184 results on '"Dudley, Edward G."'
Search Results
2. High resistance of fluoroquinolone and macrolide reported in avian pathogenic Escherichia coli isolates from the humid subtropical regions of Pakistan
- Author
-
Jalil, Amna, Masood, Saleha, Ain, Quratul, Andleeb, Saadia, Dudley, Edward G, and Adnan, Fazal
- Published
- 2023
- Full Text
- View/download PDF
3. Fluoroquinolone sales in food animals and quinolone resistance in non-typhoidal Salmonella from retail meats: United States, 2009–2018
- Author
-
Yin, Xin, Dudley, Edward G., Pinto, Casey N., and M'ikanatha, Nkuchia M.
- Published
- 2022
- Full Text
- View/download PDF
4. Genomic diversity of Campylobacter jejuni and Campylobacter coli isolated from the Ethiopian dairy supply chain.
- Author
-
Admasie, Abera, Wei, Xiaoyuan, Johnson, Beth, Burns, Logan, Pawar, Preeti, Aurand-Cravens, Ashley, Voloshchuk, Olena, Dudley, Edward G., Sisay Tessema, Tesfaye, Zewdu, Ashagrie, and Kovac, Jasna
- Abstract
Campylobacteriosis outbreaks have previously been linked to dairy foods. While the genetic diversity of Campylobacter is well understood in high-income countries, it is largely unknown in low-income countries, such as Ethiopia. This study therefore aimed to conduct the first genomic characterization of Campylobacter isolates from the Ethiopian dairy supply chain to aid in future epidemiological studies. Fourteen C. jejuni and four C. coli isolates were whole genome sequenced using an Illumina platform. Sequences were analyzed using the bioinformatics tools in the GalaxyTrakr platform to identify MLST types, and single nucleotide polymorphisms, and infer phylogenetic relationships among the studied isolates. Assembled genomes were further screened to detect antimicrobial resistance and virulence gene sequences. Among 14 C. jejuni, ST 2084 and ST 51, which belong to the clonal complexes ST-353 and ST-443, respectively, were identified. Among the 4 sequenced C. coli isolates, two isolates belonged to ST 1628 and two to ST 830 from the clonal complex ST-828. The isolates of C. jejuni ST 2084 and ST 51 carried β-lactam resistance gene blaOXA-605, a fluoroquinolone resistance-associated mutation T86I in the gryA gene, and a macrolide resistance-associated mutation A103V in 50S L22. Only ST 2084 isolates carried the tetracycline resistance gene tetO. Conversely, all four C. coli ST 830 and ST 1628 isolates carried tetO, but only ST 1628 isolates also carried blaOXA-605. Lastly, C. jejuni ST 2084 isolates carried a total of 89 virulence genes, and ST 51 isolates carried up to 88 virulence genes. Among C. coli, ST 830 isolates carried 71 genes involved in virulence, whereas two ST 1628 isolates carried up to 82 genes involved in virulence. Isolates from all identified STs have previously been isolated from human clinical cases, demonstrating a potential food safety concern. This finding warrants further monitoring of Campylobacter in dairy foods in Ethiopia to better understand and manage the risks associated with Campylobacter contamination and transmission. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
5. Microbial synergy between Pichia kudriazevii YS201 and Bacillus subtilis BS38 improves pulp degradation and aroma production in cocoa pulp simulation medium
- Author
-
Ouattara, Honoré G., Elias, Ryan J., and Dudley, Edward G.
- Published
- 2020
- Full Text
- View/download PDF
6. Exploring Antimicrobial Resistance Profiles of E. coli Isolates in Dairy Cattle: A Baseline Study across Dairy Farms with Varied Husbandry Practices in Puerto Rico.
- Author
-
Malavez, Yadira, Nieves-Miranda, Sharon M., Loperena Gonzalez, Paola N., Padin-Lopez, Adrian F., Xiaoli, Lingzi, and Dudley, Edward G.
- Subjects
ESCHERICHIA coli ,DAIRY farms ,DRUG resistance in microorganisms ,AGRICULTURE ,DAIRY cattle ,DAIRY farm management - Abstract
Antimicrobial treatment in livestock can contribute to the emergence and spread of antimicrobial-resistant (AMR) microorganisms. Despite substantial surveillance of AMR bacteria in the continental United States, the prevalence of these AMR organisms in U.S. territories, such as Puerto Rico, remains understudied. The goals of this research included obtaining baseline data on the antimicrobial profile of E. coli isolates from Puerto Rico dairy farms with different husbandry practices. Seventy-nine fecal samples were collected from two types of conventional dairy farms: those that fed calves with tank milk and those that fed calves with waste milk. These samples were collected from the animals' rectums, culture, and subsequently confirmed through biochemical tests. Out of these samples, 32 isolates were analyzed phenotypically and genotypically to elucidate their AMR profiles. The results underscore a discrepancy in the occurrence of antimicrobial resistance genes between calves and adult cattle. Notably, waste milk-fed calves exhibited a significantly higher prevalence of antibiotic-resistant E. coli when compared to their tank milk-fed counterparts. These disparities emphasize the need for more comprehensive investigations to determine causative factors. These results underscore the urgency of comprehensive strategies to raise awareness about how management practices influence antimicrobial resistance, shifting the focus from treatment to prevention. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
7. Food Microbiology: Fundamentals and Frontiers, 5th Edition
- Author
-
Dudley, Edward G.
- Subjects
Food Microbiology: Fundamentals and Frontiers, 5th ed. (Nonfiction work) -- Doyle, Michael P. -- Diez-Gonzalez, Francisco -- Hill, Colin ,Books -- Book reviews ,Health - Abstract
Michael P. Doyle, Francisco Diez-Gonzalez, Colin Hill, editors; ASM Press, Washington, DC, USA, 2019; ISBN: 978-1555819965; Pages: 1,100; Price: US $200.00 The most recent edition of Food Microbiology: Fundamentals and [...]
- Published
- 2022
8. Global Distribution of O Serotypes and Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Collected From the Blood of Patients With Bacteremia Across Multiple Surveillance Studies.
- Author
-
Weerdenburg, Eveline, Davies, Todd, Morrow, Brian, Zomer, Aldert L, Hermans, Peter, Go, Oscar, Spiessens, Bart, van den Hoven, Thijs, Geet, Gunter van, Aitabi, Moussa, DebRoy, Chitrita, Dudley, Edward G, Bonten, Marc, Poolman, Jan, and Geurtsen, Jeroen
- Subjects
ESCHERICHIA coli ,BACTEREMIA ,RETROSPECTIVE studies ,SEROTYPES ,RISK assessment ,MULTIDRUG resistance ,INTESTINAL parasites ,DESCRIPTIVE statistics ,DISEASE risk factors ,DISEASE complications - Abstract
Background Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of bacteremia worldwide, with older populations having increased risk of invasive bacterial disease. Increasing resistance to first-line antibiotics and emergence of multidrug-resistant (MDR) strains represent major treatment challenges. ExPEC O serotypes are key targets for potential multivalent conjugate vaccine development. Therefore, we evaluated the O serotype distribution and antibiotic resistance profiles of ExPEC strains causing bloodstream infections across 4 regions. Methods Blood culture isolates from patients aged ≥60 years collected during 5 retrospective E. coli surveillance studies in Europe, North America, Asia-Pacific, and South America (2011–2017) were analyzed. Isolates were O serotyped by agglutination; O genotyping was performed for nontypeable isolates. Antimicrobial susceptibility testing was also conducted. Results Among 3217 ExPEC blood culture isolates, the most ubiquitous O serotype was O25 (n = 737 [22.9%]), followed by O2, O6, O1, O75, O15, O8, O16, O4, O18, O77 group, O153, O9, O101/O162, O86, and O13 (prevalence of ≥1%). The prevalence of these O serotypes was generally consistent across regions, apart from South America; together, these 16 O serotypes represented 77.6% of all ExPEC bacteremia isolates analyzed. The overall MDR frequency was 10.7%, with limited variation between regions. Within the MDR subset (n = 345), O25 showed a dominant prevalence of 63.2% (n = 218). Conclusions Predominant O serotypes among ExPEC bacteremia isolates are widespread across different regions. O25 was the most prevalent O serotype overall and particularly dominant among MDR isolates. These findings may inform the design of multivalent conjugate vaccines that can target the predominant O serotypes associated with invasive ExPEC disease in older adults. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
9. Comparison of Genotypic and Phenotypic Predictions for Heavy Metal Resistance in Salmonella enterica and Escherichia coli.
- Author
-
Rivera-Díaz, Jeevan, Phillippi, Haley, Mbogo, Nyduta, Nawrocki, Erin M., and Dudley, Edward G.
- Subjects
HEAVY metals ,COHEN'S kappa coefficient (Statistics) ,GENOTYPES ,SALMONELLA enterica ,ESCHERICHIA coli ,SALMONELLA ,PHENOTYPES - Abstract
Salmonella enterica and Escherichia coli are two pathogenic bacteria of worldwide importance that can infect the gastrointestinal tract. Contamination in the food supply chain is an area of concern. Animal feed may be supplemented with essential trace elements, which function as nutritional additives to promote growth & health and optimize production. Bacteria have acquired many metal resistance genes to adapt to the exposure of metals. In this study, our objectives were to evaluate in S. enterica and E. coli, the correlation between the resistance genotype and phenotype to certain heavy metals, and the ability of conjugative plasmids to transfer antimicrobial resistance genes (AMRGs) and heavy metal resistance genes (HMRGs). A total of 10 strains, five S. enterica and five E. coli, were used for this study. Minimal inhibitory concentrations (MICs) were determined for heavy metals: copper, silver, arsenic, and tellurite. The tested isolates showed resistance to copper (5/10; 50%), arsenic (7/10; 70%), and silver (9/10; 90%). Cohen's Kappa statistics were used to analyze genotype to phenotype agreements. Among the 10 strains sampled, the accordance between geno- and phenotypic heavy metal resistance was fair for copper (kappa = 0.4), none to slight for arsenic (kappa = 0.19) and tellurite (kappa = 0), and no agreement for silver (kappa = -0.19). The transfer of HMRGs was determined in a conjugation experiment performed for all five Salmonella strains as donors using mixed broth cultures. Transconjugants were obtained only from the genotypically tellurite-resistant strain PSU-3260, which yielded a transfer frequency of 10-³ transconjugants per donor. In such strain, the tellurite-resistant genes reside on an IncHI2-type plasmid that shares high DNA sequence identity with known HMRG-disseminating Salmonella plasmids. Our results indicated no considerable correlation between the geno- and phenotypic resistance towards heavy metals in the sampled S. enterica and E. coli. The necessity of research in this area is supported by the lack of standardized protocols and MIC clinical breakpoints for heavy metals. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
10. Comparison of the complete genome sequences of Bifidobacterium animalis subsp, lactis DSM 10140 and B1-04
- Author
-
Barrangou, Rodolphe, Briczinski, Elizabeth P., Traeger, Lindsay L., Loquasto, Joseph R., Richards, Melissa, Horvath, Philippe, Coute-Monvoisin, Anne-Claire, Leyer, Gregory, Rendulic, Snjezana, Steele, James L., Broadbent, Jeffery R., Oberg, Taylor, Dudley, Edward G., Schuster, Stephan, Romero, Dennis A., and Roberts, Robert F.
- Subjects
Genomes -- Identification and classification ,Bacterial genetics -- Research ,Bifidobacterium -- Genetic aspects ,Biological sciences - Abstract
Bifidobacteria are important members of the human gut flora, especially in infants. Comparative genomic analysis of two Bifidobacterium animalis subsp, lactis strains revealed evolution by internal deletion of consecutive spacer-repeat units within a novel clustered regularly interspaced short palindromic repeat locus, which represented the largest differential content between the two genomes. Additionally, 47 single nucleotide polymorphisms were identified, consisting primarily of nonsynonymous mutations, indicating positive selection and/or recent divergence. A particular nonsynonymous mutation in a putative glucose transporter was linked to a negative phenotypic effect on the ability of the variant to catabolize glucose, consistent with a modification in the predicted protein transmembrane topology. Comparative genome sequence analysis of three Bifidobacterium species provided a core genome set of 1,117 orthologs complemented by a pan-genome of 2,445 genes. The genome sequences of the intestinal bacterium B. animalis subsp, lactis provide insights into rapid genome evolution and the genetic basis for adaptation to the human gut environment, notably with regard to catabolism of dietary carbohydrates, resistance to bile and acid, and interaction with the intestinal epithelium. The high degree of genome conservation observed between the two strains in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies and explains the inability to differentiate the strains by standard techniques such as pulsed-field gel electrophoresis.
- Published
- 2009
11. Low occurrence of multi‐antimicrobial and heavy metal resistance in Salmonella enterica from wild birds in the United States.
- Author
-
Fu, Yezhi, M'ikanatha, Nkuchia M., Whitehouse, Chris A., Tate, Heather, Ottesen, Andrea, Lorch, Jeffrey M., Blehert, David S., Berlowski‐Zier, Brenda, and Dudley, Edward G.
- Subjects
HEAVY metals ,SALMONELLA enterica ,DRUG resistance in bacteria ,WATER birds ,DOMESTIC animals - Abstract
Summary: Wild birds are common reservoirs of Salmonella enterica. Wild birds carrying resistant S. enterica may pose a risk to public health as they can spread the resistant bacteria across large spatial scales within a short time. Here, we whole‐genome sequenced 375 S. enterica strains from wild birds collected in 41 U.S. states during 1978–2019 to examine bacterial resistance to antibiotics and heavy metals. We found that Typhimurium was the dominant S. enterica serovar, accounting for 68.3% (256/375) of the bird isolates. Furthermore, the proportions of the isolates identified as multi‐antimicrobial resistant (multi‐AMR: resistant to at least three antimicrobial classes) or multi‐heavy metal resistant (multi‐HMR: resistant to at least three heavy metals) were both 1.87% (7/375). Interestingly, all the multi‐resistant S. enterica (n = 12) were isolated from water birds or raptors; none of them was isolated from songbirds. Plasmid profiling demonstrated that 75% (9/12) of the multi‐resistant strains carried resistance plasmids. Our study indicates that wild birds do not serve as important reservoirs of multi‐resistant S. enterica strains. Nonetheless, continuous surveillance for bacterial resistance in wild birds is necessary because the multi‐resistant isolates identified in this study also showed close genetic relatedness with those from humans and domestic animals. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
12. Where are we heading with Salmonella molecular subtyping?
- Author
-
Shariat, Nikki and Dudley, Edward G
- Published
- 2013
- Full Text
- View/download PDF
13. Peptidases and amino acid catabolism in lactic acid bacteria
- Author
-
Christensen, Jeffrey E., Dudley, Edward G., Pederson, Jeffrey A., and Steele, James L.
- Published
- 1999
- Full Text
- View/download PDF
14. Increase in quinolone resistance among salmonella isolates from retail meat samples is driven by Salmonella enteritidis and Salmonella infantis
- Author
-
Yin, Xin, Dudley, Edward G., Pinto, Casey N., and M'ikanatha, Nkuchia M.
- Published
- 2022
- Full Text
- View/download PDF
15. Corrigendum to ‘Fluoroquinolone sales in food animals and quinolone resistance in non-typhoidal Salmonella from retail meats: United States, 2009–2018’ [Journal of Global Antimicrobial Resistance 29 (2022) 163-167]
- Author
-
Yin, Xin, Dudley, Edward G., Pinto, Casey N., and M'ikanatha, Nkuchia M.
- Published
- 2022
- Full Text
- View/download PDF
16. Proteomic and microarray characterization of the AggR regulon identifies a pheU pathogenicity island in enteroaggregative Escherichia coli
- Author
-
Dudley, Edward G., Thomson, Nicholas R., Parkhill, Julian, Morin, Nicholas P., and Nataro, James P.
- Published
- 2006
17. EilA, a HilA-like regulator in enteroaggregative Escherichia coli
- Author
-
Sheikh, Jalaluddin, Dudley, Edward G., Sui, Baoquan, Tamboura, Boubou, Suleman, Altaf, and Nataro, James P.
- Published
- 2006
18. Antimicrobial‐coated films as food packaging: A review.
- Author
-
Fu, Yezhi and Dudley, Edward G.
- Subjects
PACKAGED foods ,FOOD packaging ,PACKAGING film ,ANTIMICROBIAL polymers ,COMPRESSION molding ,PACKAGING materials ,ANTI-infective agents - Abstract
Antimicrobial food packaging involves packaging the foods with antimicrobials to protect them from harmful microorganisms. In general, antimicrobials can be integrated with packaging materials via direct incorporation of antimicrobial agents into polymers or application of antimicrobial coating onto polymer surfaces. The former option is generally achieved through thermal film‐making technology such as compression molding or film extrusion, which is primarily suitable for heat‐stable antimicrobials. As a nonthermal technology, surface coating is more promising compared to molding or extrusion for manufacturing food packaging containing heat‐sensitive antimicrobials. In addition, it also has advantages over direct incorporation to preserve the packaging materials' bulk properties (e.g., mechanical and physical properties) and minimize the amount of antimicrobials to reach sufficient efficacy. Herein, antimicrobial food packaging films achieved through surface coating is explored and discussed. The two components (i.e., film substrate and antimicrobials) consisting of the antimicrobial‐coated films are reviewed as plastic/biopolymer films; and synthetic/naturally occurring antimicrobials. Furthermore, special emphasis is given to different coating technologies to deposit antimicrobials onto film substrate. Laboratory coating techniques (e.g., knife coating, bar coating, and spray coating) commonly applied in academic research are introduced briefly, and scalable coating methods (i.e., electrospinning/spraying, gravure roll coating, flexography coating) that have the potential to bring laboratory‐developed antimicrobial‐coated films to an industrial level are explained in detail. The migration profile, advantages/drawbacks of antimicrobial‐coated films for food applications, and quantitative analyses of the reviewed antimicrobial‐coated films from different aspects are also covered in this review. A conclusion is made with a discussion of the challenges that remain in bringing the production of antimicrobial‐coated films to an industrial level. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
19. A Targeted Sequencing Assay for Serotyping Escherichia coli Using AgriSeq Technology.
- Author
-
Elder, Jacob R., Fratamico, Pina M., Liu, Yanhong, Needleman, David S., Bagi, Lori, Tebbs, Robert, Allred, Adam, Siddavatam, Prasad, Suren, Haktan, Gujjula, Krishna Reddy, DebRoy, Chitrita, Dudley, Edward G., and Yan, Xianghe
- Subjects
SEROTYPING ,ESCHERICHIA coli ,GENETIC markers ,NUCLEOTIDE sequencing ,DATA analysis - Abstract
The gold standard method for serotyping Escherichia coli has relied on antisera-based typing of the O- and H-antigens, which is labor intensive and often unreliable. In the post-genomic era, sequence-based assays are potentially faster to provide results, could combine O-serogrouping and H-typing in a single test, and could simultaneously screen for the presence of other genetic markers of interest such as virulence factors. Whole genome sequencing is one approach; however, this method has limited multiplexing capabilities, and only a small fraction of the sequence is informative for subtyping or identifying virulence potential. A targeted, sequence-based assay and accompanying software for data analysis would be a great improvement over the currently available methods for serotyping. The purpose of this study was to develop a high-throughput, molecular method for serotyping E. coli by sequencing the genes that are required for production of O- and H-antigens, as well as to develop software for data analysis and serotype identification. To expand the utility of the assay, targets for the virulence factors, Shiga toxins (stx
1 , and stx2 ) and intimin (eae) were included. To validate the assay, genomic DNA was extracted from O-serogroup and H-type standard strains and from Shiga toxin-producing E. coli , the targeted regions were amplified, and then sequencing libraries were prepared from the amplified products followed by sequencing of the libraries on the Ion S5™ sequencer. The resulting sequence files were analyzed via the SeroType Caller™ software for identification of O-serogroup, H-type, and presence of stx1 , stx2 , and eae. We successfully identified 169 O-serogroups and 41 H-types. The assay also routinely detected the presence of stx1a,c,d (3 of 3 strains), stx2c−e,g (8 of 8 strains), stx2f (1 strain), and eae (6 of 6 strains). Taken together, the high-throughput, sequence-based method presented here is a reliable alternative to antisera-based serotyping methods for E. coli. [ABSTRACT FROM AUTHOR]- Published
- 2021
- Full Text
- View/download PDF
20. Whole‐genome sequencing reveals resistome of highly drug‐resistant retail meat and human Salmonella Dublin.
- Author
-
Eyler, Andrea B., M'ikanatha, Nkuchia M., Xiaoli, Lingzi, and Dudley, Edward G.
- Subjects
SALMONELLA ,SINGLE nucleotide polymorphisms ,FOODBORNE diseases ,NOROVIRUS diseases ,SYMPTOMS ,MEAT ,GASTROENTERITIS - Abstract
Non‐typhoidal Salmonella (NTS) are a significant source of foodborne illness worldwide, with disease symptoms most often presenting as self‐limiting gastroenteritis; however, occasionally the infection spreads and becomes invasive, frequently requiring anti‐microbial treatment. The cattle‐adapted Dublin serovar of NTS has commonly been associated with invasive illness and anti‐microbial resistance (AMR). Here, the enhanced resolution conferred by whole‐genome sequencing was utilized to elucidate and compare the resistome and genetic relatedness of 14 multidrug‐resistant (MDR) and one pan‐susceptible S. Dublin, isolated primarily in Pennsylvania, from fresh retail meat (one isolate) and humans (14 isolates). Twelve different genetic AMR determinants, including both acquired and chromosomal, were identified. Furthermore, comparative plasmid analysis indicated that AMR was primarily conferred by a putative IncA/C2 plasmid. A single pan‐susceptible S. Dublin isolate, collected from the same timeframe and geographical region as the MDR isolates, did not carry an IncA/C2 replicon sequence within its genome. Moreover, the pan‐susceptible isolate was genetically distinct from its MDR counterparts, as it was separated by ≥267 single nucleotide polymorphisms (SNPs), whereas there was a ≤38 SNP distance between the MDR isolates. Collectively, this data set advances our understanding of the genetic basis of the highly drug‐resistant nature of S. Dublin, a serovar with significant public health implications. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
21. Detection of CTX-M-1 extended-spectrum beta-lactamase among ceftiofur-resistant Salmonella enterica clinical isolates of poultry.
- Author
-
Denagamage, Thomas N., Wallner-Pendleton, Eva, Jayarao, Bhushan M., Xiaoli, Lingzi, Dudley, Edward G., Wolfgang, David, and Kariyawasam, Subhashinie
- Subjects
BETA lactamases ,SALMONELLA enterica ,ENTEROBACTERIACEAE ,POULTRY ,FOOD animals ,U.S. states ,PLASMIDS ,FOOD chains - Abstract
Salmonella enterica resistance to extended-spectrum cephalosporins (ESC) conferred by cefotaximases (bla
CTX-M ) is a growing concern in the United States. Among food-producing animals, poultry are a major reservoir of ESC-resistant Salmonella. A retrospective study was carried out to further characterize 38 ceftiofur-resistant clinical Salmonella enterica isolates obtained from poultry during 2007–2018. Of the isolates tested, 31 displayed resistance to ceftriaxone and harbored blaCMY-2 , whereas 7 isolates demonstrated resistance or reduced susceptibility to cefepime in addition to ceftriaxone resistance. These 7 isolates displayed extended-spectrum β-lactamase activity, harbored blaCTX-M-1 , and were recovered only from recent poultry diagnostic submissions made in 2011–2018 as opposed to the 31 isolates that were recovered in 2007–2018. Further characterization of the blaCTX-M-1 gene determined that it was located on conjugative IncN/ST1 and IncI1/ST87 plasmids in the isolates from commercial turkeys and broilers, respectively. These plasmids have been responsible for extensive spread of blaCTX-M-1 in livestock, poultry, and humans in Europe. Potential transfer of IncN and IncI1 plasmids and/or nontyphoidal Salmonella carrying these plasmids through the food chain, or by other means to humans, may result in treatment failures. Our study demonstrates the importance of further characterization of ceftiofur-resistant S. enterica isolates detected by veterinary diagnostic laboratories to identify the sources of blaCTX-M-1 and to mitigate the spread of ESC-resistant Salmonella in the poultry production pyramid. [ABSTRACT FROM AUTHOR]- Published
- 2019
- Full Text
- View/download PDF
22. Strain specific genotyping of Bifidobacterium animalis subsp. lactis by using single-nucleotide polymorphisms, insertions, and deletions
- Author
-
Briczinski, Elizabeth P., Loquasto, Joseph R., Barrangou, Rodolphe, Dudley, Edward G., Roberts, Anastasia M., and Roberts, Robert F.
- Subjects
Bifidobacterium -- Genetic aspects ,Bifidobacterium -- Physiological aspects ,Chromosome abnormalities -- Analysis ,Dextrose -- Physiological aspects ,Glucose -- Physiological aspects ,Single nucleotide polymorphisms -- Analysis ,Biological sciences - Abstract
Single-nucleotide polymorphism (SNP) and insertion and/or deletion (INDEL) sites are exploited to develop a technique capable of differentiating among a collection of Bifidobacterium animalis subsp. lactis strains. The presence of a nonsynonymous SNP within the gene encoding a putative glucose uptake protein has correlated with the ability of certain strains to transport glucose and to grow rapidly in a medium containing glucose as the sole carbon source.
- Published
- 2009
23. Non-pathogenic Escherichia coli Enhance Stx2a Production of E. coli O157: H7 Through Both bamA-Dependent and Independent Mechanisms.
- Author
-
Lingzi Xiaoli, Figler, Hillary M., Banerjee, Kakolie Goswami, Hayes, Christopher S., and Dudley, Edward G.
- Subjects
ESCHERICHIA coli ,FOOD pathogens ,COLONIZATION (Ecology) - Abstract
Intestinal colonization by the foodborne pathogen Escherichia coli O157:H7 leads to serious disease symptoms, including hemolytic uremic syndrome (HUS) and hemorrhagic colitis (HC). Synthesis of one or more Shiga toxins (Stx) is essential for HUS and HC development. The genes encoding Stx, including Stx2a, are found within a lambdoid prophage integrated in the E. coli O157:H7 chromosome. Enhanced Stx2a expression was reported when specific non-pathogenic E. coli strains were co-cultured with E. coli O157:H7, and it was hypothesized that this phenotype required the non-pathogenic E. coli to be sensitive to stx-converting phage infection. We tested this hypothesis by generating phage resistant non-pathogenic E. coli strains where bamA (an essential gene and Stx phage receptor) was replaced with an ortholog from other species. Such heterologous gene replacement abolished the ability of the laboratory strain E. coli C600 to enhance toxin production when co-cultured with E. coli O157:H7 strain PA2, which belongs to the hypervirulent clade 8. The extracellular loops of BamA (loop 4, 6, 7) were further shown to be important for infection by stx2a-converting phages. However, similar gene replacement in another commensal E. coli, designated 1.1954, revealed a bamA-independent mechanism for toxin amplification. Toxin enhancement by 1.1954 was not the result of phage infection through an alternative receptor (LamB or FadL), lysogen formation by stx2a-converting phages, or the production of a secreted molecule. Collectively, these data suggest that non-pathogenic E. coli can enhance toxin production through at least two mechanisms. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
24. Critical Synergistic Concentration of Lecithin Phospholipids Improves the Antimicrobial Activity of Eugenol against Escherichia coli.
- Author
-
Haoshu Zhang, Dudley, Edward G., and Harte, Federico
- Subjects
- *
LECITHIN , *PHOSPHOLIPIDS , *ESCHERICHIA coli , *PHOSPHOCHOLINE , *EUGENOL - Abstract
In this study, the effect of individual lecithin phospholipids on the antimicrobial properties of eugenol against Escherichia coli C600 was investigated. We tested five major phospholipids common in soy or egg lecithin (1,2-dihexadecanoylsn-glycero-3-phosphocholine [DPPC], 1,2-dioctadecanoyl-sn-glycero-3-phosphocholine [DSPC], 1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine [DPPE], 1,2-dihexadecanoylsn-glycero-3-phosphate [sodium salt] [DPPA], and 1,2-dihexadecanoyl-sn-glycero-3-phospho-L-serine [DPPS]) and one synthetic cationic phospholipid (1,2-dioctadecanoyl-snglycero-3-ethylphosphocholine [18:0 EPC]). Among the six phospholipids, DPPC, DSPC, DPPE, DPPA, and the cationic 18:0 EPC showed critical synergistic concentrations that significantly improved the inactivation effect of eugenol against E. coli after 30 min of exposure. At the critical synergistic concentration, an additional ca. 0.4 to 1.9 log reduction (ca. 0.66 to 2.17 log CFU/ml reduction) in the microbial population was observed compared to eugenol-only (control) treatments (ca. 0.25 log reduction). In all cases, increasing the phospholipid amount above the critical synergistic concentration (which was different for each phospholipid) resulted in antimicrobial properties similar to those seen with the eugenol-only (control) treatments. DPPS did not affect the antimicrobial properties of eugenol at the tested concentrations. The critical synergistic concentration of phospholipids was correlated with their critical micelle concentrations (CMC). IMPORTANCE Essential oils (EOs) are naturally occurring antimicrobials, with limited use in food due to their hydrophobicity and strong aroma. Lecithin is used as a natural emulsifier to stabilize EOs in aqueous systems. We previously demonstrated that, within a narrow critical-concentration window, lecithin can synergistically enhance the antimicrobial properties of eugenol. Since lecithin is a mixture of different phospholipids, we aimed to identify which phospholipids are crucial for the observed synergistic effect. This research studied the bioactivity of lecithin phospholipids, contributing to a rational design in using lecithin to effectively control foodborne pathogens in foods. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
25. Identification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T-β-MCA.
- Author
-
DiMarzio, Michael, Rusconi, Brigida, Yennawar, Neela H., Eppinger, Mark, Patterson, Andrew D., and Dudley, Edward G.
- Subjects
BILE salts ,HYDROLASES ,FARNESOID X receptor ,LACTOBACILLUS ,GASTROINTESTINAL system - Abstract
Bile salt hydrolase (BSH) activity against the bile acid tauro-beta-muricholic acid (T-β-MCA) was recently reported to mediate host bile acid, glucose, and lipid homeostasis via the farnesoid X receptor (FXR) signaling pathway. An earlier study correlated decreased Lactobacillus abundance in the cecum with increased concentrations of intestinal T-β-MCA, an FXR antagonist. While several studies have characterized BSHs in lactobacilli, deconjugation of T-β-MCA remains poorly characterized among members of this genus, and therefore it was unclear what strain(s) were responsible for this activity. Here, a strain of L. johnsonii with robust BSH activity against T-β-MCA in vitro was isolated from the cecum of a C57BL/6J mouse. A screening assay performed on a collection of 14 Lactobacillus strains from nine different species identified BSH substrate specificity for T-β-MCA only in two of three L. johnsonii strains. Genomic analysis of the two strains with this BSH activity revealed the presence of three bsh genes that are homologous to bsh genes in the previously sequenced human-associated strain L. johnsonii NCC533. Heterologous expression of several bsh genes in E. coli followed by enzymatic assays revealed broad differences in substrate specificity even among closely related bsh homologs, and suggests that the phylogeny of these enzymes does not closely correlate with substrate specificity. Predictive modeling allowed us to propose a potential mechanism driving differences in BSH activity for T-β-MCA in these homologs. Our data suggests that L. johnsonii regulates T-β-MCA levels in the mouse intestinal environment, and that this species may play a central role in FXR signaling in the mouse. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
26. Critical Concentration of Lecithin Enhances the Antimicrobial Activity of Eugenol against Escherichia coli.
- Author
-
Haoshu Zhang, Dudley, Edward G., Davidson, P. Michael, and Harte, Federico
- Subjects
- *
LECITHIN , *ANTI-infective agents , *EUGENOL , *ESCHERICHIA coli physiology , *STABILIZING agents , *FOODBORNE diseases , *LIGHT absorbance , *ESSENTIAL oils , *PREVENTION - Abstract
Lecithin is a natural emulsifier used in a wide range of food and nonfood applications to improve physical stability, with no known bioactive effects. In this study, the effect of lecithin on the antimicrobial performance of a constant eugenol concentration was tested against three Escherichia coli strains (C600, 0.1229, and O157:H7 strain ATCC 700728). This is the first study, to our knowledge, focusing on lecithin at concentrations below those commonly used in foods to improve the stability of oil in water emulsions (≤10 mg/100 ml). For all three cultures, significant synergistic antimicrobial effects were observed when E. coli cultures were exposed to a constant eugenol concentration (ranging from 0.043 to 0.050% [wt/wt]) together with critical lecithin concentrations ranging from 0.5 to 1 mg/100 ml. Increasing the concentration of lecithin above 1 mg/100 ml (up to 10 mg/100 ml lecithin) diminished the antibacterial effect to values similar to those with eugenol-only treatments. The formation of aggregates (<100 nm) at the critical lecithin concentration was observed using cryo-transmission electron microscopy (cryo-TEM), together with a reduction in light absorbance at 284 nm. At critically low concentrations of lecithin, the formation of nanoscale aggregates is responsible for improving eugenol antimicrobial effects. IMPORTANCE: Essential oils (EOs) are effective natural antimicrobials. However, their hydrophobicity and strong aromatic character limit the use of essential oils in food systems. Emulsifiers (e.g., lecithin) increase the stability of EOs in water-based systems but fail to consistently improve antimicrobial effects. We demonstrate that lecithin, within a narrow critical concentration window, can enhance the antimicrobial properties of eugenol. This study highlights the potential bioactivity of lecithin when utilized to effectively control foodborne pathogens. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
27. Prevalence and Phylogenetic Characterization of Escherichia coli and Hygiene Indicator Bacteria Isolated from Leafy Green Produce, Beef, and Pork Obtained from Farmers' Markets in Pennsylvania.
- Author
-
Scheinberg, Joshua A., Dudley, Edward G., Campbell, Jonathan, Roberts, Beth, DiMarzio, Michael, DebRoy, Chitrita, and Cutter, Catherine N.
- Subjects
- *
FARMERS' markets , *ESCHERICHIA coli , *FOOD recall , *COLIFORMS , *HYGIENE - Abstract
The popularity of farmers' markets in the United States has led to over 8,400 farmers' markets being in operation in 2015. As farmers' markets have increased in size and complexity in the kinds of foods sold at these venues, so have the potential food safety risks. Since 2008, seven major foodborne illness outbreaks and two recalls associated with food products from farmers' markets have occurred, causing 80 known reported illnesses and one death. Various researchers also have observed vendors performing high-risk food safety retail behaviors, and others have identified microbiological hazards in foods sold at farmers' markets. In this study, the presence of hygiene indicators (coliforms, fecal coliforms, Listeria spp., and Escherichia coli) was assessed in select samples of leafy green produce and meat obtained from farmers' markets in Pennsylvania. E. coli isolates were further characterized by phylogenetic profile and virulence potential. E. coli was present in 40% (20 of 50) and 18% (9 of 50) of beef and pork samples, respectively, and in 28% (15 of 54), 29% (15 of 52), and 17% (8 of 46) of kale, lettuce, and spinach samples, respectively. Listeria spp. was found in 8% (4 of 50) of beef samples, 2% (1 of 54) of kale samples, 4% (2 of 52) of lettuce samples, and 7% (3 of 46) of spinach samples. Among the 10 Listeria spp. isolates, 3 were identified as L. monocytogenes. E. coli isolated from meat samples mainly clustered into phylogroup B1 (66%; 19 of 29), whereas produce isolates clustered into phylogroups B2 (36%; 14 of 39) and B1 (33%; 13 of 39). These E. coli isolates possessed the fimH, iroN, hlyD, and eae genes associated with extraintestinal pathogenic E. coli and Shiga toxin–producing E. coli. The high prevalence but low levels of E. coli and Listeria spp. found on both produce and meat products obtained from farmers' markets in this study strongly indicate that farmers' market vendors would benefit greatly from food safety training and increased public health oversight. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
28. A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease.
- Author
-
Ivanov, Yury V., Shariat, Nikki, Register, Karen B., Linz, Bodo, Rivera, Israel, Kai Hu, Dudley, Edward G., and Harvill, Eric T.
- Subjects
BORDETELLA ,ENDONUCLEASES ,GENETIC transcription in bacteria ,IMMUNITY ,NUCLEOTIDE sequencing ,POLYMERASE chain reaction - Abstract
Background: Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) are widely distributed among bacteria. These systems provide adaptive immunity against mobile genetic elements specified by the spacer sequences stored within the CRISPR. Methods: The CRISPR-Cas system has been identified using Basic Local Alignment Search Tool (BLAST) against other sequenced and annotated genomes and confirmed via CRISPRfinder program. Using Polymerase Chain Reactions (PCR) and Sanger DNA sequencing, we discovered CRISPRs in additional bacterial isolates of the same species of Bordetella. Transcriptional activity and processing of the CRISPR have been assessed via RT-PCR. Results: Here we describe a novel Type II-C CRISPR and its associated genes--cas1, cas2, and cas9--in several isolates of a newly discovered Bordetella species. The CRISPR-cas locus, which is absent in all other Bordetella species, has a significantly lower GC-content than the genome-wide average, suggesting acquisition of this locus via horizontal gene transfer from a currently unknown source. The CRISPR array is transcribed and processed into mature CRISPR RNAs (crRNA), some of which have homology to prophages found in closely related species B. hinzii. Conclusions: Expression of the CRISPR-Cas system and processing of crRNAs with perfect homology to prophages present in closely related species, but absent in that containing this CRISPR-Cas system, suggest it provides protection against phage predation. The 3,117-bp cas9 endonuclease gene from this novel CRISPR-Cas system is 990 bp smaller than that of Streptococcus pyogenes, the 4,017-bp allele currently used for genome editing, and which may make it a useful tool in various CRISPR-Cas technologies. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
29. Commercially Available Rapid Methods for Detection of Selected Food-borne Pathogens.
- Author
-
Valderrama, Wladir B., Dudley, Edward G., Doores, Stephanie, and Cutter, Catherine N.
- Subjects
- *
FOOD pathogens , *SALMONELLA , *STAPHYLOCOCCUS aureus , *NUCLEIC acids , *BIOSENSORS - Abstract
Generally, the enumeration and isolation of food-borne pathogens is performed using culture-dependent methods. These methods are sensitive, inexpensive, and provide both qualitative and quantitative assessment of the microorganisms present in a sample, but these are time-consuming. For this reason, researchers are developing new techniques that allow detection of food pathogens in shorter period of time. This review identifies commercially available methods for rapid detection and quantification of Listeria monocytogenes, Salmonella spp., Staphylococcus aureus, and Shiga toxin-producing Escherichia coli in food samples. Three categories are discussed: immunologically based methods, nucleic acid-based assays, and biosensors. This review describes the basic mechanism and capabilities of each method, discusses the difficulties of choosing the most convenient method, and provides an overview of the future challenges for the technology for rapid detection of microorganisms. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
30. Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation.
- Author
-
Pettengill, Emily A., Pettengill, James B., Binet, Rachel, Dudley, Edward G., and Peritz, Adam
- Subjects
SHIGELLA ,ESCHERICHIA coli ,PHYLOGENY - Abstract
As a leading cause of bacterial dysentery, Shigella represents a significant threat to public health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC) can also cause dysentery. Current typing methods have limited ability to identify and differentiate between these pathogens despite the need for rapid and accurate identification of pathogens for clinical treatment and outbreak response. We present a comprehensive phylogeny of Shigella and EIEC using whole genome sequencing of 169 samples, constituting unparalleled strain diversity, and observe a lack of monophyly between Shigella and EIEC and among Shigella taxonomic groups. The evolutionary relationships in the phylogeny are supported by analyses of population structure and hierarchical clustering patterns of translated gene homolog abundance. Lastly, we identified a panel of 404 single nucleotide polymorphism (SNP) markers specific to each phylogenetic cluster for more accurate identification of Shigella and EIEC. Our findings show that Shigella and EIEC are not distinct evolutionary groups within the E. coli genus and, thus, EIEC as a group is not the ancestor to Shigella. The multiple analyses presented provide evidence for reconsidering the taxonomic placement of Shigella. The SNP markers offer more discriminatory power to molecular epidemiological typing methods involving these bacterial pathogens. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
31. CRISPR-Based Typing and Next-Generation Tracking Technologies.
- Author
-
Barrangou, Rodolphe and Dudley, Edward G.
- Published
- 2016
- Full Text
- View/download PDF
32. A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease.
- Author
-
Ivanov, Yury V., Shariat, Nikki, Register, Karen B., Linz, Bodo, Rivera, Israel, Hu, Kai, Dudley, Edward G., and Harvill, Eric T.
- Abstract
Background: Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) are widely distributed among bacteria. These systems provide adaptive immunity against mobile genetic elements specified by the spacer sequences stored within the CRISPR. Methods: The CRISPR-Cas system has been identified using Basic Local Alignment Search Tool (BLAST) against other sequenced and annotated genomes and confirmed via CRISPRfinder program. Using Polymerase Chain Reactions (PCR) and Sanger DNA sequencing, we discovered CRISPRs in additional bacterial isolates of the same species of Bordetella. Transcriptional activity and processing of the CRISPR have been assessed via RT-PCR. Results: Here we describe a novel Type II-C CRISPR and its associated genes—cas1, cas2, and cas9—in several isolates of a newly discovered Bordetella species. The CRISPR-cas locus, which is absent in all other Bordetella species, has a significantly lower GC-content than the genome-wide average, suggesting acquisition of this locus via horizontal gene transfer from a currently unknown source. The CRISPR array is transcribed and processed into mature CRISPR RNAs (crRNA), some of which have homology to prophages found in closely related species B. hinzii. Conclusions: Expression of the CRISPR-Cas system and processing of crRNAs with perfect homology to prophages present in closely related species, but absent in that containing this CRISPR-Cas system, suggest it provides protection against phage predation. The 3,117-bp cas9 endonuclease gene from this novel CRISPR-Cas system is 990 bp smaller than that of Streptococcus pyogenes, the 4,017-bp allele currently used for genome editing, and which may make it a useful tool in various CRISPR-Cas technologies. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
33. Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages.
- Author
-
Shuang Yin, Rusconi, Brigida, Sanjar, Fatemeh, Goswami, Kakolie, Lingzi Xiaoli, Eppinger, Mark, and Dudley, Edward G.
- Subjects
ESCHERICHIA coli ,HEMOLYTIC-uremic syndrome ,BACTERIOPHAGES ,SINGLE nucleotide polymorphisms ,VEROCYTOTOXINS ,MICROBIAL genomics - Abstract
Background: Shiga toxin-producing Escherichia coli O157:H7 is a foodborne pathogen that causes severe human diseases including hemolytic uremic syndrome (HUS). The virulence factor that mediates HUS, Shiga toxin (Stx), is encoded within the genome of a lambdoid prophage. Although draft sequences are publicly available for a large number of E. coli O157:H7 strains, the high sequence similarity of stx-converting bacteriophages with other lambdoid prophages poses challenges to accurately assess the organization and plasticity among stx-converting phages due to assembly difficulties. Methods: To further explore genome plasticity of stx-converting prophages, we enriched phage DNA from 45 ciprofloxacin-induced cultures for subsequent 454 pyrosequencing to facilitate assembly of the complete phage genomes. In total, 22 stx2a-converting phage genomes were closed. Results: Comparison of the genomes distinguished nine distinct phage sequence types (PSTs) delineated by variation in obtained sequences, such as single nucleotide polymorphisms (SNPs) and insertion sequence element prevalence and location. These nine PSTs formed three distinct clusters, designated as PST1, PST2 and PST3. The PST2 cluster, identified in two clade 8 strains, was related to stx2a-converting phages previously identified in non- O157 Shiga-toxin producing E. coli (STEC) strains associated with a high incidence of HUS. The PST1 cluster contained phages related to those from E. coli O157:H7 strain Sakai (lineage I, clade 1), and PST3 contained a single phage that was distinct from the rest but most related to the phage from E. coli O157:H7 strain EC4115 (lineage I/II, clade 8). Five strains carried identical stx2a-converting phages (PST1-1) integrated at the same chromosomal locus, but these strains produced different levels of Stx2. Conclusion: The stx2a-converting phages of E. coli O157:H7 can be categorized into at least three phage types. Diversification within a phage type is mainly driven by IS629 and by a small number of SNPs. Polymorphisms between phage genomes may help explain differences in Stx2a production between strains, however our data indicates that genes encoded external to the phage affect toxin production as well. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
34. Complete nucleotide sequence of pRS218, a large virulence plasmid that augments pathogenic potential of meningitis-associated Escherichia coli strain RS218.
- Author
-
Wijetunge, Dona Saumya S., Karunathilake, Kurundu Hewage Eranda M., Chaudhari, Atul, Katani, Robab, Dudley, Edward G., Kapur, Vivek, DebRoy, Chitrita, and Kariyawasam, Subhashinie
- Subjects
NUCLEOTIDE sequence ,ESCHERICHIA coli ,MICROBIAL virulence ,PLASMIDS ,MENINGITIS - Abstract
Background Escherichia coli is the most predominant Gram-negative bacterial pathogen associated with neonatal meningitis. Previous studies indicated that the prototypic neonatal meningitis E. coli (NMEC) strain RS218 (O18:K1:H7) harbors one large plasmid. Objectives of the present study were to analyze the complete nucleotide sequence of this large plasmid (pRS218) and its contribution to NMEC pathogenesis using in vitro and in vivo models of neonatal meningitis. Results The plasmid is 114,231 bp in size, belongs to the incompatibility group FIB/IIA (IncFIB/IIA), and contains a genetic load region that encodes several virulence and fitness traits such as enterotoxicity, iron acquisition and copper tolerance. The nucleotide sequence of pRS218 showed a 41- 46% similarity to other neonatal meningitis-causing E. coli (NMEC) plasmids and remarkable nucleotide sequence similarity (up to 100%) to large virulence plasmids of E. coli associated with acute cystitis. Some genes located on pRS218 were overly represented by NMEC strains compared to fecal E. coli isolated from healthy individuals. The plasmid-cured strain was significantly attenuated relative to the RS218 wild-type strain as determined in vitro by invasion potential to human cerebral microvascular endothelial cells and in vivo by mortalities, histopathological lesions in the brain tissue, and bacterial recovery from the cerebrospinal fluid of infected rat pups. Conclusions The pRS218 is an IncFIB/IIA plasmid which shares a remarkable nucleotide sequence similarity to large plasmids of E. coli associated with cystitis. Both in vitro and in vivo experiments indicated that pRS218 plays an important role in NMEC pathogenesis. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
35. Genomic and Transcriptomic Analyses of Foodborne Bacterial Pathogens.
- Author
-
Zhang, Wei, Dudley, Edward G., and Wade, Joseph T.
- Abstract
DNA microarrays (often interchangeably called DNA chips or DNA arrays) are among the most popular analytical tools for high-throughput comparative genomic and transcriptomic analyses of foodborne bacterial pathogens. A typical DNA microarray contains hundreds to millions of small DNA probes that are chemically attached (or ˵printed″) onto the surface of a microscopic glass slide. Depending on the specific ˵printing″ and probe synthesis technologies for different microarray platforms, such DNA probes can be PCR amplicons or in situ synthesized short oligonucleotides. DNA microarray technologies have revolutionized the way that we investigate the biology of foodborne bacterial pathogens. The major advantage of these technologies is that DNA microarrays allow comparison of subtle genomic or transcriptomic variations between two bacterial samples, such as genomic variations between two different bacterial strains or transcriptomic alterations of same bacterial strain under two different treatments. Some applications of comparative genomic hybridization microarrays and global gene expression microarrays have been covered in previous chapters of this book. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
36. Chapter 11: Genomic and Virulence Heterogeneity of Enteroaggregative Escherichia coli.
- Author
-
Dudley, Edward G. and Rasko, David A.
- Published
- 2011
37. Track antibiotic-resistant strains of Salmonella from farm to fork
- Author
-
Dudley, Edward G.
- Subjects
Drug resistance in microorganisms ,Salmonella food poisoning ,Salmonella ,Biotechnology industry ,Business ,Food and beverage industries - Abstract
Tracing the transmission of individual strains of bacteria from agricultural environments to humans is difficult because of the rapid evolution of resistance patterns among these bacteria. Resistance patterns change so [...]
- Published
- 2013
38. CRISPRs: Molecular Signatures Used for Pathogen Subtyping.
- Author
-
Shariat, Nikki and Dudley, Edward G.
- Subjects
- *
PROKARYOTES , *ENTEROBACTERIACEAE , *PHYTOPATHOGENIC microorganisms , *IMMUNE system , *MYCOBACTERIUM tuberculosis - Abstract
Rapid and accurate strain identification is paramount in the battle against microbial outbreaks, and several subtyping approaches have been developed. One such method uses clustered regular interspaced short palindromic repeats (CRISPRs), DNA repeat elements that are present in approximately half of all bacteria. Though their signature function is as an adaptive immune system against invading DNA such as bacteriophages and plasmids, CRISPRs also provide an excellent framework for pathogen tracking and evolutionary studies. Analysis of the spacer DNA sequences that reside between the repeats has been tremendously useful for bacterial subtyping during molecular epidemiological investigations. Subtyping, or strain identification, using CRISPRs has been employed in diverse Gram-positive and Gram-negative bacteria, including Mycobacterium tuberculosis, Salmonella enterica, and the plant pathogen Erwinia amylovora. This review discusses the several ways in which CRISPR sequences are exploited for subtyping. This includes the well-established spoligotyping methodologies that have been used for 2 decades to type Mycobacterium species, as well as in-depth consideration of newer, higher-throughput CRISPR-based protocols. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
39. CRISPR-MVLST subtyping of Salmonella enterica subsp. enterica serovars Typhimurium and Heidelberg and application in identifying outbreak isolates.
- Author
-
Shariat, Nikki, Sandt, Carol H., DiMarzio, Michael J., Barrangou, Rodolphe, and Dudley, Edward G.
- Subjects
SALMONELLA enterica ,FOODBORNE diseases ,PULSED-field gel electrophoresis ,DISEASE outbreaks - Abstract
Background Salmonella enterica subsp. enterica serovars Typhimurium (S. Typhimurium) and Heidelberg (S. Heidelberg) are major causes of foodborne salmonellosis, accounting for a fifth of all annual salmonellosis cases in the United States. Rapid, efficient and accurate methods for identification are required for routine surveillance and to track specific strains during outbreaks. We used Pulsed-field Gel Electrophoresis (PFGE) and a recently developed molecular subtyping approach termed CRISPR-MVLST that exploits the hypervariable nature of virulence genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) to subtype clinical S. Typhimurium and S. Heidelberg isolates. Results We analyzed a broad set of 175 S. Heidelberg and S. Typhimurium isolates collected over a five-year period. We identified 21 Heidelberg Sequence Types (HSTs) and 37 Typhimurium STs (TSTs) that were represented by 27 and 45 PFGE pulsotypes, respectively, and determined the discriminatory power of each method. Conclusions For S. Heidelberg, our data shows that combined typing by both CRISPR-MVLST and PFGE provided a discriminatory power of 0.9213. Importantly, CRISPR-MVLST was able to separate common PFGE patterns such as JF6X01.0022 into distinct STs, thus providing significantly greater discriminatory power. Conversely, we show that subtyping by either CRISPR-MVLST or PFGE independently provides a sufficient discriminatory power (0.9345 and 0.9456, respectively) for S. Typhimurium. Additionally, using isolates from two S. Typhimurium outbreaks, we demonstrate that CRISPR-MVLST provides excellent epidemiologic concordance. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
40. A Type VI Secretion System Encoding Locus Is Required for Bordetella bronchiseptica Immunomodulation and Persistence In Vivo.
- Author
-
Weyrich, Laura S., Rolin, Olivier Y., Muse, Sarah J., Park, Jihye, Spidale, Nicholas, Kennett, Mary J., Hester, Sara E., Chun Chen, Dudley, Edward G., and Harvill, Eric T.
- Subjects
GRAM-negative bacteria ,INFECTION ,GENES ,BORDETELLA bronchiseptica ,MACROPHAGES ,APOPTOSIS - Abstract
Type VI Secretion Systems (T6SSs) have been identified in numerous Gram-negative pathogens, but the lack of a natural host infection model has limited analysis of T6SS contributions to infection and pathogenesis. Here, we describe disruption of a gene within locus encoding a putative T6SS in Bordetella bronchiseptica strain RB50, a respiratory pathogen that circulates in a broad range of mammals, including humans, domestic animals, and mice. The 26 gene locus encoding the B. bronchiseptica T6SS contains apparent orthologs to all known core genes and possesses thirteen novel genes. By generating an in frame deletion of clpV, which encodes a putative ATPase required for some T6SS-dependent protein secretion, we observe that ClpV contributes to in vitro macrophage cytotoxicity while inducing several eukaryotic proteins associated with apoptosis. Additionally, ClpV is required for induction of IL-1β, IL-6, IL-17, and IL-10 production in J774 macrophages infected with RB50. During infections in wild type mice, we determined that ClpV contributes to altered cytokine production, increased pathology, delayed lower respiratory tract clearance, and long term nasal cavity persistence. Together, these results reveal a natural host infection system in which to interrogate T6SS contributions to immunomodulation and pathogenesis. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
41. Influence of indigenous eukaryotic microbial communities on the reduction of Escherichia coli O157:H7 in compost slurry A. Puri & E.G. Dudley Reduction of E. coli O157:H7 in compost.
- Author
-
Puri, Amrita and Dudley, Edward G.
- Subjects
- *
ESCHERICHIA coli , *EUKARYOTIC cells , *ORGANIC fertilizers , *ESCHERICHIA , *GEL electrophoresis - Abstract
Compost made from livestock manure is commonly used as a crop fertilizer and serves as a possible vehicle for the transmission of Escherichia coli O157:H7 to fresh produce. In this study, we hypothesized that the indigenous microbial communities present in composts adversely affects the survival of E. coli O157:H7. Escherichia coli O157:H7 was spiked into compost slurry and incubated at 25 °C. Escherichia coli O157:H7 exhibited a c. 4 log reduction over 16 days. When compost was supplemented with the eukaryotic inhibitor cycloheximide, there was a minimal decrease in E. coli O157:H7 counts over the same time period. Analysis of microbial communities present in the compost with denaturing gradient gel electrophoresis (DGGE) suggested minor differences in the fungal communities present in cycloheximide-treated compost, compared with untreated compost over a period of 12 days at 25 °C. However, the DGGE profiles of protists showed drastic differences in community complexity. Clone library sequence analysis of protist populations revealed significantly different species composition between treatment and control samples at different time points. This suggests that predation of E. coli O157:H7 by protists might be a potential mechanism for reducing E. coli O157:H7 in compost materials. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
42. Complete Genome Sequence and Comparative Metabolic Profiling of the Prototypical Enteroaggregative Escherichia coli Strain 042.
- Author
-
Chaudhuri, Roy R., Sebaihia, Mohammed, Hobman, Jon L., Webber, Mark A., Leyton, Denisse L., Goldberg, Martin D., Cunningham, Adam F., Scott-Tucker, Anthony, Ferguson, Paul R., Thomas, Christopher M., Frankel, Gad, Tang, Christoph M., Dudley, Edward G., Roberts, Ian S., Rasko, David A., Pallen, Mark J., Parkhill, Julian, Nataro, James P., Thomson, Nicholas R., and Henderson, Ian R.
- Subjects
ESCHERICHIA coli ,GENETICS ,SUMMER diseases ,GENOTYPE-environment interaction ,GENOMES ,GENOMICS ,FOODBORNE diseases ,DIARRHEA ,ENTEROBACTERIACEAE - Abstract
Background: Escherichia coli can experience a multifaceted life, in some cases acting as a commensal while in other cases causing intestinal and/or extraintestinal disease. Several studies suggest enteroaggregative E. coli are the predominant cause of E. coli-mediated diarrhea in the developed world and are second only to Campylobacter sp. as a cause of bacterialmediated diarrhea. Furthermore, enteroaggregative E. coli are a predominant cause of persistent diarrhea in the developing world where infection has been associated with malnourishment and growth retardation. Methods: In this study we determined the complete genomic sequence of E. coli 042, the prototypical member of the enteroaggregative E. coli, which has been shown to cause disease in volunteer studies. We performed genomic and phylogenetic comparisons with other E. coli strains revealing previously uncharacterised virulence factors including a variety of secreted proteins and a capsular polysaccharide biosynthetic locus. In addition, by using Biolog™ Phenotype Microarrays we have provided a full metabolic profiling of E. coli 042 and the non-pathogenic lab strain E. coli K-12. We have highlighted the genetic basis for many of the metabolic differences between E. coli 042 and E. coli K-12. Conclusion: This study provides a genetic context for the vast amount of experimental and epidemiological data published thus far and provides a template for future diagnostic and intervention strategies. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
43. The interplay of Escherichia coli O157:H7 and commensal E. coli : the importance of strain-level identification.
- Author
-
Figler, Hillary M. and Dudley, Edward G.
- Subjects
MICROBIAL virulence genetics ,ESCHERICHIA coli O157:H7 ,GENETIC regulation ,BACTERIAL genetics ,ESCHERICHIA coli ,COMMENSALISM - Abstract
The authors reflect on a study which demonstrates how the expression of critical virulence factor of Escherichia coli 0157:H7 may be regulated by the specific members of the gut microbiota. Topics discussed include the importance of the microbiome and its relationship to human health and disease, the diversity of Escherichia coli and how it interacts with commensal bacteria.
- Published
- 2016
- Full Text
- View/download PDF
44. The Escherichia coli biofilm-promoting protein Antigen 43 does not contribute to intestinal colonization.
- Author
-
de Luna, Maria das Graças, Scott-Tucker, Anthony, Desvaux, Mickael, Ferguson, Paul, Morin, Nicholas P., Dudley, Edward G., Turner, Sue, Nataro, James P., Owen, Peter, and Henderson, Ian R.
- Subjects
ESCHERICHIA coli ,INTESTINAL diseases ,ENTEROBACTERIACEAE ,FOODBORNE diseases ,MICROBIAL aggregation ,PARASITE antigens ,LABORATORY mice ,FOOD poisoning ,COLIFORMS - Abstract
Escherichia coli is a versatile organism capable of causing a variety of intestinal and extraintestinal diseases, as well as existing as part of the commensal flora. A variety of factors permit specific attachment to host receptors including fimbrial adhesins and outer membrane proteins such as autotransporters. One of the better characterized autotransporters is Antigen 43 (Ag43), the major phase-variable surface protein of E. coli. Ag43 is associated with bacterial cell–cell aggregation and biofilm formation. Nevertheless, the precise biological significance and contribution to intestinal colonization remain to be elucidated. Here we investigated the contribution of Ag43 to E. coli adherence to intestinal epithelial cells and colonization of the mouse intestine. These investigations revealed that Ag43 increased in vitro adherence of E. coli to epithelial cells by promoting bacterial cell–cell aggregation but that Ag43 did not promote specific interactions with the mammalian cells. Furthermore, Ag43 did not contribute significantly to colonization of the mouse intestine and expression of Ag43 was lost a few days after colonization of the mouse was established. Unexpectedly, considering its similarity to other adhesins, our findings suggest that Ag43 does not act as a direct colonization factor by binding to mammalian cells. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
45. Pathogenesis of enteroaggregative Escherichia coli infection.
- Author
-
Harrington, Susan M., Dudley, Edward G., and Nataro, James P.
- Subjects
- *
ESCHERICHIA coli diseases , *ESCHERICHIA coli , *HIV-positive persons , *HIV , *DIARRHEA , *BACTERIAL toxins , *PATHOGENIC microorganisms , *MICROBIAL virulence ,DEVELOPING countries - Abstract
Enteroaggregative Escherichia coli (EAEC) is emerging as a significant diarrheal pathogen in multiple population groups. Although most commonly associated with pediatric diarrhea in developing countries, EAEC is also linked to diarrhea in adults including HIV-positive patients and travelers and has been a cause of food-borne outbreaks in the industrialized world. Current data suggest that one set of virulence elements is not associated with all EAEC strains, but that combinations of multiple factors prevail. Pathogenesis is believed to be initiated with adherence to the terminal ileum and colon in an aggregative, stacked-brick-type pattern by means of one of several different hydrophobic aggregative adherence fimbriae. Some strains of EAEC may then elaborate cytotoxins including the plasmid-encoded toxin and the enterotoxins, EAST1 and ShET1. An AraC homolog termed AggR regulates several genes contributing to fimbrial biogenesis in ‘typical EAEC strains’. AggR has now also been shown to regulate genes on a chromosomal island. Sequencing of the EAEC type strain 042 completed at the Sanger Center has revealed two other chromosomal islands that are being explored for their pathogenetic potential. This article reviews these virulence elements and presents on-going areas of research in EAEC pathogenesis. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
46. Use of a microarray to assess the distribution of plasmid and chromosomal virulence genes in strains of enteroaggregative Escherichia coli
- Author
-
Jenkins, Claire, van Ijperen, Carola, Dudley, Edward G., Chart, Henrik, Willshaw, Geraldine A., Cheasty, Tom, Smith, Henry R., and Nataro, James P.
- Subjects
ESCHERICHIA coli ,GENES ,ENTEROBACTERIACEAE ,DIARRHEA - Abstract
Abstract: A DNA microarray was used to analyze the distribution of plasmid and chromosomal genes among strains of enteroaggregative Escherichia coli (EAEC) isolated from a prospective diarrhoea surveillance study in the United Kingdom. Target genes were extracted from existing databases and from the genome sequence of prototype EAEC strain 042. We found that strains exhibiting the aggregative adherence (AA) phenotype could be broadly divided into two groups depending upon whether they harboured genes from the EAEC virulence plasmid (pAA) and a set of chromosomal genes found in EAEC strain 042. Several chromosomal loci were inherited en bloc, and were more common in strains which we designated Group 1; genes at the pheU locus were particularly conserved. Genes encoded on the pAA plasmid and those under control of the master regulator AggR were also concentrated in the Group 1 EAEC. A gene encoding a type 1 pilin allele was detected more frequently in Group 2 EAEC. Our data suggest that strains previously designated as typical EAEC harbour a large number of conserved plasmid and chromosomal loci, further illuminating a package of virulence genes common to the most important EAEC. [Copyright &y& Elsevier]
- Published
- 2005
- Full Text
- View/download PDF
47. Lactococcus lactis LM0230 contains a single aminotransferase involved in aspartate biosynthesis, which is essential for growth in milk.
- Author
-
Dudley, Edward G., Steele, James L., Edward G. Dudley, and James L. Steele
- Subjects
- *
BIOSYNTHESIS , *AMINOTRANSFERASES , *LACTOCOCCUS lactis - Abstract
Examines the aspartate biosynthesis with Lactococcus lactis LM0230 aminotransferase. Duplication of aspartate ATase gene (AspC) from L. lactis by complementation into Escherichia coli DL39; Implications of substrate-specificity studies for the ATase activity of lactococcal AspC; Role of a lactococcal ATase in oxaloacetate conversion to Asp.
- Published
- 2001
- Full Text
- View/download PDF
48. Gene Cloning, Sequencing, and Inactivation of the Branched-Chain Aminotransferase of Lactococcus...
- Author
-
Atiles, Myrta W. and Dudley, Edward G.
- Subjects
- *
AMINOTRANSFERASES , *LACTOCOCCUS lactis - Abstract
Discusses gene cloning, sequencing and inactivation of the branched-chain aminotransferase of Lactococcus lactis LM0230. Cloning of the gene encoding the branched-chain aminotransferase; Aminotransferase activity of the lactococcal IlvE in Escherichia coli DL39; Growth of Lactococcus lactis LM0230 and its derivative.
- Published
- 2000
- Full Text
- View/download PDF
49. Sequencing, distribution, and inactivation of the dipeptidase A gene (pepDA) from Lactobacillus...
- Author
-
Dudley, Edward G. and Husgen, Ann C.
- Subjects
- *
LACTOBACILLUS - Abstract
Initiates the characterization of the proteolytic system of Lactobacillus helveticus CNRZ32. RNA isolation and Northern hybridization; Quantitative dipeptidase assays; Southern hybridizations; Molecular cloning and enzymatic screening; Bacterial strains, media and plasmids; DNA sequencing.
- Published
- 1996
- Full Text
- View/download PDF
50. Special Section on the Third International E. coli and the Mucosal Immune System (ECMIS) Symposium.
- Author
-
Dudley, Edward G.
- Subjects
- *
IMMUNE system , *CONFERENCES & conventions , *MICROBIAL ecology , *MICROBIOLOGY , *VACCINE development - Published
- 2020
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.