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51. 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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53. Enhanced Subtyping scheme for Salmonella Enteritidis

Author

Zheng, Jie, Keys, Christine E., Zhao, Shaohua, Meng, Jianghong, and Brown, Eric W.

Subjects
Salmonella enteritidis -- Research, Salmonella enteritidis -- Diseases, Lymphocytes -- Histology, Lymphocytes -- Methods
Abstract

To improve pulsed-field gel electrophoresis-based strain discrimination of 76 Salmonella Enteritidis strains, we evaluated 6 macro-restriction endonucleases, separately and in various combinations. One 3-enzyme subset, Sfil/Pacl/Notl, was highly discriminatory. Five [...]

Published
2007

54. Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing

Author

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

Abstract

Oxford Nanopore sequencing can be used to achieve complete bacterial genomes. However, the error rates of Oxford Nanopore long reads are greater compared to Illumina short reads. Long-read assemblers using a variety of assembly algorithms have been developed to overcome this deficiency, which have not been benchmarked for genomic analyses of bacterial pathogens using Oxford Nanopore long reads. In this study, long-read assemblers, namely Canu, Flye, Miniasm/Racon, Raven, Redbean, and Shasta, were thus benchmarked using Oxford Nanopore long reads of bacterial pathogens. Ten species were tested for mediocre- and low-quality simulated reads, and 10 species were tested for real reads. Raven was the most robust assembler, obtaining complete and accurate genomes. All Miniasm/Racon and Raven assemblies of mediocre-quality reads provided accurate antimicrobial resistance (AMR) profiles, while the Raven assembly of Klebsiella variicola with low-quality reads was the only assembly with an accurate AMR profile among all assemblers and species. All assemblers functioned well for predicting virulence genes using mediocre-quality and real reads, whereas only the Raven assemblies of low-quality reads had accurate numbers of virulence genes. Regarding multilocus sequence typing (MLST), Miniasm/Racon was the most effective assembler for mediocre-quality reads, while only the Raven assemblies of Escherichia coli O157:H7 and K. variicola with low-quality reads showed positive MLST results. Miniasm/Racon and Raven were the best performers for MLST using real reads. The Miniasm/Racon and Raven assemblies showed accurate phylogenetic inference. For the pan-genome analyses, Raven was the strongest assembler for simulated reads, whereas Miniasm/Racon and Raven performed the best for real reads. Overall, the most robust and accurate assembler was Raven, closely followed by Miniasm/Racon.

Published
2020

58. Antimicrobial resistance of Escherichia coli O26, O103, O111, O128, and O145 from animals and humans. (Research)

Author

Schroeder, Carl M., Meng, Jianghong, Zhao, Shaohua, DebRoy, Chitrita, Torcolini, Jocelyn, Zhao, Cuiwei, McDermott, Patrick F., Wagner, David D., Walker, Robert D., and White, David G.

Subjects
Cross infection -- Causes of, Nosocomial infections, Escherichia coli -- Health aspects, Meningitis -- Causes of, Urinary tract infections -- Causes of
Abstract

Susceptibilities to fourteen antimicrobial agents important in clinical medicine and agriculture were determined for 752 Escherichia coli isolates of serotypes O26, O103, Ol11, O128, and O145. Strains of these, serotypes [...]

Published
2002

59. Antimicrobial resistance of Escherichia coli O157 isolated from humans, cattle, swine, and food

Author

Schroeder, Carl M., Zhao, Cuiwei, DebRoy, Chitrita, Torcolini, Jocelyn, Zhao, Shaohua, White, David G., Wagner, David D., McDermott, Patrick F., Walker, Robert D., and Meng, Jianghong

Subjects
Microbiological research -- Analysis, Escherichia coli -- Physiological aspects, Toxins -- Physiological aspects, Tetracycline -- Physiological aspects, Biological sciences
Abstract

Research has been conducted on the Escherichia coli O157 isolates, recovered from human, swine, food and cattle. The prevalence of the antimicrobial resistance in these isolates has been investigated and the results indicate that selection pressure caused by the use of the tetracycline derivatives affect antimicrobial resistance in Shiga- and non-Shiga toxin-producing Escherichia coli O157.

Published
2002

60. Prevalence of Campylobacter spp. Escherichia coli, and Salmonella serovars in retail chicken, turkey, pork, and beef from the Greater Washington, D.C. area

Author

Zhao, Cuiwei, Ge, Beilei, De Villena, Juan, Sudler, Robert, Yeh, Emily, Zhao, Shaohua, White, David G., Wagner, David, and Meng, Jianghong

Subjects
Meat -- Contamination, Foodborne diseases -- Research, Biological sciences
Abstract

Raw meat at many retail stores may be contaminated with bacteria that cause food poisoning. Analysis of meat samples from 59 stores in Washington, DC, found that 71% of the chicken samples were contaminated with Campylobacter and 39% were contaminated with E. coli. Turkey, beef, and pork were less likely to be contaminated.

Published
2001

61. The isolation of antibiotic-resistant Salmonella from retail ground meats

Author

White, David G., Zhao, Shaohua, Sudler, Robert, Ayers, Sherry, Friedman, Sharon, Chen, Sheng, McDermott, Patrick F., McDermott, Shawn, Wagner, David D., and Meng, Jianghong

Subjects
Salmonella, Drug resistance in microorganisms -- Statistics, Meat -- Contamination
Abstract

Researchers discovered that 20% of 200 meat samples they tested from three grocery stores were contaminated with Salmonella. Eighty-four percent of the Salmonella strains were resistant to one antibiotic, half were resistant to three antibiotics, and some were resistant to nine or more different antibiotics. This is a direct result of the use of antibiotics in food animals.

Published
2001

62. Availability of glutamate and arginine during acid challenge determines cell density-dependent survival phenotype of Escherichia coli strains

Author

Cui, Shenghui, Meng, Jianghong, and Bhagwat, Arvind A.

Subjects
Escherichia coli -- Research, Stress (Physiology) -- Environmental aspects, Biological sciences
Abstract

Escherichia coli does not produce a diffusible substance that protects the bacterium from an acid challenge. Acid tolerance appears to involve the induction of glutamate- and arginine-decarboxylase acid survival pathways.

Published
2001

63. Identification and characterization of integron-mediated antibiotic resistance among Shiga toxin-producing Escherichia coli isolates

Author

Zhao, Shaohua, White, David G., Ge, Beilei, Ayers, Sherry, Friedman, Sharon, English, Linda, Wagner, David, Gaines, Stuart, and Meng, Jianghong

Subjects
Drug resistance in microorganisms -- Reports, Escherichia coli, Biological sciences
Abstract

Researchers report the first documentation of genes for antibiotic resistance in Shiga toxin-producing E. coli, including strain O157:H7. Seventy-eight percent of the 50 isolates examined were resistant to two or more antibiotic classes, with resistance to streptomycin, sulfamethoxazole, and tetracycline being most common.

Published
2001

72. 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, Zhang,Jianmin, 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

Abstract

Zeqiang Zhan,1 Xuebin Xu,2 Zhen Gu,3 Jianghong Meng,4 Xiayidan Wufuer,5 Mingliu Wang,6 Meilian Huang,7 Jianhui Chen,8 Chunmei Jing,9 Zhiying Xiong,1 Mei Zeng,10 Ming Liao,1 Jianmin Zhang1 1National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Key Laboratory of Zoonoses, Ministry of Agriculture, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; 2Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China; 3Emerging Infections Program China Office, Beijing, 102206, China; 4Department of Food Science and Nutrition, University of Maryland, College Park, Maryland 20742, USA; 5Xinjiang Uygur Autonomous Region Center for Disease Control and Prevention, Urumchi 830001, China; 6Guangxi Zhuang Autonomous Region Disease Prevention and Control Center, Nanning 530028, China; 7Xiamen City Children’s Hospital, Xiamen 361006, China; 8Fujian Provincial Center for Disease Control and Prevention, Fuzhou 350001, China; 9Chongqing City Children’s Hospital, Chongqing 400014, China; 10Department of Infectious Diseases, Children’s Hospital of Fudan University, Shanghai 200336, ChinaCorrespondence: Mei ZengDepartment of Infectious Diseases, Children’s Hospital of Fudan University, 399 Wanyuan Road, Shanghai 201102, ChinaEmail zengmeigao@aliyun.comJianmin ZhangCollege of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, ChinaTel +86 20 8528 0240Fax +86 20 8528 5282Email junfeng-v@163.comPurpose: 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 clinic

Published
2019

82. Resistant bacteria in retail meats and antimicrobial use in animals

Author

Barber, David, Miller, Gay, McNamara, Paul, Sundberg, Paul, Vogel, Lyle P., Blackman, Burton T., White, David G., McDermott, Patrick F., Meng, Jianghong, McDonald, L. Clifford, Sorensen, Thomas Lund, Wegener, Henrick Caspar, and Frimodt-Moller, Niels

Published
2002

83. Genomic characterisation of the population structure and antibiotic resistance of Salmonella entericaserovar 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.

Abstract

Multidrug-resistant (MDR) SalmonellaInfantis has disseminated worldwide, mainly linked to the consumption of poultry products. Evidence shows dissemination of this pathogen in Chile; however, studies are primarily limited to phenotypic data or involve few isolates. As human cases of SalmonellaInfantis infections have substantially increased in recent years, this study aimed to characterise the genomic epidemiology and antimicrobial-resistance profiles of isolates obtained from different sources, aiming to inform effective surveillance and control measures.

Published
2024
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85. Proposed Epidemiological Cutoff Values for Ceftriaxone, Cefepime, and Colistin in Salmonella

Author

Tyson, Gregory H., primary, Bodeis-Jones, Sonya, additional, Caidi, Hayat, additional, Cook, Kimberly, additional, Dessai, Uday, additional, Haro, Jovita, additional, McCullough, Andre E., additional, Meng, Jianghong, additional, Morales, Cesar A., additional, Lawrence, Jodie Plumblee, additional, Tillman, Glenn E., additional, Winslow, Angela, additional, and Miller, Ron A., additional

Published
2018
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90. Metagenomic Analysis of Bacteria, Fungi, Bacteriophages, and Helminths in the Gut of Giant Pandas

Author

Yang, Shengzhi, primary, Gao, Xin, additional, Meng, Jianghong, additional, Zhang, Anyun, additional, Zhou, Yingmin, additional, Long, Mei, additional, Li, Bei, additional, Deng, Wenwen, additional, Jin, Lei, additional, Zhao, Siyue, additional, Wu, Daifu, additional, He, Yongguo, additional, Li, Caiwu, additional, Liu, Shuliang, additional, Huang, Yan, additional, Zhang, Hemin, additional, and Zou, Likou, additional

Published
2018
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94. Isolation and characterization of Listeria monocytogenes isolates from ready-to-eat foods in Florida

Author

Yuelian Shen, Yan Liu, Yifan Zhang, Cripe, Jennifer, Conway, William, Meng, Jianghong, Hall, Grace, and Bhagwat, Arvind A.

Subjects
Listeria monocytogenes -- Research, Convenience foods -- Research, Convenience foods -- Contamination, Convenience foods -- Health aspects, Biological sciences
Abstract

A study aimed to analyze ready-to-eat food samples for the presence of Listeria monocytogenes, determine the pulsed-field gel electrophoresis (PFGE) patterns and antimicrobial susceptibility profiles of the isolates, measure the efficiency of an Listeria monocytogenes-specific bacteriophage cocktail for lysing the isolates and examine and characterize the isolates ability to withstand acid challenge. It was able to differentiate food-borne isolates based on antibiotic resistance and acid tolerance phenotypes in combination with phenotypic analysis.

Published
2006

100. Characterization of multiple-antimicrobial-resistant Salmonella serovars isolated from retail meats

Author

Chen, Sheng, Zhao, Shaohua, White, David G., Schroeder, Carl M., Lu, Ran, yang, Hanchun, McDermott, Patrick F., Ayers, Sherry, and Meng, Jianghong

Subjects
Statistics, Salmonella, Meat, Drug resistance in microorganisms, Biological sciences
Abstract

Research demonstrates 82% of the 133 Salmonella isolates are resistant to at least one antimicrobial agent. The isolates collected from the meats purchased in the United States and China display resistance to different types of antimicrobials, indicating that the isolates are commonly resistant to multiple antimicrobials, including ceftriaxone. Genes conferring this resistance are examined.

Published
2004

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