Changes detected in the genome sequences of Escherichia coli, Listeria monocytogenes, Vibrio parahaemolyticus, and Salmonella enterica after serial subculturing

2019 ◽  
Vol 65 (11) ◽  
pp. 842-850
Author(s):  
Nicholas Petronella ◽  
Palni Kundra ◽  
Olivia Auclair ◽  
Karine Hébert ◽  
Mary Rao ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Listeria Monocytogenes ◽  
Foodborne Pathogens ◽  
Salmonella Enterica ◽  
Vibrio Parahaemolyticus ◽  
Molecular Techniques ◽  
Genomic Variation ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genomic Changes

Whole genome sequencing (WGS) is rapidly replacing other molecular techniques for identifying and subtyping bacterial isolates. The resolution or discrimination offered by WGS is significantly higher than that offered by other molecular techniques, and WGS readily allows infrequent differences that occur between 2 closely related strains to be found. In this investigation, WGS was used to identify the changes that occurred in the genomes of 13 strains of bacterial foodborne pathogens after 100 serial subcultures. Pure cultures of Shiga-toxin-producing Escherichia coli, Salmonella enterica, Listeria monocytogenes, and Vibrio parahaemolyticus were subcultured daily for 100 successive days. The 1st and 100th subcultures were whole-genome sequenced using short-read sequencing. Single nucleotide polymorphisms (SNPs) were identified between the 1st and final culture using 2 different approaches, and multilocus sequence typing of the whole genome was also performed to detect any changes at the allelic level. The number of observed genomic changes varied by strain, species, and the SNP caller used. This study provides insight into the genomic variation that can be detected using next-generation sequencing and analysis methods after repeated subculturing of 4 important bacterial pathogens.

scholarly journals Emergence of a novel Salmonella enterica serotype Reading clone is linked to its expansion in commercial turkey production, resulting in unanticipated human illness in North America

2019 ◽  
Author(s):  
Elizabeth A. Miller ◽  
Ehud Elnekave ◽  
Cristian Flores Figueroa ◽  
Abigail Johnson ◽  
Ashley Kearney ◽  
...  
Keyword(s):  
North America ◽  
Foodborne Pathogens ◽  
Salmonella Enterica ◽  
The United States ◽  
Common Source ◽  
Whole Genome ◽  
Genomic Context ◽  
Genomic Changes ◽  
Human Illness ◽  
Commercial Turkey

AbstractConcurrent separate human outbreaks of Salmonella enterica serotype Reading occurred in 2017-2019 in the United States and Canada, which were both linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of S. Reading from turkeys, and to determine the genomic context of outbreaks involving this rarely isolated Salmonella serotype. A total of 988 isolates of U.S. origin were examined using whole genome-based approaches, including current and historical isolates from humans, meat, and live food animals. Broadly, isolates clustered into three major clades, with one apparently highly adapted turkey clade. Within the turkey clade isolates clustered into three subclades, including an “emergent” clade that only contained isolates dated 2016 or later, including many of the isolates from these outbreaks. Genomic differences were identified between emergent and other turkey subclades suggesting that the apparent success of currently circulating subclades clade is, in part, attributable to plasmid acquisitions conferring antimicrobial resistance, gain of phage-like sequences with cargo virulence factors, and mutations in systems that may be involved in beta-glucuronidase activity and resistance towards colicins. U.S. and Canadian outbreak isolates were found interspersed throughout the emergent subclade and the other circulating subclade. The emergence of a novel S. Reading turkey subclade, coinciding temporally with expansion in commercial turkey production and with U.S. and Canadian human outbreaks, indicates that emergent strains with higher potential for niche success were likely vertically transferred and rapidly disseminated from a common source.ImportanceIncreasingly, outbreak investigations involving foodborne pathogens are confounded by the inter-connectedness of food animal production and distribution, necessitating high-resolution genomic investigations to determine their basis. Fortunately, surveillance and whole genome sequencing, combined with the public availability of these data, enable comprehensive queries to determine underlying causes of such outbreaks. Utilizing this pipeline, it was determined that a novel clone of Salmonella Reading has emerged that coincides with increased abundance in raw turkey products and two outbreaks of human illness in North America. The rapid dissemination of this highly adapted and conserved clone indicates that it was likely obtained from a common source and rapidly disseminated across turkey production. Key genomic changes may have contributed to its apparent continued success in the barn environment, and ability to cause illness in humans.

scholarly journals Influence of Bacterial Competitors on Salmonella enterica and Enterohemorrhagic Escherichia coli Growth in Microbiological Media and Attachment to Vegetable Seeds

Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 285
Author(s):  
Da Liu ◽  
Ronald Walcott ◽  
Kevin Mis Solval ◽  
Jinru Chen
Keyword(s):  
Escherichia Coli ◽  
Foodborne Pathogens ◽  
Salmonella Enterica ◽  
Lactobacillus Rhamnosus ◽  
Probiotic Bacterium ◽  
Enterohemorrhagic Escherichia Coli ◽  
Biocontrol Agents ◽  
Human Pathogens ◽  
Bacterial Strains ◽  
Pathogen Populations

Interests in using biological agents for control of human pathogens on vegetable seeds are rising. This study evaluated whether probiotic bacterium Lactobacillus rhamnosus GG, bacterial strains previously used as biocontrol agents in plant science, as well as a selected plant pathogen could compete with foodborne human pathogens, such as Salmonella enterica and enterohemorrhagic Escherichia coli (EHEC), for growth in microbiological media and attachment to vegetable seeds; and to determine whether the metabolites in cell-free supernatants of competitive bacterial spent cultures could inhibit the growth of the two pathogens. The results suggest that the co-presence of competitive bacteria, especially L. rhamnosus GG, significantly (p < 0.05) inhibited the growth of Salmonella and EHEC. Cell-free supernatants of L. rhamnosus GG cultures significantly reduced the pathogen populations in microbiological media. Although not as effective as L. rhamnosus GG in inhibiting the growth of Salmonella and EHEC, the biocontrol agents were more effective in competing for attachment to vegetable seeds. The study observed the inhibition of human bacterial pathogens by competitive bacteria or their metabolites and the competitive attachment to sprout seeds among all bacteria involved. The results will help strategize interventions to produce vegetable seeds and seed sprouts free of foodborne pathogens.

scholarly journals Experimental evolution of gallium resistance in Escherichia coli

2019 ◽  
Vol 2019 (1) ◽  
pp. 169-180
Author(s):  
Joseph L Graves ◽  
Akamu J Ewunkem ◽  
Jason Ward ◽  
Constance Staley ◽  
Misty D Thomas ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Experimental Evolution ◽  
Molecular Mechanisms ◽  
Gallium Nitrate ◽  
Whole Genome ◽  
Mechanisms Of Resistance ◽  
Genomic Changes ◽  
K 12

Abstract Background and Objectives Metallic antimicrobial materials are of growing interest due to their potential to control pathogenic and multidrug-resistant bacteria. Yet we do not know if utilizing these materials can lead to genetic adaptations that produce even more dangerous bacterial varieties. Methodology Here we utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance. Results By day 10 of evolution, increased gallium resistance was evident in populations cultured in medium containing a sublethal concentration of gallium. Furthermore, these populations showed increased resistance to ionic silver and iron (III), but not iron (II) and no increase in traditional antibiotic resistance compared with controls and the ancestral strain. In contrast, the control populations showed increased resistance to rifampicin relative to the gallium-resistant and ancestral population. Genomic analysis identified hard selective sweeps of mutations in several genes in the gallium (III)-resistant lines including: fecA (iron citrate outer membrane transporter), insl1 (IS30 tranposase) one intergenic mutations arsC →/→ yhiS; (arsenate reductase/pseudogene) and in one pseudogene yedN ←; (iapH/yopM family). Two additional significant intergenic polymorphisms were found at frequencies &gt; 0.500 in fepD ←/→ entS (iron-enterobactin transporter subunit/enterobactin exporter, iron-regulated) and yfgF ←/→ yfgG (cyclic-di-GMP phosphodiesterase, anaerobic/uncharacterized protein). The control populations displayed mutations in the rpoB gene, a gene associated with rifampicin resistance. Conclusions This study corroborates recent results observed in experiments utilizing pathogenic Pseudomonas strains that also showed that Gram-negative bacteria can rapidly evolve resistance to an atom that mimics an essential micronutrient and shows the pleiotropic consequences associated with this adaptation. Lay summary We utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.

scholarly journals ATIVIDADE ANTIMICROBIANA DE MICRORGANISMOS ISOLADOS DE GRÃOS DE KEFIR

2018 ◽  
Vol 19 (0) ◽  
Author(s):  
Priscila Alves Dias ◽  
Daiani Teixeira Silva ◽  
Cláudio Dias Timm
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Listeria Monocytogenes ◽  
Salmonella Typhimurium ◽  
Salmonella Enterica ◽  
Escherichia Coli O157 ◽  
E Coli

Resumo Kefir é o produto da fermentação do leite pelos grãos de kefir. Esses grãos contêm uma mistura simbiótica de bactérias e leveduras imersas em uma matriz composta de polissacarídeos e proteínas. Muitos benefícios à saúde humana têm sido atribuídos ao kefir, incluindo atividade antimicrobiana contra bactérias Gram positivas e Gram negativas. A atividade antimicrobiana de 60 microrganismos isolados de grãos de kefir, frente à Escherichia coli O157:H7, Salmonella enterica subsp. enterica sorotipos Typhimurium e Enteritidis, Staphylococcus aureus e Listeria monocytogenes, foi estudada através do teste do antagonismo. A ação antimicrobiana dos sobrenadantes das bactérias ácido-lácticas que apresentaram atividade no teste do antagonismo foi testada. O experimento foi repetido usando sobrenadantes com pH neutralizado. Salmonella Typhimurium e Enteritidis sobreviveram por 24 horas no kefir em fermentação. E. coli O157:H7, S. aureus e L. monocytogenes foram recuperados até 72 horas após o início da fermentação. Todos os isolados apresentaram atividade antimicrobiana contra pelo menos um dos patógenos usados no teste do antagonismo. Sobrenadantes de 25 isolados apresentaram atividade inibitória e três mantiveram essa atividade com pH neutralizado. As bactérias patogênicas estudadas sobreviveram por tempo superior àquele normalmente utilizado para a fermentação do kefir artesanal, o que caracteriza perigo em potencial para o consumidor quando a matéria-prima não apresentar segurança sanitária. Lactobacillus isolados de grãos de kefir apresentam atividade antimicrobiana contra cepas de E. coli O157:H7, Salmonella sorotipos Typhimurium e Enteritidis, S. aureus e L. monocytogenes além daquela exercida pela diminuição do pH.

Changes in Aerobic Plate and Escherichia coli–Coliform Counts and in Populations of Inoculated Foodborne Pathogens on Inshell Walnuts during Storage

2016 ◽  
Vol 79 (7) ◽  
pp. 1143-1153 ◽  
Author(s):  
JOHN C. FRELKA ◽  
GORDON R. DAVIDSON ◽  
LINDA J. HARRIS
Keyword(s):  
Escherichia Coli ◽  
Listeria Monocytogenes ◽  
Relative Humidity ◽  
Low Temperature ◽  
Foodborne Pathogens ◽  
Limit Of Detection ◽  
Sampling Time ◽  
E Coli ◽  
Plate Counts ◽  
Forced Air

ABSTRACT After harvest, inshell walnuts are dried using low-temperature forced air and are then stored in bins or silos for up to 1 year. To better understand the survival of bacteria on inshell walnuts, aerobic plate counts (APCs) and Escherichia coli–coliform counts (ECCs) were evaluated during commercial storage (10 to 12°C and 63 to 65% relative humidity) over 9 months. APCs decreased by 1.4 to 2.0 log CFU per nut during the first 5 months of storage, and ECCs decreased by 1.3 to 2.2 log CFU per nut in the first month of storage. Through the remaining 4 to 8 months of storage, APCs and ECCs remained unchanged (P &gt; 0.05) or decreased by &lt;0.15 log CFU per nut per month. Similar trends were observed on kernels extracted from the inshell walnuts. APCs and ECCs were consistently and often significantly higher on kernels extracted from visibly broken inshell walnuts than on kernels extracted from visibly intact inshell walnuts. Parameters measured in this study were used to determine the survival of five-strain cocktails of E. coli O157:H7, Listeria monocytogenes, and Salmonella inoculated onto freshly hulled inshell walnuts (~8 log CFU/g) after simulated commercial drying (10 to 12 h; 40°C) and simulated commercial storage (12 months at 10°C and 65% relative humidity). Populations declined by 2.86, 5.01, and 4.40 log CFU per nut for E. coli O157:H7, L. monocytogenes, and Salmonella, respectively, after drying and during the first 8 days of storage. Salmonella populations changed at a rate of −0.33 log CFU per nut per month between days 8 and 360, to final levels of 2.83 ± 0.79 log CFU per nut. E. coli and L. monocytogenes populations changed by −0.17 log CFU per nut per month and −0.26 log CFU per nut per month between days 8 and 360, respectively. For some samples, E. coli or L. monocytogenes populations were below the limit of detection by plating (0.60 log CFU per nut) by day 183 or 148, respectively; at least one of the six samples was positive at each subsequent sampling time by either plating or by enrichment.

Evaluation of Gaseous Chlorine Dioxide as a Sanitizer for Killing Salmonella, Escherichia coli O157:H7, Listeria monocytogenes, and Yeasts and Molds on Fresh and Fresh-Cut Produce

2005 ◽  
Vol 68 (6) ◽  
pp. 1176-1187 ◽  
Author(s):  
KAYE V. SY ◽  
MELINDA B. MURRAY ◽  
M. DAVID HARRISON ◽  
LARRY R. BEUCHAT
Keyword(s):  
Escherichia Coli ◽  
Listeria Monocytogenes ◽  
Chlorine Dioxide ◽  
Foodborne Pathogens ◽  
Escherichia Coli O157 ◽  
Gaseous Chlorine Dioxide ◽  
Sensory Qualities ◽  
A Cell ◽  
Fresh Cut ◽  
Yeasts And Molds

Gaseous chlorine dioxide (ClO2) was evaluated for effectiveness in killing Salmonella, Escherichia coli O157:H7, and Listeria monocytogenes on fresh-cut lettuce, cabbage, and carrot and Salmonella, yeasts, and molds on apples, peaches, tomatoes, and onions. Inoculum (100 μl, ca. 6.8 log CFU) containing five serotypes of Salmonella enterica, five strains of E. coli O157:H7, or five strains of L. monocytogenes was deposited on the skin and cut surfaces of fresh-cut vegetables, dried for 30 min at 22°C, held for 20 h at 4°C, and then incubated for 30 min at 22°C before treatment. The skin surfaces of apples, peaches, tomatoes, and onions were inoculated with 100 μl of a cell suspension (ca. 8.0 log CFU) containing five serotypes of Salmonella, and inoculated produce was allowed to dry for 20 to 22 h at 22°C before treatment. Treatment with ClO2 at 4.1 mg/liter significantly (α = 0.05) reduced the population of foodborne pathogens on all produce. Reductions resulting from this treatment were 3.13 to 4.42 log CFU/g for fresh-cut cabbage, 5.15 to 5.88 log CFU/g for fresh-cut carrots, 1.53 to 1.58 log CFU/g for fresh-cut lettuce, 4.21 log CFU per apple, 4.33 log CFU per tomato, 1.94 log CFU per onion, and 3.23 log CFU per peach. The highest reductions in yeast and mold populations resulting from the same treatment were 1.68 log CFU per apple and 2.65 log CFU per peach. Populations of yeasts and molds on tomatoes and onions were not significantly reduced by treatment with 4.1 mg/liter ClO2. Substantial reductions in populations of pathogens on apples, tomatoes, and onions but not peaches or fresh-cut cabbage, carrot, and lettuce were achieved by treatment with gaseous ClO2 without markedly adverse effects on sensory qualities.

Inactivation of Escherichia coli O157:H7, Salmonella enterica Serotype Enteritidis, and Listeria monocytogenes on Lettuce by Hydrogen Peroxide and Lactic Acid and by Hydrogen Peroxide with Mild Heat

2002 ◽  
Vol 65 (8) ◽  
pp. 1215-1220 ◽  
Author(s):  
CHIA-MIN LIN ◽  
SARAH S. MOON ◽  
MICHAEL P. DOYLE ◽  
KAY H. McWATTERS
Keyword(s):  
Escherichia Coli ◽  
Hydrogen Peroxide ◽  
Lactic Acid ◽  
Listeria Monocytogenes ◽  
Salmonella Enterica ◽  
Salmonella Enteritidis ◽  
Sensory Characteristics ◽  
Escherichia Coli O157 ◽  
E Coli ◽  
Log Reduction

Iceberg lettuce is a major component in vegetable salad and has been associated with many outbreaks of foodborne illnesses. In this study, several combinations of lactic acid and hydrogen peroxide were tested to obtain effective antibacterial activity without adverse effects on sensory characteristics. A five-strain mixture of Escherichia coli O157:H7, Salmonella enterica serotype Enteritidis, and Listeria monocytogenes was inoculated separately onto fresh-cut lettuce leaves, which were later treated with 1.5% lactic acid plus 1.5% hydrogen peroxide (H2O2) at 40°C for 15 min, 1.5% lactic acid plus 2% H2O2 at 22°C for 5 min, and 2% H2O2 at 50°C for 60 or 90 s. Control lettuce leaves were treated with deionized water under the same conditions. A 4-log reduction was obtained for lettuce treated with the combinations of lactic acid and H2O2 for E. coli O157:H7 and Salmonella Enteritidis, and a 3-log reduction was obtained for L. monocytogenes. However, the sensory characteristics of lettuce were compromised by these treatments. The treatment of lettuce leaves with 2% H2O2 at 50°C was effective not only in reducing pathogenic bacteria but also in maintaining good sensory quality for up to 15 days. A ≤4-log reduction of E. coli O157:H7 and Salmonella Enteritidis was achieved with the 2% H2O2 treatment, whereas a 3-log reduction of L. monocytogenes was obtained. There was no significant difference (P &gt; 0.05) between pathogen population reductions obtained with 2% H2O2 with 60- and 90-s exposure times. Hydrogen peroxide residue was undetectable (the minimum level of sensitivity was 2 ppm) on lettuce surfaces after the treated lettuce was rinsed with cold water and centrifuged with a salad spinner. Hence, the treatment of lettuce with 2% H2O2 at 50°C for 60 s is effective in initially reducing substantial populations of foodborne pathogens and maintaining high product quality.

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