Jonathan G Frye | USDA Agricultural Research Service (original) (raw)

Papers by Jonathan G Frye

Tropical Medicine and Health, Feb 12, 2018

Journal of Food Safety, Jun 7, 2016

There are multiple ways to sample broiler chicken carcasses for the prevalence of Salmonella. A c... more There are multiple ways to sample broiler chicken carcasses for the prevalence of Salmonella. A common method in the USA is a whole carcass rinse and culture of an aliquot of the rinse. The objective of this study was to compare the sensitivity of the rinse aliquot method to overnight enrichment of the entire carcass in the rinse liquid. Fourteen replicate samplings of eight carcasses each were done at two commercial broiler processing plants. Carcasses were subjected to a whole carcass rinse in buffered peptone from which 30 mL was removed and added to 30 mL fresh buffered peptone (rinse aliquot sample). The aliquot sample and the carcass, in the remaining buffered peptone, were incubated overnight prior to standard selective enrichment and plating for Salmonella detection. Salmonella was detected in 15% of rinse aliquot samples and 59% of whole carcass enrichment samples. When detected by both methods, for the most part, the same serotypes were found on individual carcasses. Whole carcass enrichment was shown to be more sensitive than rinse aliquot method, and likely detects Salmonellae even when tightly bound to the carcass or present in very low numbers. As such, whole carcass enrichment is a useful research tool to determine Salmonella prevalence.Practical ApplicationsWhole broiler carcass enrichment is a more sensitive method for detection of Salmonella than whole carcass rinse and aliquot incubation. Logistical requirements, however, make it impractical for routine or large scale investigations. Whole carcass enrichment has utility for research purposes to determine relative sensitivity of other methods or for testing of broiler processing microbial interventions.

Applied and Environmental Microbiology, Dec 1, 2007

Three strains of Salmonella enterica serotype Enteritidis were compared to Salmonella enterica se... more Three strains of Salmonella enterica serotype Enteritidis were compared to Salmonella enterica serotype Heidelberg, Salmonella enterica serotype Newport, and Salmonella enterica serovar Typhimurium for growth in the presence of 240 antibiotics arranged within a commercial high-throughput phenotype microarray. The results show that antibiotic resistances were different for subpopulations of serotype Enteritidis separated only by genetic drift.

The Journal of applied poultry research, Dec 1, 2016

Abstract Salmonella and Campylobacter are frequent colonizers of the intestinal tracts of poultry... more Abstract Salmonella and Campylobacter are frequent colonizers of the intestinal tracts of poultry and have often been associated with human foodborne illness. The entry, transmission, and prevalence of both pathogens have been extensively studied in chickens but little information is available for turkeys. This project monitored turkey breeder hens and toms from d of hatch to 65 wk of age with the objective of determining routes of transmission for Salmonella and Campylobacter throughout the turkey production cycle. Breeder poults were separated by sex and then into 2 groups (control and inoculated) for each sex. The inoculated group was orally gavaged with marker strains of both Salmonella and Campylobacter. The inoculated groups (toms and hens) were placed on the opposite side of a growout house from the uninoculated groups. Fecal samples, intestinal samples and organs, feed, drinkers, and potential vectors such as insects and mice, were analyzed at different times until 65 wk. Monitoring showed that Campylobacter spread rapidly and cross-contaminated turkeys throughout the growout house. For both Salmonella and Campylobacter, naturally occurring strains that were first isolated in control groups at wk 3 and 4, respectively, outcompeted marker strains several wk post inoculation and persisted in the flock. The most common naturally occurring strains were C. jejuni (tetracycline resistant), C. coli (kanamycin resistant), and S. Agona. Campylobacter and Salmonella also were isolated from flies and from a mouse, confirming the importance of proper pest control and biosecurity to reduce the spread of the bacteria.

Genome Announcements, Oct 27, 2016

Here, we report a 4.87-Mbp draft genome sequence of the multidrug-resistant (MDR) Salmonella ente... more Here, we report a 4.87-Mbp draft genome sequence of the multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Bardo strain CRJJGF_00099, isolated from dairy cattle in 2005.

Genome Announcements, Oct 27, 2016

Here, we report a 4.70-Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar O... more Here, we report a 4.70-Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar Orion strain CRJJGF_00093, isolated from a dog in 2005.

Zoonoses and Public Health, Feb 4, 2015

SummaryThe presence and transfer of antimicrobial resistance genes from commensal bacteria in com... more SummaryThe presence and transfer of antimicrobial resistance genes from commensal bacteria in companion animals to more pathogenic bacteria may contribute to dissemination of antimicrobial resistance. The purpose of this study was to determine antimicrobial resistance gene content and the presence of genetic elements in antimicrobial resistant Escherichia coli from healthy companion animals. In our previous study, from May to August, 2007, healthy companion animals (155 dogs and 121 cats) from three veterinary clinics in the Athens, GA, USA area were sampled and multidrug‐resistant E. coli (n = 36; MDR, resistance to ≥2 antimicrobial classes) were obtained. Of the 25 different plasmid replicon types tested by PCR, at least one plasmid replicon type was detected in 94% (34/36) of the MDR E. coli; four isolates contained as many as five different plasmid replicons. Nine replicon types (FIA, FIB, FII, I2, A/C, U, P, I1 and HI2) were identified with FIB, FII, I2 as the most common pattern. The presence of class I integrons (intI) was detected in 61% (22/36) of the isolates with eight isolates containing aminoglycoside‐ and/or trimethoprim‐resistance genes in the variable cassette region of intI. Microarray analysis of a subset of the MDR E. coli (n = 9) identified the presence of genes conferring resistance to aminoglycosides (aac, aad, aph and strA/B), β‐lactams (ampC, cmy, tem and vim), chloramphenicol (cat), sulfonamides (sulI and sulII), tetracycline [tet(A), tet(B), tet(C), tet(D) and regulator, tetR] and trimethoprim (dfrA). Antimicrobial resistance to eight antimicrobials (ampicillin, cefoxitin, ceftiofur, amoxicillin/clavulanic acid, streptomycin, gentamicin, sulfisoxazole and trimethoprim‐sulfamethoxazole) and five plasmid replicons (FIA, FIB, FII, I1 and I2) were transferred via conjugation. The presence of antimicrobial resistance genes, intI and transferable plasmid replicons indicate that E. coli from companion animals may play an important role in the dissemination of antimicrobial resistance, particularly to human hosts during contact.

Journal of Clinical Microbiology, 2009

During 6 months, we obtained Enterobacteriaceae isolates from patients with gram-negative bactere... more During 6 months, we obtained Enterobacteriaceae isolates from patients with gram-negative bacteremia at a 1,250-bed teaching hospital in St. Louis, MO, and compared carbapenem susceptibilities with the presence of bla KPC , a transferable carbapenemase gene. Three (1.2%) out of 243 isolates were bla KPC positive. Ertapenem nonsusceptibility had a low positive predictive value.

Journal of Clinical Microbiology, Sep 1, 2008

An isolate of Proteus mirabilis recovered from blood cultures of a diabetic patient was shown to ... more An isolate of Proteus mirabilis recovered from blood cultures of a diabetic patient was shown to be resistant to imipenem, meropenem, and ertapenem by disk diffusion susceptibility testing. Amplification of whole-cell and/or plasmid DNA recovered from the isolate with primers specific for the bla KPC carbapenemase gene produced an amplicon of the expected size which was confirmed to be bla KPC-2 by sequence analysis. Transformation of a susceptible Escherichia coli host with plasmid preparations from the isolate generated a transformant for which the MICs of all of the carbapenems tested were increased three-to fourfold. We believe this to be the first report of carbapenem resistance in P. mirabilis caused by the acquisition of bla KPC .

Scientific Reports, Jun 16, 2021

Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable... more Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable whole genome sequencing, in silico approaches to assessing AMR gene content can be used to detect known resistance mechanisms and potentially identify novel mechanisms. To enable accurate assessment of AMR gene content, as part of a multi-agency collaboration, NCBI developed a comprehensive AMR gene database, the Bacterial Antimicrobial Resistance Reference Gene Database and the AMR gene detection tool AMRFinder. Here, we describe the expansion of the Reference Gene Database, now called the Reference Gene Catalog, to include putative acid, biocide, metal, stress resistance genes, in addition to virulence genes and species-specific point mutations. Genes and point mutations are classified by broad functions, as well as more detailed functions. As we have expanded both the functional repertoire of identified genes and functionality, NCBI released a new version of AMRFinder, known as AMRFinderPlus. This new tool allows users the option to utilize only the core set of AMR elements, or include stress response and virulence genes, too. AMRFinderPlus can detect acquired genes and point mutations in both protein and nucleotide sequence. In addition, the evidence used to identify the gene has been expanded to include whether nucleotide or protein sequence was used, its location in the contig, and presence of an internal stop codon. These database improvements and functional expansions will enable increased precision in identifying AMR genes, linking AMR genotypes and phenotypes, and determining possible relationships between AMR, virulence, and stress response. Antimicrobial resistance (AMR) is a significant public health threat, resulting in tens of thousands of deaths annually from antimicrobial resistant infections in the United States alone (https:// www. cdc. gov/ drugr esist ance/ threat-report-2013/ index. html). With the advent of affordable whole genome sequencing, often for surveillance purposes 1 and as part of existing surveillance programs 2 , in silico approaches to assess AMR gene content are routinely used 3,4. Identifying AMR gene content can lead to the discovery of novel resistance mechanisms 5 , and also can be used to predict resistance phenotypes without time-consuming phenotypic methods 6,7. To enable accurate assessment of AMR gene content, as part of a multi-agency collaboration, NCBI previously developed a comprehensive AMR gene database, the Bacterial Antimicrobial Resistance Reference Gene Database, and AMRFinder, an AMR gene detection tool 8. Here, we describe the expansion of the Reference Gene Database, now called the Reference Gene Catalog, to include acid, biocide, metal, and heat resistance genes, as well as virulence genes. Users have the option to use only the core set of AMR genes, or include these genes too.

Emerging Infectious Diseases, Sep 1, 2014

Molecular Microbiology, Jan 28, 2013

To cause disease, Salmonella must invade the intestinal epithelium employing genes encoded within... more To cause disease, Salmonella must invade the intestinal epithelium employing genes encoded within Salmonella Pathogenicity Island 1 (SPI1). We show here that propionate, a fatty acid abundant in the intestine of animals, repressed SPI1 at physiologically relevant concentration and pH, reducing expression of SPI1 transcriptional regulators and consequently decreasing expression and secretion of effector proteins, leading to reduced bacterial penetration of cultured epithelial cells. Essential to repression was hilD, which occupies the apex of the regulatory cascade within SPI1, as loss of only this gene among those of the regulon prevented repression of SPI1 transcription by propionate. Regulation through hilD, however, was achieved through the control of neither transcription nor translation. Instead, growth of Salmonella in propionate significantly reduced the stability of HilD. Extending protein half-life using a Lon protease mutant demonstrated that protein stability itself did not dictate the effects of propionate and suggested modification of HilD with subsequent degradation as the means of action. Furthermore, repression was significantly lessened in a mutant unable to produce propionyl-CoA, while further metabolism of propionyl-CoA appeared not to be required. These results suggest a mechanism of control of Salmonella virulence in which HilD is post-translationally modified using the high energy intermediate propionyl-CoA.

Journal of Food Protection, Feb 1, 2023

Letters in Applied Microbiology, May 10, 2020

Significance and Impact of the Study: Surface water is prone to bacterial contamination as it rec... more Significance and Impact of the Study: Surface water is prone to bacterial contamination as it receives wastes and pollutants from human and animal sources, and contaminated water may expose local populations to health risks. Studies have demonstrated the widespread distribution of pathogenic and antimicrobial resistant bacteria in surface waters of both developing and developed countries, confirming the importance of environmental waters as a reservoir for these bacteria and the need for more attention on the environmental bacteria for emerging antimicrobial resistance. This review discusses the prevalence and diversity of pathogenic and commensal bacteria, namely Salmonella, E. coli, and Enterococcus, present in surface waters and provides a basic understanding of the occurrence and persistence of antimicrobial resistance in these bacteria.

Journal of Applied Microbiology, Jan 20, 2020

Aim: It is well-known that enterococci are abundant in the environment; however, the role of surf... more Aim: It is well-known that enterococci are abundant in the environment; however, the role of surface water as a reservoir of antimicrobial-resistant enterococci remains largely undefined. In this study, surface water samples were collected over a 2-year period from the Upper Oconee watershed, Athens, GA to examine enterococci and their antimicrobial resistance. Methods and Results: Approximately 97% (445/458) of the samples were positive for enterococci and a total of 637 enterococci were isolated. The predominant species were Enterococcus casseliflavus (33Á6%) followed by Enterococcus faecalis (26Á5%) and Enterococcus hirae (13Á2%). Regardless of species, the highest levels of resistance were to lincomycin (88Á5%) and tetracycline (13%); isolates also exhibited resistance to newer antimicrobials, daptomycin (8Á9%) and tigecycline (6Á4%). Multidrug resistance (resistance ≥3 antimicrobial classes) was observed to as many as five classes of antimicrobials. Resistant enterococci appeared to be randomly dispersed over the seasons rather than clustered by species or antimicrobial resistance. Conclusions: This study demonstrated that surface waters contain a large population of diverse species of antimicrobial-resistant enterococci, including resistance to new antimicrobials. Significance and Impact of the Study: These results may indicate the potential of human intestinal illness and/or colonization of the human gut with resistant enterococci as enterococci correlate with increased disease risk to humans during recreational exposure to water.

Applied and Environmental Microbiology, May 24, 2022

Salmonella has been traditionally considered a foodborne pathogen, as it is one of the most commo... more Salmonella has been traditionally considered a foodborne pathogen, as it is one of the most common etiologies of foodborne illnesses worldwide; however, recent Salmonella outbreaks attributed to fresh produce and water suggest a potential environmental source of Salmonella that causes some human illnesses. Here, we investigated the prevalence, diversity, and antimicrobial resistance of Salmonella isolated from a mixed-use watershed in Georgia, USA, in order to enhance the overall understanding of waterborne Salmonella .

Poultry Science, Nov 1, 2020

Quail (Coturnix japonica) is processed and marketed as fresh meat, with limited shelf life. The o... more Quail (Coturnix japonica) is processed and marketed as fresh meat, with limited shelf life. The objective of this study was to evaluate the efficacy of antimicrobial interventions during slaughter on reducing Salmonella and Campylobacter contamination and to determine the microbiological shelf life of quail during refrigerated (4 C) storage. Three antimicrobials, peracetic acid (400 ppm; PAA), Citrilow (pH 1.2), and Cecure (cetylpyridinium chloride [CPC], 450 ppm), along with a water and no-treatment control were evaluated. Quail carcasses (n 5 75) were inoculated with a cocktail of nalidixic acid-resistant Salmonella Typhimurium and gentamicin-resistant Campylobacter coli. After 30 min of attachment time, quail carcasses were submerged in each antimicrobial solution for 20 s with air agitation. Noninoculated quail carcasses (n 5 25) were similarly treated, packaged, and stored under refrigeration (4 C). Aerobic plate counts (APC), psychrotroph counts (PC), Enterobacteriaceae counts (ENT), total coliform counts (TCC), and Escherichia coli counts on quail carcasses were determined on 1, 4, 7, and 10 d. Salmonella and Campylobacter populations were determined by plating on Petrifilm APC supplemented with 200-ppm nalidixic acid and Campy Cefex agar supplemented with 200-ppm gentamycin, respectively. No significant reductions in (P. 0.01 log cfu/mL) in APC, PC, ENT, TCC, and E. coli counts were observed on carcasses submerged in water. However, treatments with PAA, Citrilow, and CPC significantly reduced (P 0.05) Salmonella and Campylobacter coli contamination. Citrilow showed greater (P 0.05) reduction in Salmonella and Campylobacter population (1.90 and 3.82 log cfu/mL reduction, respectively) to PAA and CPC. Greater (P 0.05) reductions in APC, PC, ENT, TCC, and E. coli counts (2.22, 1.26, 1.47, 1.52, and 1.59 log cfu/mL, respectively) were obtained with the application of CPC. Application of antimicrobial interventions resulted in a reduction in Campylobacter and Salmonella, APC, PC, and ENT populations after treatments (day 0) and throughout the storage period (day 10). Use of antimicrobial interventions after slaughter can improve the microbiological safety and shelf life of quail.

Genome Announcements, Oct 27, 2016

Here, we report a 4.72-Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar B... more Here, we report a 4.72-Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar Blockley strain CRJJGF_00147, isolated from chicken rinse in 2009.

Journal of Food Protection, Jul 1, 2014

Salmonella enterica is not able to grow at water activity (a w) levels below 0.94, but it can sur... more Salmonella enterica is not able to grow at water activity (a w) levels below 0.94, but it can survive in low-a w foods for long periods of time. Temperature, a w , substrate, and serotype affect its persistence. The aim of this study was to evaluate the influence of temperature and a w on the relative persistence among four serotypes of Salmonella enterica in low-a w whey protein powder. Whey protein powder was equilibrated to a w s 0.18 ¡ 0.02 and 0.54 ¡ 0.03, inoculated with a cocktail of Salmonella serovars (Agona, Tennessee, Montevideo, and Typhimurium), vacuum sealed, and stored at 36uC for 6 months and at 70uC for 48 h. Presumptive Salmonella colonies (30 to 32) were randomly picked from each plate at the end of each survival study. PCR multiplex serotyping was used to identify the isolates. A multinomial mixed logistic model with Salmonella Tennessee as a reference was used to test for significant differences in frequency distribution of the surviving serotypes. Salmonella Tennessee and Salmonella Agona were the most prevalent surviving serotypes, followed in decreasing order by Salmonella Montevideo and Salmonella Typhimurium. Statistical analysis indicated that temperature (P~0.003) and a w (P~0.012) influenced the relative prevalence of the Salmonella serotypes. If other environmental conditions are equal, Salmonella Tennessee is better able to survive than Salmonella Montevideo and Salmonella Typhimurium at higher temperatures and higher a w levels in low-a w whey protein powder held at 36 and 70uC. The relative prevalence of Salmonella Agona to Salmonella Tennessee did not change with increasing temperature (P~0.211) or a w (P~0.453). These results should be considered in risk assessment and when developing predictive models for survival of Salmonella in low-a w foods.

Tropical Medicine and Health, Feb 12, 2018

Journal of Food Safety, Jun 7, 2016

There are multiple ways to sample broiler chicken carcasses for the prevalence of Salmonella. A c... more There are multiple ways to sample broiler chicken carcasses for the prevalence of Salmonella. A common method in the USA is a whole carcass rinse and culture of an aliquot of the rinse. The objective of this study was to compare the sensitivity of the rinse aliquot method to overnight enrichment of the entire carcass in the rinse liquid. Fourteen replicate samplings of eight carcasses each were done at two commercial broiler processing plants. Carcasses were subjected to a whole carcass rinse in buffered peptone from which 30 mL was removed and added to 30 mL fresh buffered peptone (rinse aliquot sample). The aliquot sample and the carcass, in the remaining buffered peptone, were incubated overnight prior to standard selective enrichment and plating for Salmonella detection. Salmonella was detected in 15% of rinse aliquot samples and 59% of whole carcass enrichment samples. When detected by both methods, for the most part, the same serotypes were found on individual carcasses. Whole carcass enrichment was shown to be more sensitive than rinse aliquot method, and likely detects Salmonellae even when tightly bound to the carcass or present in very low numbers. As such, whole carcass enrichment is a useful research tool to determine Salmonella prevalence.Practical ApplicationsWhole broiler carcass enrichment is a more sensitive method for detection of Salmonella than whole carcass rinse and aliquot incubation. Logistical requirements, however, make it impractical for routine or large scale investigations. Whole carcass enrichment has utility for research purposes to determine relative sensitivity of other methods or for testing of broiler processing microbial interventions.

Applied and Environmental Microbiology, Dec 1, 2007

Three strains of Salmonella enterica serotype Enteritidis were compared to Salmonella enterica se... more Three strains of Salmonella enterica serotype Enteritidis were compared to Salmonella enterica serotype Heidelberg, Salmonella enterica serotype Newport, and Salmonella enterica serovar Typhimurium for growth in the presence of 240 antibiotics arranged within a commercial high-throughput phenotype microarray. The results show that antibiotic resistances were different for subpopulations of serotype Enteritidis separated only by genetic drift.

The Journal of applied poultry research, Dec 1, 2016

Abstract Salmonella and Campylobacter are frequent colonizers of the intestinal tracts of poultry... more Abstract Salmonella and Campylobacter are frequent colonizers of the intestinal tracts of poultry and have often been associated with human foodborne illness. The entry, transmission, and prevalence of both pathogens have been extensively studied in chickens but little information is available for turkeys. This project monitored turkey breeder hens and toms from d of hatch to 65 wk of age with the objective of determining routes of transmission for Salmonella and Campylobacter throughout the turkey production cycle. Breeder poults were separated by sex and then into 2 groups (control and inoculated) for each sex. The inoculated group was orally gavaged with marker strains of both Salmonella and Campylobacter. The inoculated groups (toms and hens) were placed on the opposite side of a growout house from the uninoculated groups. Fecal samples, intestinal samples and organs, feed, drinkers, and potential vectors such as insects and mice, were analyzed at different times until 65 wk. Monitoring showed that Campylobacter spread rapidly and cross-contaminated turkeys throughout the growout house. For both Salmonella and Campylobacter, naturally occurring strains that were first isolated in control groups at wk 3 and 4, respectively, outcompeted marker strains several wk post inoculation and persisted in the flock. The most common naturally occurring strains were C. jejuni (tetracycline resistant), C. coli (kanamycin resistant), and S. Agona. Campylobacter and Salmonella also were isolated from flies and from a mouse, confirming the importance of proper pest control and biosecurity to reduce the spread of the bacteria.

Genome Announcements, Oct 27, 2016

Here, we report a 4.87-Mbp draft genome sequence of the multidrug-resistant (MDR) Salmonella ente... more Here, we report a 4.87-Mbp draft genome sequence of the multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Bardo strain CRJJGF_00099, isolated from dairy cattle in 2005.

Genome Announcements, Oct 27, 2016

Here, we report a 4.70-Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar O... more Here, we report a 4.70-Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar Orion strain CRJJGF_00093, isolated from a dog in 2005.

Zoonoses and Public Health, Feb 4, 2015

SummaryThe presence and transfer of antimicrobial resistance genes from commensal bacteria in com... more SummaryThe presence and transfer of antimicrobial resistance genes from commensal bacteria in companion animals to more pathogenic bacteria may contribute to dissemination of antimicrobial resistance. The purpose of this study was to determine antimicrobial resistance gene content and the presence of genetic elements in antimicrobial resistant Escherichia coli from healthy companion animals. In our previous study, from May to August, 2007, healthy companion animals (155 dogs and 121 cats) from three veterinary clinics in the Athens, GA, USA area were sampled and multidrug‐resistant E. coli (n = 36; MDR, resistance to ≥2 antimicrobial classes) were obtained. Of the 25 different plasmid replicon types tested by PCR, at least one plasmid replicon type was detected in 94% (34/36) of the MDR E. coli; four isolates contained as many as five different plasmid replicons. Nine replicon types (FIA, FIB, FII, I2, A/C, U, P, I1 and HI2) were identified with FIB, FII, I2 as the most common pattern. The presence of class I integrons (intI) was detected in 61% (22/36) of the isolates with eight isolates containing aminoglycoside‐ and/or trimethoprim‐resistance genes in the variable cassette region of intI. Microarray analysis of a subset of the MDR E. coli (n = 9) identified the presence of genes conferring resistance to aminoglycosides (aac, aad, aph and strA/B), β‐lactams (ampC, cmy, tem and vim), chloramphenicol (cat), sulfonamides (sulI and sulII), tetracycline [tet(A), tet(B), tet(C), tet(D) and regulator, tetR] and trimethoprim (dfrA). Antimicrobial resistance to eight antimicrobials (ampicillin, cefoxitin, ceftiofur, amoxicillin/clavulanic acid, streptomycin, gentamicin, sulfisoxazole and trimethoprim‐sulfamethoxazole) and five plasmid replicons (FIA, FIB, FII, I1 and I2) were transferred via conjugation. The presence of antimicrobial resistance genes, intI and transferable plasmid replicons indicate that E. coli from companion animals may play an important role in the dissemination of antimicrobial resistance, particularly to human hosts during contact.

Journal of Clinical Microbiology, 2009

During 6 months, we obtained Enterobacteriaceae isolates from patients with gram-negative bactere... more During 6 months, we obtained Enterobacteriaceae isolates from patients with gram-negative bacteremia at a 1,250-bed teaching hospital in St. Louis, MO, and compared carbapenem susceptibilities with the presence of bla KPC , a transferable carbapenemase gene. Three (1.2%) out of 243 isolates were bla KPC positive. Ertapenem nonsusceptibility had a low positive predictive value.

Journal of Clinical Microbiology, Sep 1, 2008

An isolate of Proteus mirabilis recovered from blood cultures of a diabetic patient was shown to ... more An isolate of Proteus mirabilis recovered from blood cultures of a diabetic patient was shown to be resistant to imipenem, meropenem, and ertapenem by disk diffusion susceptibility testing. Amplification of whole-cell and/or plasmid DNA recovered from the isolate with primers specific for the bla KPC carbapenemase gene produced an amplicon of the expected size which was confirmed to be bla KPC-2 by sequence analysis. Transformation of a susceptible Escherichia coli host with plasmid preparations from the isolate generated a transformant for which the MICs of all of the carbapenems tested were increased three-to fourfold. We believe this to be the first report of carbapenem resistance in P. mirabilis caused by the acquisition of bla KPC .

Scientific Reports, Jun 16, 2021

Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable... more Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable whole genome sequencing, in silico approaches to assessing AMR gene content can be used to detect known resistance mechanisms and potentially identify novel mechanisms. To enable accurate assessment of AMR gene content, as part of a multi-agency collaboration, NCBI developed a comprehensive AMR gene database, the Bacterial Antimicrobial Resistance Reference Gene Database and the AMR gene detection tool AMRFinder. Here, we describe the expansion of the Reference Gene Database, now called the Reference Gene Catalog, to include putative acid, biocide, metal, stress resistance genes, in addition to virulence genes and species-specific point mutations. Genes and point mutations are classified by broad functions, as well as more detailed functions. As we have expanded both the functional repertoire of identified genes and functionality, NCBI released a new version of AMRFinder, known as AMRFinderPlus. This new tool allows users the option to utilize only the core set of AMR elements, or include stress response and virulence genes, too. AMRFinderPlus can detect acquired genes and point mutations in both protein and nucleotide sequence. In addition, the evidence used to identify the gene has been expanded to include whether nucleotide or protein sequence was used, its location in the contig, and presence of an internal stop codon. These database improvements and functional expansions will enable increased precision in identifying AMR genes, linking AMR genotypes and phenotypes, and determining possible relationships between AMR, virulence, and stress response. Antimicrobial resistance (AMR) is a significant public health threat, resulting in tens of thousands of deaths annually from antimicrobial resistant infections in the United States alone (https:// www. cdc. gov/ drugr esist ance/ threat-report-2013/ index. html). With the advent of affordable whole genome sequencing, often for surveillance purposes 1 and as part of existing surveillance programs 2 , in silico approaches to assess AMR gene content are routinely used 3,4. Identifying AMR gene content can lead to the discovery of novel resistance mechanisms 5 , and also can be used to predict resistance phenotypes without time-consuming phenotypic methods 6,7. To enable accurate assessment of AMR gene content, as part of a multi-agency collaboration, NCBI previously developed a comprehensive AMR gene database, the Bacterial Antimicrobial Resistance Reference Gene Database, and AMRFinder, an AMR gene detection tool 8. Here, we describe the expansion of the Reference Gene Database, now called the Reference Gene Catalog, to include acid, biocide, metal, and heat resistance genes, as well as virulence genes. Users have the option to use only the core set of AMR genes, or include these genes too.

Emerging Infectious Diseases, Sep 1, 2014

Molecular Microbiology, Jan 28, 2013

To cause disease, Salmonella must invade the intestinal epithelium employing genes encoded within... more To cause disease, Salmonella must invade the intestinal epithelium employing genes encoded within Salmonella Pathogenicity Island 1 (SPI1). We show here that propionate, a fatty acid abundant in the intestine of animals, repressed SPI1 at physiologically relevant concentration and pH, reducing expression of SPI1 transcriptional regulators and consequently decreasing expression and secretion of effector proteins, leading to reduced bacterial penetration of cultured epithelial cells. Essential to repression was hilD, which occupies the apex of the regulatory cascade within SPI1, as loss of only this gene among those of the regulon prevented repression of SPI1 transcription by propionate. Regulation through hilD, however, was achieved through the control of neither transcription nor translation. Instead, growth of Salmonella in propionate significantly reduced the stability of HilD. Extending protein half-life using a Lon protease mutant demonstrated that protein stability itself did not dictate the effects of propionate and suggested modification of HilD with subsequent degradation as the means of action. Furthermore, repression was significantly lessened in a mutant unable to produce propionyl-CoA, while further metabolism of propionyl-CoA appeared not to be required. These results suggest a mechanism of control of Salmonella virulence in which HilD is post-translationally modified using the high energy intermediate propionyl-CoA.

Journal of Food Protection, Feb 1, 2023

Letters in Applied Microbiology, May 10, 2020

Significance and Impact of the Study: Surface water is prone to bacterial contamination as it rec... more Significance and Impact of the Study: Surface water is prone to bacterial contamination as it receives wastes and pollutants from human and animal sources, and contaminated water may expose local populations to health risks. Studies have demonstrated the widespread distribution of pathogenic and antimicrobial resistant bacteria in surface waters of both developing and developed countries, confirming the importance of environmental waters as a reservoir for these bacteria and the need for more attention on the environmental bacteria for emerging antimicrobial resistance. This review discusses the prevalence and diversity of pathogenic and commensal bacteria, namely Salmonella, E. coli, and Enterococcus, present in surface waters and provides a basic understanding of the occurrence and persistence of antimicrobial resistance in these bacteria.

Journal of Applied Microbiology, Jan 20, 2020

Aim: It is well-known that enterococci are abundant in the environment; however, the role of surf... more Aim: It is well-known that enterococci are abundant in the environment; however, the role of surface water as a reservoir of antimicrobial-resistant enterococci remains largely undefined. In this study, surface water samples were collected over a 2-year period from the Upper Oconee watershed, Athens, GA to examine enterococci and their antimicrobial resistance. Methods and Results: Approximately 97% (445/458) of the samples were positive for enterococci and a total of 637 enterococci were isolated. The predominant species were Enterococcus casseliflavus (33Á6%) followed by Enterococcus faecalis (26Á5%) and Enterococcus hirae (13Á2%). Regardless of species, the highest levels of resistance were to lincomycin (88Á5%) and tetracycline (13%); isolates also exhibited resistance to newer antimicrobials, daptomycin (8Á9%) and tigecycline (6Á4%). Multidrug resistance (resistance ≥3 antimicrobial classes) was observed to as many as five classes of antimicrobials. Resistant enterococci appeared to be randomly dispersed over the seasons rather than clustered by species or antimicrobial resistance. Conclusions: This study demonstrated that surface waters contain a large population of diverse species of antimicrobial-resistant enterococci, including resistance to new antimicrobials. Significance and Impact of the Study: These results may indicate the potential of human intestinal illness and/or colonization of the human gut with resistant enterococci as enterococci correlate with increased disease risk to humans during recreational exposure to water.

Applied and Environmental Microbiology, May 24, 2022

Salmonella has been traditionally considered a foodborne pathogen, as it is one of the most commo... more Salmonella has been traditionally considered a foodborne pathogen, as it is one of the most common etiologies of foodborne illnesses worldwide; however, recent Salmonella outbreaks attributed to fresh produce and water suggest a potential environmental source of Salmonella that causes some human illnesses. Here, we investigated the prevalence, diversity, and antimicrobial resistance of Salmonella isolated from a mixed-use watershed in Georgia, USA, in order to enhance the overall understanding of waterborne Salmonella .

Poultry Science, Nov 1, 2020

Quail (Coturnix japonica) is processed and marketed as fresh meat, with limited shelf life. The o... more Quail (Coturnix japonica) is processed and marketed as fresh meat, with limited shelf life. The objective of this study was to evaluate the efficacy of antimicrobial interventions during slaughter on reducing Salmonella and Campylobacter contamination and to determine the microbiological shelf life of quail during refrigerated (4 C) storage. Three antimicrobials, peracetic acid (400 ppm; PAA), Citrilow (pH 1.2), and Cecure (cetylpyridinium chloride [CPC], 450 ppm), along with a water and no-treatment control were evaluated. Quail carcasses (n 5 75) were inoculated with a cocktail of nalidixic acid-resistant Salmonella Typhimurium and gentamicin-resistant Campylobacter coli. After 30 min of attachment time, quail carcasses were submerged in each antimicrobial solution for 20 s with air agitation. Noninoculated quail carcasses (n 5 25) were similarly treated, packaged, and stored under refrigeration (4 C). Aerobic plate counts (APC), psychrotroph counts (PC), Enterobacteriaceae counts (ENT), total coliform counts (TCC), and Escherichia coli counts on quail carcasses were determined on 1, 4, 7, and 10 d. Salmonella and Campylobacter populations were determined by plating on Petrifilm APC supplemented with 200-ppm nalidixic acid and Campy Cefex agar supplemented with 200-ppm gentamycin, respectively. No significant reductions in (P. 0.01 log cfu/mL) in APC, PC, ENT, TCC, and E. coli counts were observed on carcasses submerged in water. However, treatments with PAA, Citrilow, and CPC significantly reduced (P 0.05) Salmonella and Campylobacter coli contamination. Citrilow showed greater (P 0.05) reduction in Salmonella and Campylobacter population (1.90 and 3.82 log cfu/mL reduction, respectively) to PAA and CPC. Greater (P 0.05) reductions in APC, PC, ENT, TCC, and E. coli counts (2.22, 1.26, 1.47, 1.52, and 1.59 log cfu/mL, respectively) were obtained with the application of CPC. Application of antimicrobial interventions resulted in a reduction in Campylobacter and Salmonella, APC, PC, and ENT populations after treatments (day 0) and throughout the storage period (day 10). Use of antimicrobial interventions after slaughter can improve the microbiological safety and shelf life of quail.

Genome Announcements, Oct 27, 2016

Here, we report a 4.72-Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar B... more Here, we report a 4.72-Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar Blockley strain CRJJGF_00147, isolated from chicken rinse in 2009.

Journal of Food Protection, Jul 1, 2014

Salmonella enterica is not able to grow at water activity (a w) levels below 0.94, but it can sur... more Salmonella enterica is not able to grow at water activity (a w) levels below 0.94, but it can survive in low-a w foods for long periods of time. Temperature, a w , substrate, and serotype affect its persistence. The aim of this study was to evaluate the influence of temperature and a w on the relative persistence among four serotypes of Salmonella enterica in low-a w whey protein powder. Whey protein powder was equilibrated to a w s 0.18 ¡ 0.02 and 0.54 ¡ 0.03, inoculated with a cocktail of Salmonella serovars (Agona, Tennessee, Montevideo, and Typhimurium), vacuum sealed, and stored at 36uC for 6 months and at 70uC for 48 h. Presumptive Salmonella colonies (30 to 32) were randomly picked from each plate at the end of each survival study. PCR multiplex serotyping was used to identify the isolates. A multinomial mixed logistic model with Salmonella Tennessee as a reference was used to test for significant differences in frequency distribution of the surviving serotypes. Salmonella Tennessee and Salmonella Agona were the most prevalent surviving serotypes, followed in decreasing order by Salmonella Montevideo and Salmonella Typhimurium. Statistical analysis indicated that temperature (P~0.003) and a w (P~0.012) influenced the relative prevalence of the Salmonella serotypes. If other environmental conditions are equal, Salmonella Tennessee is better able to survive than Salmonella Montevideo and Salmonella Typhimurium at higher temperatures and higher a w levels in low-a w whey protein powder held at 36 and 70uC. The relative prevalence of Salmonella Agona to Salmonella Tennessee did not change with increasing temperature (P~0.211) or a w (P~0.453). These results should be considered in risk assessment and when developing predictive models for survival of Salmonella in low-a w foods.