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26


Casirivimab-Imdevimab for Treatment of COVID-19 in Solid Organ Transplant Recipients: an Early Experience

Dhand, Abhay; Lobo, Stephen A; Wolfe, Kevin; Feola, Nicholas; Lee, Leslie; Nog, Rajat; Chen, Donald; Glicklich, Daniel; Diflo, Thomas; Nabors, Christopher
PMID: 33724242
ISSN: 1534-6080
CID: 4817612

Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections

Huang, Weihua; Wang, Guiqing; Yin, Changhong; Chen, Donald; Dhand, Abhay; Chanza, Melissa; Dimitrova, Nevenka; Fallon, John T
The surveillance of health care-associated infection (HAI) is an essential element of the infection control program. While whole-genome sequencing (WGS) has widely been adopted for genomic surveillance, its data processing remains to be improved. Here, we propose a three-level data processing pipeline for the precision genomic surveillance of microorganisms without prior knowledge: species identification, multi-locus sequence typing (MLST), and sub-MLST clustering. The former two are closely connected to what have widely been used in current clinical microbiology laboratories, whereas the latter one provides significantly improved resolution and accuracy in genomic surveillance. Comparing to a broadly used reference-dependent alignment/mapping method and an annotation-dependent pan-/core-genome analysis, we implemented our reference- and annotation-independent, k-mer-based, simplified workflow to a collection of Acinetobacter and Enterococcus clinical isolates for tests. By taking both single nucleotide variants and genomic structural changes into account, the optimized k-mer-based pipeline demonstrated a global view of bacterial population structure in a rapid manner and discriminated the relatedness between bacterial isolates in more detail and precision. The newly developed WGS data processing pipeline would facilitate WGS application to the precision genomic surveillance of HAI. In addition, the results from such a WGS-based analysis would be useful for the precision laboratory diagnosis of infectious microorganisms.
PMCID:6843764
PMID: 31554234
ISSN: 2076-2607
CID: 4690152

Complete Genome Sequences of Four Toxigenic Clostridium difficile Clinical Isolates from Patients of the Lower Hudson Valley, New York, USA

Yin, Changhong; Chen, Donald S; Zhuge, Jian; McKenna, Donna; Sagurton, Joan; Wang, Guiqing; Huang, Weihua; Dimitrova, Nevenka; Fallon, John T
Complete genome sequences of four toxigenic Clostridium difficile isolates from patients in the lower Hudson Valley, New York, USA, were achieved. These isolates represent four common sequence types (ST1, ST2, ST8, and ST42) belonging to two distinct phylogenetic clades. All isolates have a 4.0- to 4.2-Mb circular chromosome, and one carries a phage.
PMCID:5786687
PMID: 29371361
ISSN: 2169-8287
CID: 4690032

Complete Genome Sequences of Four Toxigenic Clostridium difficile Clinical Isolates from Patients of the Lower Hudson Valley, New York, USA

Yin, Changhong; Chen, Donald S.; Zhuge, Jian; McKenna, Donna; Sagurton, Joan; Wang, Guiqing; Huang, Weihua; Dimitrova, Nevenka; Fallon, John T.
ISI:000452311000020
ISSN: 2576-098x
CID: 4690602

Evolutionary structure of Plasmodium falciparum major variant surface antigen genes in South America: Implications for epidemic transmission and surveillance

Rougeron, Virginie; Tiedje, Kathryn E; Chen, Donald S; Rask, Thomas S; Gamboa, Dionicia; Maestre, Amanda; Musset, Lise; Legrand, Eric; Noya, Oscar; Yalcindag, Erhan; Renaud, François; Prugnolle, Franck; Day, Karen P
Strong founder effects resulting from human migration out of Africa have led to geographic variation in single nucleotide polymorphisms (SNPs) and microsatellites (MS) of the malaria parasite, Plasmodium falciparum. This is particularly striking in South America where two major founder populations of P. falciparum have been identified that are presumed to have arisen from the transatlantic slave trade. Given the importance of the major variant surface antigen of the blood stages of P. falciparum as both a virulence factor and target of immunity, we decided to investigate the population genetics of the genes encoding "Plasmodium falciparum Erythrocyte Membrane Protein 1" (Pf EMP1) among several countries in South America, in order to evaluate the transmission patterns of malaria in this continent. Deep sequencing of the DBLα domain of var genes from 128 P. falciparum isolates from five locations in South America was completed using a 454 high throughput sequencing protocol. Striking geographic variation in var DBLα sequences, similar to that seen for SNPs and MS markers, was observed. Colombia and French Guiana had distinct var DBLα sequences, whereas Peru and Venezuela showed an admixture. The importance of such geographic variation to herd immunity and malaria vaccination is discussed.
PMCID:5696401
PMID: 29187975
ISSN: 2045-7758
CID: 3153452

Complete Genome Sequence of a Colistin-Resistant Escherichia coli Strain Harboring mcr-1 on an IncHI2 Plasmid in the United States

Gilrane, Victoria L; Lobo, Stephen; Huang, Weihua; Zhuge, Jian; Yin, Changhong; Chen, Donald; Alvarez, Kimberly J; Budhai, Alexandra; Nadelman, Ilana; Dimitrova, Nevenka; Fallon, John T; Wang, Guiqing
We report here the incidental detection and complete genome sequence of a urinary Escherichia coli strain harboring mcr-1 and resistant to colistin in a New York patient returning from Portugal in 2016. This strain, with sequence type 1485 (ST1485), was a non-extended-spectrum beta-lactamase (ESBL) and non-carbapenemase producer and carried the mcr-1 gene on an IncHI2 plasmid.
PMCID:5646399
PMID: 29051246
ISSN: 2169-8287
CID: 4690022

Evidence of strain structure in Plasmodium falciparum var gene repertoires in children from Gabon, West Africa

Day, Karen P; Artzy-Randrup, Yael; Tiedje, Kathryn E; Rougeron, Virginie; Chen, Donald S; Rask, Thomas S; Rorick, Mary M; Migot-Nabias, Florence; Deloron, Philippe; Luty, Adrian J F; Pascual, Mercedes
Existing theory on competition for hosts between pathogen strains has proposed that immune selection can lead to the maintenance of strain structure consisting of discrete, weakly overlapping antigenic repertoires. This prediction of strain theory has conceptual overlap with fundamental ideas in ecology on niche partitioning and limiting similarity between coexisting species in an ecosystem, which oppose the hypothesis of neutral coexistence. For Plasmodium falciparum, strain theory has been specifically proposed in relation to the major surface antigen of the blood stage, known as PfEMP1 and encoded by the multicopy multigene family known as the var genes. Deep sampling of the DBLalpha domain of var genes in the local population of Bakoumba, West Africa, was completed to define whether patterns of repertoire overlap support a role of immune selection under the opposing force of high outcrossing, a characteristic of areas of intense malaria transmission. Using a 454 high-throughput sequencing protocol, we report extremely high diversity of the DBLalpha domain and a large parasite population with DBLalpha repertoires structured into nonrandom patterns of overlap. Such population structure, significant for the high diversity of var genes that compose it at a local level, supports the existence of "strains" characterized by distinct var gene repertoires. Nonneutral, frequency-dependent competition would be at play and could underlie these patterns. With a computational experiment that simulates an intervention similar to mass drug administration, we argue that the observed repertoire structure matters for the antigenic var diversity of the parasite population remaining after intervention.
PMCID:5441825
PMID: 28461509
ISSN: 1091-6490
CID: 2545852

Complete Genome Sequence of a Colistin-Resistant Escherichia coli Strain Harboring mcr-1 on an IncHI2 Plasmid in the United States

Gilrane, Victoria L.; Lobo, Stephen; Huang, Weihua; Zhuge, Jian; Yin, Changhong; Chen, Donald; Alvarez, Kimberly J.; Budhai, Alexandra; Nadelman, Ilana; Dimitrova, Nevenka; Fallon, John T.; Wang, Guiqing
ISI:000460738700015
ISSN: 2576-098x
CID: 4690652

Complete Genome Sequences of Nine Enterovirus D68 Strains from Patients of the Lower Hudson Valley, New York, 2016

Huang, Weihua; Yin, Changhong; Zhuge, Jian; Farooq, Taliya; Yoon, Esther C; Nolan, Sheila M; Chen, Donald; Fallon, John T; Wang, Guiqing
Complete genome sequences of nine enterovirus D68 (EV-D68) strains from patients in New York were obtained in 2016 by metagenomic next-generation sequencing. Comparative genomic analysis suggests that a new subclade B3, with ~4.5% nucleotide divergence from subclade B1 strains causing the 2014 outbreak, is circulating in the United States in 2016.
PMCID:5159578
PMID: 27979945
ISSN: 2169-8287
CID: 2699422

Initial Therapy for Mild to Moderate Clostridium difficile Infection Exploring the Role of Oral Metronidazole Versus Vancomycin in 168 Hospitalized Patientsl

Siegfried, Justin; Dubrovskaya, Yanina; Flagiello, Thomas; Scipione, Marco R.; Phillips, Michael; Papadopoulos, John; Chen, Donald; Safdar, Amar
Background: Oral vancomycin is being increasingly used for treatment of Clostridium difficile infection (CDI), although the feasibility for such approach and avoidance of currently recommended oral metronidazole for mild to moderate (mm)-CDI remain uncertain. We sought to assess treatment response in hospitalized patients with mm-CDI at our university medical center.
ISI:000378861200007
ISSN: 1056-9103
CID: 3853712