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584 results on '"Meng, Jianghong"'

2. Integrative genome-centric metagenomics for surface water surveillance: Elucidating microbiomes, antimicrobial resistance, and their associations

Author

Huang, Xinyang, Toro, Magaly, Reyes-Jara, Angélica, Moreno-Switt, Andrea I, Adell, Aiko D, Oliveira, Celso J․B, Bonelli, Raquel R, Gutiérrez, Sebastián, Álvarez, Francisca P, Rocha, Alan Douglas de Lima, Kraychete, Gabriela B, Chen, Zhao, Grim, Christopher, Brown, Eric, Bell, Rebecca, and Meng, Jianghong

Published
2024
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4. Genomic characterisation of the population structure and antibiotic resistance of Salmonella enterica serovar Infantis in Chile, 2009–2022

Author

Piña-Iturbe, Alejandro, Díaz-Gavidia, Constanza, Álvarez, Francisca P., Barron-Montenegro, Rocio, Álvarez-Espejo, Diana M., García, Patricia, Solís, Doina, Constenla-Albornoz, Rodrigo, Toro, Magaly, Olivares-Pacheco, Jorge, Reyes-Jara, Angélica, Meng, Jianghong, Bell, Rebecca L., and Moreno-Switt, Andrea I.

Published
2024
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8. Unveiling the genomic landscape of Salmonella enterica serotypes Typhimurium, Newport, and Infantis in Latin American surface waters: a comparative analysis

Author

Chen, Zhao, primary, Toro, Magaly, additional, Moreno-Switt, Andrea I., additional, Adell, Aiko D., additional, Delgado-Suárez, Enrique J., additional, Bonelli, Raquel R., additional, Oliveira, Celso J. B., additional, Reyes-Jara, Angélica, additional, Huang, Xinyang, additional, Albee, Brett, additional, Grim, Christopher J., additional, Allard, Marc, additional, Tallent, Sandra M., additional, Brown, Eric W., additional, Bell, Rebecca L., additional, and Meng, Jianghong, additional

Published
2024
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9. Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California

Author

Worley, Jay N, Flores, Kristopher A, Yang, Xun, Chase, Jennifer A, Cao, Guojie, Tang, Shuai, Meng, Jianghong, and Atwill, Edward R

Subjects
Microbiology, Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Foodborne Illness, Biotechnology, Digestive Diseases, Vaccine Related, Prevention, Infectious Diseases, Biodefense, 2.2 Factors relating to the physical environment, Aetiology, Infection, Animals, California, Cattle, Cattle Diseases, Escherichia coli Infections, Escherichia coli O157, Feces, Genomics, Phylogeny, Escherichia coli, O157:H7, STEC, cattle, food-borne pathogens, genomics, Medical microbiology
Abstract

Escherichia coli serotype O157:H7 is a zoonotic food- and waterborne bacterial pathogen that causes a high hospitalization rate and can cause life-threatening complications. Increasingly, E. coli O157:H7 infections appear to originate from fresh produce. Ruminants, such as cattle, are a prominent reservoir of E. coli O157:H7 in the United States. California is one of the most agriculturally productive regions in the world for fresh produce, beef, and milk. The close proximity of fresh produce and cattle presents food safety challenges on a uniquely large scale. We performed a survey of E. coli O157:H7 on 20 farms in California to observe the regional diversity and prevalence of E. coli O157:H7. Isolates were obtained from enrichment cultures of cow feces. Some farms were sampled on two dates. Genomes from isolates were sequenced to determine their relatedness and pathogenic potential. E. coli O157:H7 was isolated from approximately half of the farms. The point prevalence of E. coli O157:H7 on farms was highly variable, ranging from zero to nearly 90%. Within farms, generally one or a few lineages were found, even when the rate of isolation was high. On farms with high isolation rates, a single clonal lineage accounted for most of the isolates. Farms that were visited months after the first visit might have had the same lineages of E. coli O157:H7. Strains of E. coli O157:H7 may be persistent for months on farms.IMPORTANCE This survey of 20 cow-calf operations from different regions of California provides an in depth look at resident Escherichia coli O157:H7 populations at the molecular level. E. coli O157:H7 is found to have a highly variable prevalence, and with whole-genome sequencing, high prevalences in herds were found to be due to a single lineage shed from multiple cows. Few repeat lineages were found between farms in this area; therefore, we predict that E. coli O157:H7 has significant diversity in this area beyond what is detected in this survey. All isolates from this study were found to have pathogenic potential based on the presence of key virulence gene sequences. This represents a novel insight into pathogen diversity within a single subtype and will inform future attempts to survey regional pathogen populations.

Published
2017

12. Tracing Origins of the Salmonella Bareilly Strain Causing a Food-borne Outbreak in the United States

Author

Hoffmann, Maria, Luo, Yan, Monday, Steven R., Gonzalez-Escalona, Narjol, Ottesen, Andrea R., Muruvanda, Tim, Wang, Charles, Kastanis, George, Keys, Christine, Janies, Daniel, Senturk, Izzet F., Catalyurek, Umit V., Wang, Hua, Hammack, Thomas S., Wolfgang, William J., Schoonmaker-Bopp, Dianna, Chu, Alvina, Myers, Robert, Haendiges, Julie, Evans, Peter S., Meng, Jianghong, Strain, Errol A., Allard, Marc W., and Brown, Eric W.

Published
2016

17. Bacteria in Food and Beverage Production

Author

Doyle, Michael P., Steenson, Larry R., Meng, Jianghong, Rosenberg, Eugene, editor, DeLong, Edward F., editor, Lory, Stephen, editor, Stackebrandt, Erko, editor, and Thompson, Fabiano, editor

Published
2013
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20. Escherichia coli

Author

Meng, Jianghong, Schroeder, Carl M., Georgiev, Vassil St., editor, and Simjee, Shabbir, editor

Published
2007
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24. Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health

Author

Rocha, Alan Douglas de Lima, primary, Ferrari, Rafaela Gomes, additional, Pereira, Walter Esfrain, additional, Lima, Laiorayne Araújo de, additional, Givisiez, Patrícia Emília Naves, additional, Moreno-Switt, Andrea Isabel, additional, Toro, Magaly, additional, Delgado-Suárez, Enrique Jesús, additional, Meng, Jianghong, additional, and Oliveira, Celso José Bruno de, additional

Published
2022
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25. Critical Assessment of Short-Read Assemblers for the Metagenomic Identification of Foodborne and Waterborne Pathogens Using Simulated Bacterial Communities

Author

Chen, Zhao, Chen, Zhao, Meng, Jianghong, Chen, Zhao, Chen, Zhao, and Meng, Jianghong

Abstract

Metagenomics offers the highest level of strain discrimination of bacterial pathogens from complex food and water microbiota. With the rapid evolvement of assembly algorithms, defining an optimal assembler based on the performance in the metagenomic identification of foodborne and waterborne pathogens is warranted. We aimed to benchmark short-read assemblers for the metagenomic identification of foodborne and waterborne pathogens using simulated bacterial communities. Bacterial communities on fresh spinach and in surface water were simulated by generating paired-end short reads of Illumina HiSeq, MiSeq, and NovaSeq at different sequencing depths. Multidrug-resistant Salmonella Indiana SI43 and Pseudomonas aeruginosa PAO1 were included in the simulated communities on fresh spinach and in surface water, respectively. ABySS, IDBA-UD, MaSuRCA, MEGAHIT, metaSPAdes, and Ray Meta were benchmarked in terms of assembly quality, identifications of plasmids, virulence genes, Salmonella pathogenicity island, antimicrobial resistance genes, chromosomal point mutations, serotyping, multilocus sequence typing, and whole-genome phylogeny. Overall, MEGHIT, metaSPAdes, and Ray Meta were more effective for metagenomic identification. We did not obtain an optimal assembler when using the extracted reads classified as Salmonella or P. aeruginosa for downstream genomic analyses, but the extracted reads showed consistent phylogenetic topology with the reference genome when they were aligned with Salmonella or P. aeruginosa strains. In most cases, HiSeq, MiSeq, and NovaSeq were comparable at the same sequencing depth, while higher sequencing depths generally led to more accurate results. As assembly algorithms advance and mature, the evaluation of assemblers should be a continuous process.

Published
2022

26. Machine learning-based predictive modeling to identify genotypic traits associated with Salmonella enterica disease endpoints in isolates from ground chicken

Author

Tanui, Collins K., Karanth, Shraddha, Njage, Patrick M.K., Meng, Jianghong, Pradhan, Abani K., Tanui, Collins K., Karanth, Shraddha, Njage, Patrick M.K., Meng, Jianghong, and Pradhan, Abani K.

Abstract

As the cost of genome sequencing of foodborne pathogens decreases, it has become possible to sequence a large number of isolates and evaluate those using machine learning algorithms. This study aimed to utilize machine learning algorithms to predict the disease endpoints in untagged Salmonella genome sequences isolated from ground chicken. Our models recognized genetic patterns in the test dataset based on our training dataset obtained from an extensive literature review, using a semi-supervised approach. Using known genotypes as input features, the semi-supervised random forest model showed the highest overall accuracy of 0.94 (95% confidence interval: 0.85–0.99), and a Kappa value of 0.82, and predicted 87% of the disease endpoints. The model predicted genes associated with specific disease endpoints that were associated with virulence, which could be used as features in predictive modeling endeavors in the future. Our machine learning approach would be useful in different areas of food safety, including identifying pathogen sources, predicting antibiotic resistance, and risk assessment of foodborne pathogens.

Published
2022

34. Molecular epidemiology and antimicrobial resistance of invasive non-typhoidal Salmonella in China, 2007–2016

Author

Zhan, Zeqiang, Xu, Xuebin, Gu, Zhen, Meng, Jianghong, Wufuer, Xiayidan, Wang, Mingliu, Huang, Meilian, Chen, Jianhui, Jing, Chunmei, Xiong, Zhiying, Zeng, Mei, Liao, Ming, and Zhang, Jianmin

Subjects
beta-lactamases, China, multidrug resistant, invasive non-typhoidal Salmonella, pulsed field gel electrophoresis, fluoroquinolones, Original Research
Abstract

Purpose Human infections caused by invasive non-typhoidal Salmonella (iNTS) are highly prevalent worldwide. However, data for such infections in China are scarce. This study reports the epidemiology of iNTS in China. Methods INTS isolates were recovered from blood and other clinical specimens collected during 2007–2016 across five provinces (Shanghai, Xinjiang, Fujian, Guangxi, and Chongqing) in China. Antimicrobial susceptibility was performed using the agar dilution method and molecular epidemiology was performed using standard microbiological techniques. Results A total of 178 iNTS isolates were recovered from approximately 9700 patient specimens during 2007–2016. The predominant serovars were Salmonella Enteritidis (57/178, 32%), Salmonella Choleraesuis (47/178, 26.4%), and Salmonella Typhimurium (24/178, 13.5%). Up to 50 isolates (28.1%) were from patients who were ≤1 year of age, while 28 (15.7%) were from patients who were ≥60 years. Among these isolates, high rates of resistance to nalidixic acid (114/178, 64%), sulfisoxazole (59%), ciprofloxacin (15.2%), and cefotaxime (8.4%) were found. Moreover, 53.4% (95/178) exhibited multidrug resistance, and 3.9% (7/178) showed co-resistance to third-generation cephalosporins and ciprofloxacin. Steadily increasing numbers of nalidixic acid, cefotaxime, and ciprofloxacin-resistant isolates, but decreasing numbers of multidrug resistance isolates were detected during the study period. Detection of quinolone genes in 114 nalidixic acid-resistant isolates showed that 58.3% (67/114) harbored plasmid-mediated quinolone resistance (PMQR) genes [aac(6´)-Ib-cr, qnrA, qnrB, oqxAB, qepA, qnrS, and qnrD] and 98.2% (112/114) exhibited mutations in quinolone resistance determining regions [gyrA, parC, and parE]. Furthermore, we detected beta-lactamases genes in the ceftriaxone-resistant isolates. The most common were blaTEM-1 (93.3%), followed by blaCTX-M-55 (40%), blaCMY-2 (33.3%), and blaOXA-1 (33.3%). Finally, a range of pulsed-field gel electrophoresis patterns were detected among the Salmonella Enteritidis and Salmonella Typhimurium isolates. Conclusion High rates of multidrug resistance and steadily increasing cefotaxime and ciprofloxacin-resistant iNTS could pose a significant challenge for the effective treatment of salmonellosis in China.

Published
2019

36. Diversity of Non-O157 Shiga Toxin-Producing Escherichia coli Isolated from Cattle from Central and Southern Chile

Author

Díaz, Leonela, primary, Gutierrez, Sebastian, additional, Moreno-Switt, Andrea I, additional, Hervé, Luis Pablo, additional, Hamilton-West, Christopher, additional, Padola, Nora Lía, additional, Navarrete, Paola, additional, Reyes-Jara, Angélica, additional, Meng, Jianghong, additional, González-Escalona, Narjol, additional, and Toro, Magaly, additional

Published
2021
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40. Osmoregulated periplasmic glucans of Salmonella enterica serovar Typhimurium are required for optimal virulence in mice

Author

Bhagwat, Arvind A., Jun, Won, Liu, Liu, Kannan, Porteen, Dharne, Mahesh, Pheh, Benedict, Tall, Ben D., Kothary, Mahendra H., Gross, Kenneth C., Angle, Scott, Meng, Jianghong, and Smith, Alien

Subjects
Glucans -- Physiological aspects, Glucans -- Genetic aspects, Glucans -- Research, Microbial metabolism -- Genetic aspects, Microbial metabolism -- Research, Salmonella typhimurium -- Physiological aspects, Salmonella typhimurium -- Genetic aspects, Salmonella typhimurium -- Research, Biological sciences
Abstract

We purified osmoregulated periplasmic glucans (OPGs) from Salmonella enterica serovar Typhimurium and found them to be composed of 100% glucose with 2-linked glucose as the most abundant residue, with terminal glucose, 2,3-linked and 2,6-linked glucose also present in high quantities. The two structural genes for OPG biosynthesis, opgG and opgH, form a bicistronic operon, and insertion of a kanamycin resistance gene cassette into this operon resulted in a strain devoid of OPGs. The opgGH mutant strain was impaired in motility and growth under low osmolarity conditions. The opgGH mutation also resulted in a 2 log increase in the [LD.sub.50] in mice compared to the wild-type strain SL1344. Inability to synthesize OPGs had no significant impact on the organism's lipopolysaccharide pattern or its ability to survive antimicrobial peptides-, detergent-, pH- and nutrient-stress conditions. We observed that the opgGH-defective strain respired at a reduced rate under acidic growth conditions (pH 5.0) and had lower ATP levels compared to the wild-type strain. These data indicate that OPGs of S. Typhimurium contribute towards mouse virulence as well as growth and motility under low osmolarity growth conditions.

Published
2009

43. Additional file 12 of Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing

Author

Chen, Zhao, Erickson, David L., and Meng, Jianghong

Abstract

Additional file 12: Table S12. Numbers of single nucleotide polymorphisms (SNPs) in the hybrid assemblies of bacterial strains with simulated Illumina short reads and mediocre-quality Oxford Nanopore long reads using MaSuRCA, SPAdes, and Unicycler, as determined by aligning to their corresponding reference genomes and expressed as SNPs per 1 million bp of the reference genome.

Published
2020
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46. Additional file 9 of Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing

Author

Chen, Zhao, Erickson, David L., and Meng, Jianghong

Abstract

Additional file 9: Table S9. Genome completeness of the hybrid assemblies of bacterial strains with simulated Illumina short reads and mediocre-quality Oxford Nanopore long reads using MaSuRCA, SPAdes, and Unicycler compared to their corresponding reference genomes.

Published
2020
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50. Additional file 20 of Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing

Author

Chen, Zhao, Erickson, David L., and Meng, Jianghong

Abstract

Additional file 20: Table S20. Plasmids of bacterial strains with real Illumina short reads and Oxford Nanopore long reads, as predicted based on their MaSuRCA, SPAdes, and Unicycler assemblies and compared to their corresponding reference genomes.

Published
2020
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