type 38 Strain Isolated from Dry Cow Feces on a Commercial Dairy Operation.

Escherichia coli is a diverse species of commensal and pathogenic strains, of which some can cause extraintestinal infections, such as sequence type 38 (ST38) strains. Here, we report the genome sequence of E. coli ARS-CC7049, an ST38 strain that was isolated from a composite fecal sample on a dairy farm.

Genomic diversity and resistome profiles of Salmonella enterica subsp. enterica serovar Kentucky isolated from food and animal sources in Ireland.

Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from poultry, dairy and beef cattle, the environment and people with clinical salmonellosis globally. However, the sources of this serovar and its diversity and antimicrobial resistance capacities remain poorly described in many regions.

Genome sequences of antibiotic-resistant Escherichia coli isolated from veal calves in the USA.

Objectives: The aim of this study was to describe the genome sequences of 38 antibiotic-resistant Escherichia coli isolated from veal calves.

Methods: The isolates were recovered in 2015 from nine veal farms in the eastern USA and were screened for antibiotic susceptibility using an automated microdilution procedure. The draft genomes were sequenced on an Illumina NextSeq 500 platform and were assembled using SPAdes.

Genomic Analysis of Antibiotic-Resistant and -Susceptible Isolated from Bovine Sources in Maputo, Mozambique.

This study reports a genomic analysis of isolates recovered from 25 bovine fecal composite samples collected from four different production units in Maputo city and around Maputo Province, Mozambique. The genomes were analyzed to determine the presence of antibiotic resistance genes (ARGs), genetic relatedness, and virulence factors known to cause diseases in humans. Whole-genome sequencing was conducted on 28 isolates using an Illumina NextSeq 500 sequencing platform.

Metagenomic Analysis of the Microbial Communities and Resistomes of Veal Calf Feces.

Antimicrobial resistance (AMR) is a major public health concern, and dairy calves, including veal calves, are known reservoirs of resistant bacteria. To investigate AMR in the fecal microbial communities of veal calves, we conducted metagenomic sequencing of feces collected from individual animals on four commercial veal operations in Pennsylvania. Fecal samples from three randomly selected calves on each farm were collected soon after the calves were brought onto the farms ( = 12), and again, just before the calves from the same cohorts were ready for slaughter ( = 12).

Differences in the Microbial Community and Resistome Structures of Feces from Preweaned Calves and Lactating Dairy Cows in Commercial Dairy Herds.

Preweaned dairy calves and lactating dairy cows are known reservoirs of antibiotic-resistant bacteria. To further understand the differences in the resistomes and microbial communities between the two, we sequenced the metagenomes of fecal composite samples from preweaned dairy calves and lactating dairy cows on 17 commercial dairy farms ( = 34 samples). Results indicated significant differences in the structures of the microbial communities (analysis of similarities [ANOSIM]  = 0.

Interaction of with Bovine Epithelial Cells Demonstrates Serovar-Specific Association and Invasion Patterns.

Dairy cows are known reservoirs of and human salmonellosis has been attributed to the consumption of contaminated dairy and beef products as well as poultry meat and eggs. Although many serovars are known to colonize the gastrointestinal tract of cattle, the interactions between dairy commensal (or persistent) and transient serovars with bovine epithelial cells are not well understood. Association-invasion assays were used to characterize the interactions of 26 strains from bovine origins, comprising serovars Anatum, Cerro, Dublin, Give, Kentucky, Mbandaka, Meleagridis, Montevideo, Muenster, Newport, Oranienburg, Senftenberg, and Typhimurium, with cultured bovine epithelial cells.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly.

Salmonella enterica serovar Kentucky recovered from human clinical cases in Maryland, USA (2011-2015).

Salmonella Kentucky is among the most frequently isolated S. enterica serovars from food animals in the United States. Recent research on isolates recovered from these animals suggests there may be geographic and host specificity signatures associated with S.

Diversity of Extended-Spectrum Cephalosporin-Resistant in Feces from Calves and Cows on Pennsylvania Dairy Farms.

The global incidence of human infections associated with extended-spectrum β-lactamase (ESBL)-producing is increasing. Dairy animals are reservoirs of ESBL-producing , especially, third-generation cephalosporin (3GC)-resistant strains. To further understand the diversity of 3GC-resistant across animals of different age groups (e.

Antimicrobial Resistance Among Escherichia coli Isolated from Veal Calf Operations in Pennsylvania.

Antimicrobial resistance (AR) is a pressing public health concern, and agricultural operations such as dairy and beef cattle production have been implicated as potential sources of resistant bacteria or genetic elements. This study aimed to determine the prevalence of antimicrobial-resistant Escherichia coli from calf pens in 6 auction houses (56 manure composite samples) and 12 veal calf operations (240 fecal samples in 2 visits: after the calves arrived at the farm and shortly before the animals were sent to slaughter) in the Commonwealth of Pennsylvania. A total of 1567 generic E.

Complete Genome Sequence of a Salmonella enterica subsp. enterica Serovar Fresno Isolate Recovered from a Bovine Lymph Node.

Salmonella enterica serovar Fresno is an infrequently isolated serovar whose ecology and genomic characteristics have not yet been described. To further understand the genomic characteristics of this serovar, we sequenced the complete genome of a single isolate recovered from a bovine lymph node at harvest.

Age-Associated Distribution of Antimicrobial-Resistant Salmonella enterica and Escherichia coli Isolated from Dairy Herds in Pennsylvania, 2013-2015.

Antimicrobial resistance has become a major global public health concern, and agricultural operations are often implicated as a source of resistant bacteria. This study characterized the prevalence of antimicrobial-resistant Salmonella enterica and Escherichia coli from a total of 443 manure composite samples from preweaned calves, postweaned calves, dry cows, and lactating cows from 80 dairy operations in Pennsylvania. A total of 1095 S.

Complete Closed Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Dublin Strains Isolated from Cattle at Harvest.

Salmonella enterica subsp. enterica serovar Dublin is a host-adapted pathogen for cattle that can cause invasive disease in humans. To facilitate genomic comparisons characterizing virulence determinants of this pathogen, we present the complete genome sequences of three S.

Fecal Metagenome Sequences from Lactating Dairy Cows Shedding Escherichia coli O157:H7.

Cattle are primary reservoirs of Escherichia coli O157:H7, a causative agent of severe human infections. To facilitate analyses of the communities in which this pathogen is found, we sequenced the fecal metagenomes of 10 dairy cows shedding E. coli O157:H7 and added them to the public domain.

Antimicrobial Resistance in Fecal Escherichia coli and Salmonella enterica from Dairy Calves: A Systematic Review.

The discovery of antibiotics brought with it many advances in the health and well-being of humans and animals; however, in recent years development of antimicrobial resistance (AMR) has increasingly become a concern. Much of the antibiotic use on dairy farms is for disease management in mature cattle, and AMR in fecal organisms is relatively rare in this group. However, young dairy calves often carry high levels of AMR in their fecal Escherichia coli and Salmonella enterica, which could provide a potential reservoir of AMR genes on dairy farms.

Genetic diversity and virulence profiles of Listeria monocytogenes recovered from bulk tank milk, milk filters, and milking equipment from dairies in the United States (2002 to 2014).

Unpasteurized dairy products are known to occasionally harbor Listeria monocytogenes and have been implicated in recent listeriosis outbreaks and numerous sporadic cases of listeriosis. However, the diversity and virulence profiles of L. monocytogenes isolates recovered from these products have not been fully described.