Publications by authors named "Jo Ann S Van Kessel"

48 Publications

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

Zoonoses Public Health 2022 Feb 30;69(1):1-12. Epub 2021 Oct 30.

Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.

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. To further understand the genetic diversity and antimicrobial sensitivity patterns among S. Kentucky strains isolated from non-human sources in Ireland, we sequenced and analysed the genomes of 61 isolates collected from avian, bovine, canine, ovine, piscine, porcine, environmental and vegetation sources between 2000 and 2016. The majority of isolates (n = 57, 93%) were sequence type (ST) 314, while only three isolates were ST198 and one was ST152. Several isolates were multidrug-resistant (MDR) and 14 carried at least one acquired antimicrobial resistance gene. When compared to a database of publicly available ST314, four distinct clades were identified (clades I-IV), with the majority of isolates from Ireland clustering together in Clade I. Two of the three ST198 isolates were characteristic of those originating outside of the Americas (Clade ST198.2), while one was distantly clustered with isolates from South and North America (Clade ST198.1). The genomes of the two clade ST198.2 isolates encoded Salmonella Genomic Island 1 (SGI1), were multidrug-resistant and encoded polymorphisms in the DNA gyrase (gyrA) and DNA topoisomerase (parC) known to confer resistance to fluoroquinolones. The single ST152 isolate was from raw beef, clustered with isolates from food and bovine sources in North America and was pan-susceptible. Results of this study indicate that most S. Kentucky isolates from non-human sources in Ireland are closely related ST314 and only a few isolates are antimicrobial-resistant. This study also demonstrates the presence of multidrug-resistant ST198 in food sources in Ireland.
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http://dx.doi.org/10.1111/zph.12884DOI Listing
February 2022

The resistome of the bovine gastrointestinal tract.

Curr Opin Biotechnol 2021 Sep 4;73:213-219. Epub 2021 Sep 4.

Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.

The gastrointestinal tracts of beef and dairy cattle are reservoirs of antimicrobial-resistant bacteria, and our knowledge of the ecology of resistance in these animals has changed with the advent of novel molecular technologies. Application of metagenomics and qPCR to the study of bovine gut ecology has demonstrated that there is overlap, with some differences, between beef and dairy cattle fecal resistomes, that treatment with antimicrobials often transiently influences the resistome, and young calves carry a high abundance of ARGs. Future work should harness emerging metagenome sequencing technologies to better describe the taxa harboring ARGs and collocated non-resistance genes and use these data along with identifying the multiplicity of factors driving resistance to develop strategies to reduce AMR carriage in cattle.
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http://dx.doi.org/10.1016/j.copbio.2021.07.025DOI Listing
September 2021

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

J Glob Antimicrob Resist 2021 09 27;26:69-73. Epub 2021 May 27.

Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA. Electronic address:

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.

Results: In total, 294 resistance genes, categorised into 42 unique genes, conferring resistance to seven different antibiotic classes were detected. Extended-spectrum β-lactamase (ESBL) genes (bla and bla) and the azithromycin resistance gene mph(A) were detected in multiple genomes. Furthermore, mutations in gyrA, parC and parE conferring resistance to fluoroquinolones were detected, as were mutations in the ampC promoter responsible for hyperproduction of β-lactamases. We identified 25 unique sequence types (STs), including STs that are associated with extraintestinal infections.

Conclusion: The results of this study indicate a high level of diversity among multidrug-resistant E. coli isolates from veal operations. The identification of multiple isolates encoding resistance to β-lactams, macrolides and fluoroquinolones as well as virulence factors responsible for human infections warrants more study on the ecology of antibiotic resistance in veal operations.
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http://dx.doi.org/10.1016/j.jgar.2021.04.024DOI Listing
September 2021

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

Foodborne Pathog Dis 2021 06 11;18(6):426-435. Epub 2021 May 11.

Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland, USA.

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. The genomes were analyzed using BLASTN for the presence of resistance genes and virulence factors, as well as to determine their phylogenetic groups, sequence types (ST), and ST complexes (ST Cplxs). The majority of the isolates (85%) were identified as members of phylogenetic groups B1, with fewer isolates identified as members of group A, and a single isolate identified as group "E/Clade I." The ST analysis demonstrated a higher level of diversity than the phylogenetic group analysis. Sixteen different STs, five ST Cplxs, and seven singleton complexes were identified. A strain identified as a novel ST (ST9215) showed a high level of similarity with an isolate recovered from a wild animal in the Gambia. Seven different ARGs were identified, with being the most frequently detected, followed by , , , , and . Three isolates encoded β-lactam-conferring point mutations in the promoter (-42C>T). In total, 51 different virulence factors were identified among the genomes. This study demonstrates that from bovine sources in Mozambique encoded multiple antibiotic resistance elements, plasmids, and virulence factors. To the best of our knowledge, this is the first genomic description of antibiotic-resistant isolated from bovine sources in Mozambique.
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http://dx.doi.org/10.1089/fpd.2020.2901DOI Listing
June 2021

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

Front Microbiol 2020 9;11:609950. Epub 2021 Feb 9.

Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States.

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). Results indicated that the most frequently identified phyla were Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Fecal microbial communities in samples collected from the calves at the early and late stages of production were significantly different at the genus level (analysis of similarities [ANOSIM] on Bray-Curtis distances, = 0.37, < 0.05), but not at the phylum level. Variances among microbial communities in the feces of the younger calves were significantly higher than those from the feces of calves at the late stage of production (betadisper = 8.25, < 0.05). Additionally, our analyses identified a diverse set of mobile antimicrobial resistance genes (ARGs) in the veal calf feces. The fecal resistomes mostly consisted of ARGs that confer resistance to aminoglycosides, tetracyclines, and macrolide-lincosamide-streptogramin B (MLS), and these ARGs represented more than 70% of the fecal resistomes. Factors that are responsible for selection and persistence of resistant bacteria in the veal calf gut need to be identified to implement novel control points and interrupt detrimental AMR occurrence and shedding.
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http://dx.doi.org/10.3389/fmicb.2020.609950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7899987PMC
February 2021

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

Foodborne Pathog Dis 2020 08 13;17(8):494-503. Epub 2020 Mar 13.

Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland.

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]  = 0.81,  = 0.001) and resistomes (ANOSIM  = 0.93 to 0.96,  = 0.001) between the two age groups. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the predominant members of the communities, but when the groups were compared, Bacteroidetes and Verrumicrobia were significantly more abundant in calf fecal composite samples, whereas Firmicutes, Spirochaetes, Deinococcus-Thermus, Lentisphaerae, Planctomycetes, Chlorofexi, and Saccharibacteria-(TM7) were more abundant in lactating cow samples. Diverse suites of antibiotic resistance genes (ARGs) were identified in all samples, with the most frequently detected being assigned to tetracycline and aminoglycoside resistance. When the two groups were compared, ARGs were significantly more abundant in composite fecal samples from calves than those from lactating cows (calf median ARG abundance = 1.8 × 10 ARG/16S ribosomal RNA [rRNA], cow median ARG abundance = 1.7 × 10 ARG/16S rRNA) and at the antibiotic resistance class level, the relative abundance of tetracycline, trimethoprim, aminoglycoside, macrolide-lincosamide-streptogramin B, β-lactam, and phenicol resistance genes was significantly higher in calf samples than in cow samples. Results of this study indicate that composite feces from preweaned calves harbor different bacterial communities and resistomes than composite feces from lactating cows, with a greater abundance of resistance genes detected in preweaned calf feces.
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http://dx.doi.org/10.1089/fpd.2019.2768DOI Listing
August 2020

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

Foodborne Pathog Dis 2020 10 5;17(10):608-610. Epub 2020 Mar 5.

Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, Maryland, USA.

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. There were significant differences in the association with and invasion of bovine epithelial cells within and across serovars (Tukey's Honestly Significant Difference test,  < 0.05). serovar Dublin strains were the most invasive, whereas Kentucky, Mbandaka, Cerro, and Give strains were the least invasive ( < 0.05). Significant differences in motility on semisolid medium were also observed between strains from different serovars. Findings from this study demonstrate an underappreciated level of phenotypic diversity among strains within and across serovars and serve as a baseline for future studies that may identify the molecular mechanisms of asymptomatic carriage and bovine salmonellosis.
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http://dx.doi.org/10.1089/fpd.2019.2765DOI Listing
October 2020

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

Genome Biol 2019 08 2;20(1):153. Epub 2019 Aug 2.

USDA-ARS U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.

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. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.
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http://dx.doi.org/10.1186/s13059-019-1760-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6676630PMC
August 2019

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

Zoonoses Public Health 2019 06 19;66(4):382-392. Epub 2019 Mar 19.

Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland.

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. Kentucky strains. However, the sources and genomic features of human clinical S. Kentucky isolated in the United States remain poorly described. To investigate the characteristics of clinical S. Kentucky and the possible sources of these infections, the genomes of all S. Kentucky isolates recovered from human clinical cases in the State of Maryland between 2011 and 2015 (n = 12) were sequenced and compared to a database of 525 previously sequenced S. Kentucky genomes representing 12 sequence types (ST) collected from multiple sources on several continents. Of the 12 human clinical S. Kentucky isolates from Maryland, nine were ST198, two were ST152, and one was ST314. Forty-one per cent of isolates were recovered from patients reporting recent international travel and 58% of isolates encoded genomic characteristics similar to those originating outside of the United States. Of the five isolates not associated with international travel, three encoded antibiotic resistance genes conferring resistance to tetracycline or aminoglycosides, while two others only encoded the cryptic aac(6')-Iaa gene. Five isolates recovered from individuals with international travel histories (ST198) and two for which travel was not recorded (ST198) encoded genes conferring resistance to between 4 and 7 classes of antibiotics. Seven ST198 genomes encoded the Salmonella Genomic Island 1 and substitutions in the gyrA and parC genes known to confer resistance to ciprofloxacin. Case report data on food consumption and travel were, for the most part, consistent with the inferred S. Kentucky phylogeny. Results of this study indicate that the majority of S. Kentucky infections in Maryland are caused by ST198 which may originate outside of North America.
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http://dx.doi.org/10.1111/zph.12571DOI Listing
June 2019

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

Foodborne Pathog Dis 2019 05 4;16(5):368-370. Epub 2019 Feb 4.

1 Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, Maryland.

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.g., pre- and postweaned calves, lactating cows, and dry cows) and farms, we used pulsed-field gel electrophoresis (PFGE) to characterize 70 fecal isolates from 14 dairy farms located in nine Pennsylvania counties. Results of this analysis indicated that 3GC-resistant were highly diverse and grouped into 27 PFGE clades (80% similarity cutoff) and 24 unique antimicrobial resistance patterns were observed among the isolates. For eight farms, clonal with the same resistance patterns were isolated from two or more age groups, indicating that strains were carried in both the calves and adult cows within the same herd. However, there were also several isolates with the same resistance pattern that were distributed to different clades, including isolates from different animal age groups on the same farm, suggesting different strains of within a farm harbored the same resistance-conferring elements. Results of this analysis indicated that 3GC-resistant were highly diverse, associated with multidrug resistance, and circulated through different (noncommingled) animal groups on individual farms.
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http://dx.doi.org/10.1089/fpd.2018.2579DOI Listing
May 2019

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

Foodborne Pathog Dis 2019 01;16(1):74-80

1 Environmental Microbial and Food Safety Laboratory, USDA-Agricultural Research Service, Beltsville, Maryland.

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. coli were isolated and screened for resistance phenotypes. Resistant E. coli were isolated from all auction houses and farms sampled. Based on nonparametric Kruskal-Wallis tests, incremental prevalence of E. coli resistant to ampicillin, azithromycin, cefoxitin, ceftiofur, ceftriaxone, chloramphenicol, streptomycin, sulfisoxazole, trimethoprim-sulfamethoxazole, and tetracycline in the samples from auction houses and the first and second farm visits was observed (χ 6.98-15.91, p < 0.05). Multidrug-resistant E. coli (resistant to more than three antimicrobial classes) were identified in 76.8%, 90.8%, and 100% of samples collected from the auction houses, first farm visits, and second farm visits, respectively. The presence of bla-E. coli in 11 of the 12 farms presents the possibility of veal production environments being a reservoir for resistant genetic materials that may pose a risk to human health if they are transferred to human pathogens. Additional research on the impact of various management strategies in veal calf rearing is needed for a complete scenario of AR in these production environments.
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http://dx.doi.org/10.1089/fpd.2018.2530DOI Listing
January 2019

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

Microbiol Resour Announc 2019 Jan 10;8(2). Epub 2019 Jan 10.

USDA ARS U.S. Meat Animal Research Center, Clay Center, Nebraska, USA.

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.
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http://dx.doi.org/10.1128/MRA.01338-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328650PMC
January 2019

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

Foodborne Pathog Dis 2019 01 31;16(1):60-67. Epub 2018 Dec 31.

2 Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland.

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. enterica and 2370 E. coli isolates were screened and tested for resistance to 14 antimicrobials on the National Antimicrobial Resistance Monitoring System Gram-negative (NARMS GN) panel. Salmonellae were isolated from 67% of dairy operations, and 99% of the isolates were pan-susceptible. Salmonella were isolated more frequently from lactating and dry cow samples than from pre- and postweaned calf samples. Overall, the most prevalent serotypes were Cerro, Montevideo, Kentucky, and Newport. E. coli were isolated from all the manure composite samples, and isolates were commonly resistant to tetracyclines, sulfonamides, and aminoglycosides. Resistance was detected more frequently in the E. coli isolates from pre- and postweaned calf samples than in isolates from dry and lactating cow samples (p < 0.05). Multidrug-resistant E. coli (i.e., resistant to >3 antimicrobial classes) were isolated from 66 farms (83%) with significantly greater prevalence in preweaned calves (p < 0.05) than in the older age groups. The bla and bla genes were detected in the cephalosporin-resistant E. coli from 4% and 35% of the farms, respectively. These findings indicate that dairy animals, especially the calf population, serve as significant reservoirs for antimicrobial-resistant bacteria. Additional research on the colonization and persistence of resistant E. coli in calves is warranted to identify potential avenues for mitigation.
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http://dx.doi.org/10.1089/fpd.2018.2519DOI Listing
January 2019

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

Microbiol Resour Announc 2018 Nov 29;7(21). Epub 2018 Nov 29.

USDA ARS Environmental Microbial Food Safety Laboratory, Beltsville, Maryland, USA.

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. Dublin strains isolated from bovine sources at harvest.
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http://dx.doi.org/10.1128/MRA.01334-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284729PMC
November 2018

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

Microbiol Resour Announc 2018 Nov 8;7(18). Epub 2018 Nov 8.

Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland, USA.

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.
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http://dx.doi.org/10.1128/MRA.01279-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256543PMC
November 2018

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

Foodborne Pathog Dis 2019 01 27;16(1):23-34. Epub 2018 Nov 27.

1 Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania.

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. To develop practical and effective antibiotic stewardship policies for dairy calf rearing, it is vital to have a solid understanding of the current state of knowledge regarding AMR in these animals. A systematic review process was used to summarize the current scientific literature regarding AMR in fecal S. enterica and E. coli and associations between management practices and AMR prevalence in dairy calves in the United States and Canada. Seven online databases were searched for literature published from 1997 to 2018. Multiple studies indicated an association between preweaned calves and increased risk of fecal shedding of resistant bacteria, compared to other animal groups on dairy farms. There also was evidence, although less consistent, of an impact of antibiotic treatment, antibiotic-containing milk replacer feeding, and feeding nonsalable or waste milk (WM) on the presence of AMR bacteria. Overall, the research summarized in this systematic review highlights the need for continued research on the impact of management practices, including antibiotic use, WM feeding, and disease prevention practices in reducing AMR in E. coli and S. enterica in dairy calves. In addition, few data were available on physiological and microbiological factors that may contribute to the high relative populations of resistant bacteria in young calves, suggesting another valuable area of future research.
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http://dx.doi.org/10.1089/fpd.2018.2529DOI Listing
January 2019

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).

PLoS One 2018 9;13(5):e0197053. Epub 2018 May 9.

Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America.

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. Here we report a genomic analysis of 121 L. monocytogenes isolates recovered from milk, milk filters, and milking equipment collected from bovine dairy farms in 19 states over a 12-year period. In a multi-virulence-locus sequence typing (MVLST) analysis, 59 Virulence Types (VT) were identified, of which 25% were Epidemic Clones I, II, V, VI, VII, VIII, IX, or X, and 31 were novel VT. In a multi-locus sequence typing (MLST) analysis, 60 Sequence Types (ST) of 56 Clonal Complexes (CC) were identified. Within lineage I, CC5 and CC1 were among the most abundant, and within lineage II, CC7 and CC37 were the most abundant. Multiple CCs previously associated with central nervous system and maternal-neonatal infections were identified. A genomic analysis identified variable distribution of virulence markers, Listeria pathogenicity islands (LIPI) -1, -3, and -4, and stress survival island-1 (SSI-1). Of these, 14 virulence markers, including LIPI-3 and -4 were more frequently detected in one lineage (I or II) than the other. LIPI-3 and LIPI-4 were identified in 68% and 28% of lineage I CCs, respectively. Results of this analysis indicate that there is a high level of genetic diversity among the L. monocytogenes present in bulk tank milk in the United States with some strains being more frequently detected than others, and some being similar to those that have been isolated from previous non-dairy related outbreaks. Results of this study also demonstrate significant number of strains isolated from dairy farms encode virulence markers associated with severe human disease.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197053PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5942804PMC
August 2018

Prevalence of Salmonella enterica, Listeria monocytogenes, and pathogenic Escherichia coli in bulk tank milk and milk filters from US dairy operations in the National Animal Health Monitoring System Dairy 2014 study.

J Dairy Sci 2018 Mar 21;101(3):1943-1956. Epub 2017 Dec 21.

Environmental Microbial and Food Safety Laboratory, USDA, Agricultural Research Service, Beltsville, MD 20705. Electronic address:

The dairy farm environment is a well-documented reservoir for zoonotic pathogens such as Salmonella enterica, Shiga-toxigenic Escherichia coli, and Listeria monocytogenes, and humans may be exposed to these pathogens via consumption of unpasteurized milk and dairy products. As part of the National Animal Health Monitoring System Dairy 2014 study, bulk tank milk (BTM, n = 234) and milk filters (n = 254) were collected from a total of 234 dairy operations in 17 major dairy states and analyzed for the presence of these pathogens. The invA gene was detected in samples from 18.5% of operations and Salmonella enterica was isolated from 18.0% of operations. Salmonella Dublin was detected in 0.7% of operations. Sixteen Salmonella serotypes were isolated, and the most common serotypes were Cerro, Montevideo, and Newport. Representative Salmonella isolates (n = 137) were tested against a panel of 14 antimicrobials. Most (85%) were pansusceptible; the remaining were resistant to 1 to 9 antimicrobials, and within the resistant strains the most common profile was resistance to ampicillin/clavulanic acid, ampicillin, cefoxitin, ceftiofur, ceftriaxone, chloramphenicol, streptomycin, sulfisoxazole, and tetracycline. Listeria spp. were isolated from 19.9% of operations, and L. monocytogenes was isolated from 3.0% of operations. Serogroups 1/2a and 1/2b were the most common, followed by 4b and 4a. One or more E. coli virulence genes were detected in the BTM from 30.5% of operations and in the filters from 75.3% of operations. A combination of stx, eaeA, and γ-tir genes was detected in the BTM from 0.5% of operations and in the filters from 6.6% of operations. The results of this study indicate an appreciable prevalence of bacterial pathogens in BTM and filters, including serovars known to infect humans.
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http://dx.doi.org/10.3168/jds.2017-13546DOI Listing
March 2018

Alternative Growth Promoters Modulate Broiler Gut Microbiome and Enhance Body Weight Gain.

Front Microbiol 2017 26;8:2088. Epub 2017 Oct 26.

Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States.

Antibiotic growth promoters (AGPs) are frequently used to enhance weight-gain in poultry production. However, there has been increasing concern over the impact of AGP on the emergence of antibiotic resistance in zoonotic bacterial pathogens in the microbial community of the poultry gut. In this study, we adopted mass-spectrophotometric, phylogenetic, and shotgun-metagenomic approaches to evaluate bioactive phenolic extracts (BPE) from blueberry () and blackberry () pomaces as AGP alternatives in broilers. We conducted two trials with 100 Cobb-500 broiler chicks (in each trial) in four equal groups that were provided water with no supplementation, supplemented with AGP (tylosin, neomycin sulfate, bacitracin, erythromycin, and oxytetracycline), or supplemented with 0.1 g Gallic acid equivalent (GAE)/L or 1.0 g GAE/L (during the last 72 h before euthanasia) of BPE for 6 weeks. When compared with the control group (water only), the chickens supplemented with AGP and 0.1 g GAE/L of BPE gained 9.5 and 5.8% more body weight, respectively. The microbiomes of both the AGP- and BPE-treated chickens had higher Firmicutes to Bacteroidetes ratios. AGP supplementation appeared to be associated with higher relative abundance of bacteriophages and unique cecal resistomes compared with BPE supplementation or control. Functional characterization of cecal microbiomes revealed significant animal-to-animal variation in the relative abundance of genes involved in energy and carbohydrate metabolism. These findings established a baseline upon which mechanisms of plant-based performance enhancers in regulation of animal growth can be investigated. In addition, the data will aid in designing alternate strategies to improve animal growth performance and consequently production.
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http://dx.doi.org/10.3389/fmicb.2017.02088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662582PMC
October 2017

Genome Sequences of subsp. Serovar Kentucky Sequence Type 152 Isolated from Dairy Cows in the United States.

Genome Announc 2017 Oct 19;5(42). Epub 2017 Oct 19.

Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, Maryland, USA

subsp. serovar Kentucky ( Kentucky) is frequently isolated from dairy cows in the United States, but is an infrequent cause of human salmonellosis. To investigate the genomic features of  Kentucky strains isolated from a single dairy farm, the genomes of eight isolates were sequenced and added to the public domain.
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http://dx.doi.org/10.1128/genomeA.01119-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5646404PMC
October 2017

Genome Sequences of 30 O157:H7 Isolates Recovered from a Single Dairy Farm and Its Associated Off-Site Heifer-Raising Facility.

Genome Announc 2017 Aug 31;5(35). Epub 2017 Aug 31.

Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland, USA

Cattle are the primary reservoir of O157:H7, the most frequently isolated serotype of enterohemorrhagic infections among humans in North America. To evaluate the diversity of O157:H7 isolates within a single dairy herd, the genomes of 30 isolates collected over a 7-year period were sequenced.
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http://dx.doi.org/10.1128/genomeA.00814-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578836PMC
August 2017

Genome Sequences of Five Multidrug-Resistant Sequence Type 117 Isolates Recovered from Dairy Calves.

Genome Announc 2017 Aug 17;5(33). Epub 2017 Aug 17.

Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland, USA

sequence type 117 (ST117) strains have been recovered from poultry with colibacillosis, as well as from urinary tract infections and fatal septic infections in humans. To further investigate ST117 isolates recovered from nonpoultry food animals, we sequenced the genomes of five ST117 isolates from dairy calves in Pennsylvania.
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http://dx.doi.org/10.1128/genomeA.00732-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604762PMC
August 2017

Genome Sequences of Four Nonhuman/Nonclinical Serovar Kentucky ST198 Isolates Recovered between 1972 and 1973.

Genome Announc 2017 Mar 16;5(11). Epub 2017 Mar 16.

Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland, USA

serovar Kentucky is a polyphyletic member of subclade A1 with multiple sequence types that often colonize the same hosts but in different frequencies on different continents. To evaluate the genomic features involved in  Kentucky host specificity, we sequenced the genomes of four isolates recovered in the 1970s.
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http://dx.doi.org/10.1128/genomeA.01699-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5356063PMC
March 2017

Prevalence, antimicrobial resistance, and molecular characterization of Campylobacter spp. in bulk tank milk and milk filters from US dairies.

J Dairy Sci 2017 May 23;100(5):3470-3479. Epub 2017 Feb 23.

Environmental Microbial and Food Safety Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705. Electronic address:

Campylobacter spp. are frequently isolated from dairy cows as commensal organisms. Sporadic Campylobacter infections in humans in the United States are generally attributed to poultry, but outbreaks are also commonly associated with dairy products, particularly unpasteurized or raw milk. Bulk tank milk samples and milk filters from US dairy operations were collected during the National Animal Health Monitoring System Dairy 2014 study and analyzed using real-time PCR and traditional culture techniques for the presence of thermophilic Campylobacter species. The weighted prevalence of operations from which we detected Campylobacter spp. in either bulk tank milk or milk filters was 24.9%. We detected Campylobacter spp. in a higher percentage of operations with 100-499 cows (42.8%) and 500 or more cows (47.5%) than in operations with 30-99 cows (6.5%). Campylobacter spp. were also more frequently detected in operations in the west than the east (45.9 and 22.6%, respectively). We isolated Campylobacter spp. from approximately half of PCR-positive samples, representing 12.5% (weighted prevalence) of operations. The majority (91.8%) of isolates were C. jejuni, but C. lari and C. coli were also isolated. We detected resistance to tetracycline in 68.4% of C. jejuni isolates, and resistance to ciprofloxacin and nalidixic acid in 13.2% of C. jejuni isolates. Based on pulsed-field gel electrophoresis, we found that dairy-associated C. jejuni were genotypically diverse, although clonal strains were isolated from different geographic regions. These results suggest that bulk tank milk can be contaminated with pathogenic Campylobacter spp., and that the consumption of unpasteurized or raw milk presents a potential human health risk.
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http://dx.doi.org/10.3168/jds.2016-12084DOI Listing
May 2017

Genome Sequences of Two Salmonella enterica Serovar Kentucky Isolates Recovered from Poultry Carcasses in the United States.

Genome Announc 2016 Nov 17;4(6). Epub 2016 Nov 17.

United States Department of Agriculture, Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, Beltsville, Maryland, USA

We report here the draft genome sequences of two Salmonella enterica serovar Kentucky eBurstGroup 15 isolates collected from poultry carcasses in Georgia (USA).
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http://dx.doi.org/10.1128/genomeA.01289-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114379PMC
November 2016

Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America.

PLoS One 2016 3;11(10):e0161225. Epub 2016 Oct 3.

Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America.

Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from healthy poultry and dairy cows and is occasionally isolated from people with clinical disease. A genomic analysis of 119 isolates collected in the United States from dairy cows, ground beef, poultry and poultry products, and human clinical cases was conducted. Results of the analysis demonstrated that the majority of poultry and bovine-associated S. Kentucky were sequence type (ST) 152. Several bovine-associated (n = 3) and food product isolates (n = 3) collected from the United States and the majority of human clinical isolates were ST198, a sequence type that is frequently isolated from poultry and occasionally from human clinical cases in Northern Africa, Europe and Southeast Asia. A phylogenetic analysis indicated that both STs are more closely related to other Salmonella serovars than they are to each other. Additionally, there was strong evidence of an evolutionary divergence between the poultry-associated and bovine-associated ST152 isolates that was due to polymorphisms in four core genome genes. The ST198 isolates recovered from dairy farms in the United States were phylogenetically distinct from those collected from human clinical cases with 66 core genome SNPs differentiating the two groups, but more isolates are needed to determine the significance of this distinction. Identification of S. Kentucky ST198 from dairy animals in the United States suggests that the presence of this pathogen should be monitored in food-producing animals.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161225PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047448PMC
June 2017

Comparison of Microbial Communities Isolated from Feces of Asymptomatic Salmonella-Shedding and Non-Salmonella Shedding Dairy Cows.

Front Microbiol 2016 1;7:691. Epub 2016 Jun 1.

Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Agricultural Research Service Beltsville, MD, USA.

In the United States Salmonella enterica subsp. enterica serotypes Kentucky and Cerro are frequently isolated from asymptomatic dairy cows. However, factors that contribute to colonization of the bovine gut by these two serotypes have not been identified. To investigate associations between Salmonella status and bacterial diversity, as well as the diversity of the microbial community in the dairy cow hindgut, the bacterial and archaeal communities of fecal samples from cows on a single dairy farm were determined by high-throughput sequencing of 16S rRNA gene amplicons. Fecal grab samples were collected from two Salmonella-positive cows and two Salmonella-negative cows on five sampling dates (n = 20 cows), and 16S rRNA gene amplicons from these samples were sequenced on the Illumina MiSeq platform. A high level of alpha (within) and beta diversity (between) samples demonstrated that microbial profiles of dairy cow hindguts are quite diverse. To determine whether Salmonella presence, sampling year, or sampling date explained a significant amount of the variation in microbial diversity, we performed constrained ordination analyses (distance based RDA) on the unifrac distance matrix produced with QIIME. Results indicated that there was not a significant difference in the microbial diversity associated with Salmonella presence (P > 0.05), but there were significant differences between sampling dates and years (Pseudo-F = 2.157 to 4.385, P < 0.05). Based on these data, it appears that commensal Salmonella infections with serotypes Cerro and Kentucky in dairy cows have little or no association with changes in the abundance of major bacterial groups in the hindgut. Rather, our results indicated that temporal dynamics and other undescribed parameters associated with them were the most influential drivers of the differences in microbial diversity and community structure in the dairy cow hindgut.
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http://dx.doi.org/10.3389/fmicb.2016.00691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4887466PMC
June 2016

Complete Genome Sequence and Methylome of Salmonella enterica subsp. enterica Cerro, a Frequent Dairy Cow Serovar.

Genome Announc 2016 Jan 28;4(1). Epub 2016 Jan 28.

Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, USDA-ARS, Beltsville, Maryland, USA

Salmonella enterica subsp. enterica serovar Cerro is an infrequent pathogen of humans and other mammals but is frequently isolated from the hindgut of asymptomatic cattle in the United States. To further understand the genomic determinants of S. Cerro specificity for the bovine hindgut, the genome of isolate CFSAN001588 was fully sequenced and deposited in the GenBank database.
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http://dx.doi.org/10.1128/genomeA.01350-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4732324PMC
January 2016

Irrigation waters and pipe-based biofilms as sources for antibiotic-resistant bacteria.

Environ Monit Assess 2016 Jan 24;188(1):56. Epub 2015 Dec 24.

USDA-ARS Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Ave. Bldg. 173, Beltsville, MD, 20705, USA.

The presence of antibiotic-resistant bacteria in environmental surface waters has gained recent attention. Wastewater and drinking water distribution systems are known to disseminate antibiotic-resistant bacteria, with the biofilms that form on the inner-surfaces of the pipeline as a hot spot for proliferation and gene exchange. Pipe-based irrigation systems that utilize surface waters may contribute to the dissemination of antibiotic-resistant bacteria in a similar manner. We conducted irrigation events at a perennial stream on a weekly basis for 1 month, and the concentrations of total heterotrophic bacteria, total coliforms, and fecal coliforms, as well as the concentrations of these bacterial groups that were resistant to ampicillin and tetracycline, were monitored at the intake water. Prior to each of the latter three events, residual pipe water was sampled and 6-in. sections of pipeline (coupons) were detached from the system, and biofilm from the inner-wall was removed and analyzed for total protein content and the above bacteria. Isolates of biofilm-associated bacteria were screened for resistance to a panel of seven antibiotics, representing five antibiotic classes. All of the monitored bacteria grew substantially in the residual water between irrigation events, and the biomass of the biofilm steadily increased from week to week. The percentages of biofilm-associated isolates that were resistant to antibiotics on the panel sometimes increased between events. Multiple-drug resistance was observed for all bacterial groups, most often for fecal coliforms, and the distributions of the numbers of antibiotics that the total coliforms and fecal coliforms were resistant to were subject to change from week to week. Results from this study highlight irrigation waters as a potential source for antibiotic-resistant bacteria, which can subsequently become incorporated into and proliferate within irrigation pipe-based biofilms.
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http://dx.doi.org/10.1007/s10661-015-5067-4DOI Listing
January 2016

Diversity of Listeria monocytogenes within a U.S. dairy herd, 2004-2010.

Foodborne Pathog Dis 2015 Oct 1;12(10):844-50. Epub 2015 Sep 1.

1 Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center , Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland.

Listeria monocytogenes, the causative agent of listeriosis, is frequently isolated from the environment. Dairy cows and dairy farm environments are reservoirs of this pathogen, where fecal shedding contributes to its environmental dispersal and contamination of milk, dairy products, and meat. The molecular diversity of 40 L. monocytogenes isolates representing 3 serogroups (1/2a, 1/2b, and 4b) collected between 2004 and 2010 from the feces of dairy cattle on a single dairy farm was assessed using a multivirulence locus sequence typing (MVLST) assay. The dairy farm L. monocytogenes MVLST patterns were compared to those from 138 strains isolated globally from clinical cases, foods, and the environment. Results of the study demonstrated that several distantly related L. monocytogenes strains persisted among members of the herd over the course of the study while other strains were transient. Furthermore, some strains isolated during this study appear to be distantly related to previously isolated L. monocytogenes while others are closely related to Epidemic Clones associated with human illness. This work demonstrates that dairy cows can be reservoirs of a diverse population of potentially human pathogenic L. monocytogenes that represents a risk to consumers of milk, dairy products, and meat.
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http://dx.doi.org/10.1089/fpd.2014.1886DOI Listing
October 2015
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