Peixuan Zhu

University of Missouri

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Cha‐Mei Tang

Creatv MicroTech (United States)

Pete Amstutz

Creatv MicroTech (United States)

Mark Achtman

University of Warwick

Daniel L. Adams

Creatv MicroTech (United States)

Jeffrey S. Karns

Agricultural Research Service

Daniel R. Shelton

Agricultural Research Service

Luther E. Lindler

Armed Forces Health Surveillance Center

Viviane Chenal‐Francisque

Institut Pasteur

Shuhong Li

Tianjin University of Science and Technology

Pierre Nicolas

Mathématiques et Informatique Appliquées du Génome à l'Environnement

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Institut Pasteur

Max Planck Institute for Infection Biology

Centers for Disease Control and Prevention

Wellcome Sanger Institute

Max Planck Institute for Molecular Genetics

Max Planck Society

Washington University in St. Louis

Academic Medical Center

United States Army Medical Research Institute of Infectious Diseases

Institut Pasteur de Madagascar

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Detection of water-borne E. coli O157 using the integrating waveguide biosensor

Biosensors and Bioelectronics (2005)

Peixuan Zhu Daniel R. Shelton Jeffrey S. Karns Appavu K. Sundaram Shuhong Li

10.1016/j.bios.2005.01.005

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Citations (65)

Microevolution and history of the plague bacillus, Yersinia pestis

Proceedings of the National Academy of Sciences (2004)

Mark Achtman Giovanna Morelli Peixuan Zhu Thierry Wirth Ines Diehl

The association of historical plague pandemics with Yersinia pestis remains controversial, partly because the evolutionary history of this largely monomorphic bacterium was unknown. The microevolution of Y. pestis was therefore investigated by three different multilocus molecular methods, targeting genomewide synonymous SNPs, variation in number of tandem repeats, and insertion of IS 100 insertion elements. Eight populations were recognized by the three methods, and we propose an evolutionary tree for these populations, rooted on Yersinia pseudotuberculosis . The tree invokes microevolution over millennia, during which enzootic pestoides isolates evolved. This initial phase was followed by a binary split 6,500 years ago, which led to populations that are more frequently associated with human disease. These populations do not correspond directly to classical biovars that are based on phenotypic properties. Thus, we recommend that henceforth groupings should be based on molecular signatures. The age of Y. pestis inferred here is compatible with the dates of historical pandemic plague. However, it is premature to infer an association between any modern molecular grouping and a particular pandemic wave that occurred before the 20th century.

Yersinia pestis

Microevolution

Yersinia pseudotuberculosis

plague

Enzootic

10.1073/pnas.0408026101

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Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis

Proceedings of the National Academy of Sciences (2001)

Peixuan Zhu Arie van der Ende Daniel Falush Norbert Brieske Giovanna Morelli

The genetic variability at six polymorphic loci was examined within a global collection of 502 isolates of subgroup III, serogroup A Neisseria meningitidis. Nine "genoclouds" were identified, consisting of genotypes that were isolated repeatedly plus 48 descendent genotypes that were isolated rarely. These genoclouds have caused three pandemic waves of disease since the mid-1960s, the most recent of which was imported from East Asia to Europe and Africa in the mid-1990s. Many of the genotypes are escape variants, resulting from positive selection that we attribute to herd immunity. Despite positive selection, most escape variants are less fit than their parents and are lost because of competition and bottlenecks during spread from country to country. Competition between fit genotypes results in dramatic changes in population composition over short time periods.

Herd Immunity

Pandemic

Microevolution

10.1073/pnas.061386098

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Enrichment and Molecular Analysis of Breast Cancer Disseminated Tumor Cells from Bone Marrow Using Microfiltration

PLoS ONE (2017)

Sreeraj G. Pillai Peixuan Zhu Chidananda Mudalagiriyappa Daniel L. Adams Shuhong Li

Molecular characterization of disseminated tumor cells (DTCs) in the bone marrow (BM) of breast cancer (BC) patients has been hindered by their rarity. To enrich for these cells using an antigen-independent methodology, we have evaluated a size-based microfiltration device in combination with several downstream biomarker assays.BM aspirates were collected from healthy volunteers or BC patients. Healthy BM was mixed with a specified number of BC cells to calculate recovery and fold enrichment by microfiltration. Specimens were pre-filtered using a 70 μm mesh sieve and the effluent filtered through CellSieve microfilters. Captured cells were analyzed by immunocytochemistry (ICC), FISH for HER-2/neu gene amplification status, and RNA in situ hybridization (RISH). Cells eluted from the filter were used for RNA isolation and subsequent qRT-PCR analysis for DTC biomarker gene expression.Filtering an average of 14×106 nucleated BM cells yielded approximately 17-21×103 residual BM cells. In the BC cell spiking experiments, an average of 87% (range 84-92%) of tumor cells were recovered with approximately 170- to 400-fold enrichment. Captured BC cells from patients co-stained for cytokeratin and EpCAM, but not CD45 by ICC. RNA yields from 4 ml of patient BM after filtration averaged 135ng per 10 million BM cells filtered with an average RNA Integrity Number (RIN) of 5.3. DTC-associated gene expression was detected by both qRT-PCR and RISH in filtered spiked or BC patient specimens but, not in control filtered normal BM.We have tested a microfiltration technique for enrichment of BM DTCs. DTC capture efficiency was shown to range from 84.3% to 92.1% with up to 400-fold enrichment using model BC cell lines. In patients, recovered DTCs can be identified and distinguished from normal BM cells using multiple antibody-, DNA-, and RNA-based biomarker assays.

10.1371/journal.pone.0170761

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Detection of E. coli O157:H7 by immunomagnetic separation coupled with fluorescence immunoassay

Biosensors and Bioelectronics (2011)

Peixuan Zhu Daniel R. Shelton Shuhong Li Daniel L. Adams Jeffrey S. Karns

Immunomagnetic separation

Magnetic bead

10.1016/j.bios.2011.09.029

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Citations (79)