Sandor Karpathy - Academia.edu (original) (raw)

Papers by Sandor Karpathy

Research paper thumbnail of Colicins produced by the Escherichia fergusonii strains closelyresemble colicins coded by E. coli

Plasmid DNA of six Escherichia fergusonii colicinogenic strains (three producers of colicin E1, t... more Plasmid DNA of six Escherichia fergusonii colicinogenic strains (three producers of colicin E1, two of Ib and one of Ia) was isolated and the colicin-encoding regions of the corresponding Col plasmids were sequenced. Two new variants of colicin E1, one of colicin Ib, and one of colicin Ia were identified as well as new variants of the colicin E1 and colicin Ib immunity proteins and the colicin E1 lysis polypeptide. The recombinant Escherichia coli producer harboring pColE1 from E. fergusonii strain EF36 (pColE1-EF36) was found to be only partially immune to E1 colicins produced by two other E. fergusonii strains suggesting that pColE1-EF36 may represent an ancestor ColE1 plasmid.

Research paper thumbnail of Multi-Locus Sequence Typing of Ehrlichia chaffeensis Reveals Extensive Genotypic Variation across the United States

The American journal of tropical medicine and hygiene, 2021

Ehrlichia chaffeensis causes human monocytic ehrlichiosis, and its principal vector is the Amblyo... more Ehrlichia chaffeensis causes human monocytic ehrlichiosis, and its principal vector is the Amblyomma americanum tick. The most frequently identified cases of ehrlichiosis come from the southeastern and south central states of the United States. In this study, a molecular typing system was developed that allows for the genetic differentiation of E. chaffeensis isolates. This multi-locus typing system included sequencing and analyzing intergenic regions ECH0033-ECH0035 and ECH0217-ECH0218, plus, variable genes variable length PCR target, 28-kDa, 120-kDa, and hemE. We examined a total of 31 unique isolates from humans and white-tailed deer, and eight DNA samples extracted from infected A. americanum collected from multiple states. This is the largest evaluation of E. chaffeensis isolates and their genotypes. Our findings show that when sequences of all six loci were concatenated and compared, the 39 samples could be separated into 23 genotypes and further grouped into six phylogenetic ...

Research paper thumbnail of Complete Genome Sequence of Rickettsia parkeri Strain Black Gap

Microbiology Resource Announcements

A unique genotype of Rickettsia parkeri , designated R. parkeri strain Black Gap, has thus far be... more A unique genotype of Rickettsia parkeri , designated R. parkeri strain Black Gap, has thus far been associated exclusively with the North American tick, Dermacentor parumapertus . The compete genome consists of a single circular chromosome with 1,329,522 bp and a G+C content of 32.5%.

Research paper thumbnail of Phylogenetic Differentiation of Rickettsia parkeri Reveals Broad Dispersal and Distinct Clustering within North American Strains

Microbiology Spectrum

Since 1937, when Rickettsia parkeri was originally identified in Amblyomma maculatum group ticks,... more Since 1937, when Rickettsia parkeri was originally identified in Amblyomma maculatum group ticks, the recognized range and associated vectors for this pathogen have expanded significantly. In recent years, R. parkeri has been identified in 12 tick species from seven countries in the Americas.

Research paper thumbnail of Characterization of a novel transitional group Rickettsia species (Rickettsia tillamookensis sp. nov.) from the western black-legged tick, Ixodes pacificus

International Journal of Systematic and Evolutionary Microbiology

A previously unrecognized Rickettsia species was isolated in 1976 from a pool of Ixodes pacificus... more A previously unrecognized Rickettsia species was isolated in 1976 from a pool of Ixodes pacificus ticks collected in 1967 from Tillamook County, Oregon, USA. The isolate produced low fever and mild scrotal oedema following intraperitoneal injection into male guinea pigs (Cavia porcellus). Subsequent serotyping characterized this isolate as distinct from recognized typhus and spotted fever group Rickettsia species; nonetheless, the isolate remained unevaluated by molecular techniques and was not identified to species level for the subsequent 30 years. Ixodes pacificus is the most frequently identified human-biting tick in the western United States, and as such, formal identification and characterization of this potentially pathogenic Rickettsia species is warranted. Whole-genome sequencing of the Tillamook isolate revealed a genome 1.43 Mbp in size with 32.4 mol% G+C content. Maximum-likelihood phylogeny of core proteins places it in the transitional group of Rickettsia basal to both...

Research paper thumbnail of Performance of Repeat BinaxNOW Severe Acute Respiratory Syndrome Coronavirus 2 Antigen Testing in a Community Setting, Wisconsin, November 2020–December 2020

Clinical Infectious Diseases

Repeating the BinaxNOW antigen test for severe acute respiratory syndrome coronavirus 2 using 2 g... more Repeating the BinaxNOW antigen test for severe acute respiratory syndrome coronavirus 2 using 2 groups of readers within 30 minutes resulted in high concordance (98.9%) in 2110 encounters. Same-day repeat antigen testing did not significantly improve test sensitivity (77.2% to 81.4%) while specificity remained high (99.6%).

Research paper thumbnail of Isolate-Dependent Differences in Clinical, Pathological, and Transcriptional Profiles following In Vitro and In Vivo Infections with Rickettsia rickettsii

Infection and Immunity

Rickettsia rickettsii , the etiological agent of Rocky Mountain spotted fever (RMSF), a life-thre... more Rickettsia rickettsii , the etiological agent of Rocky Mountain spotted fever (RMSF), a life-threatening tick-borne disease that affects humans and various animal species, has been recognized in medicine and science for more than 100 years. Isolate-dependent differences in virulence of R. rickettsii have been documented for many decades; nonetheless, the specific genetic and phenotypic factors responsible for these differences have not been characterized.

Research paper thumbnail of Integrating population genetic structure, microbiome, and pathogens presence data in Dermacentor variabilis

PeerJ

Tick-borne diseases (TBDs) continue to emerge and re-emerge in several regions of the world, high... more Tick-borne diseases (TBDs) continue to emerge and re-emerge in several regions of the world, highlighting the need for novel and effective control strategies. The development of effective strategies requires a better understanding of TBDs ecology, and given the complexity of these systems, interdisciplinary approaches are required. In recent years, the microbiome of vectors has received much attention, mainly because associations between native microbes and pathogens may provide a new promising path towards the disruption of pathogen transmission. However, we still do not fully understand how host genetics and environmental factors interact to shape the microbiome of organisms, or how pathogenic microorganisms affect the microbiome and vice versa. The integration of different lines of evidence may be the key to improve our understanding of TBDs ecology. In that context, we generated microbiome and pathogen presence data for Dermacentor variabilis, and integrated those data sets with...

Research paper thumbnail of COVID-19 Among Workers in Meat and Poultry Processing Facilities ― 19 States, April 2020

MMWR. Morbidity and Mortality Weekly Report

Research paper thumbnail of Distribution and Occurrence of Amblyomma maculatum sensu lato (Acari: Ixodidae) and Rickettsia parkeri (Rickettsiales: Rickettsiaceae), Arizona and New Mexico, 2017–2019

Journal of Medical Entomology

Amblyomma maculatum Koch sensu lato (s.l.) ticks are the vector of Rickettsia parkeri in Arizona,... more Amblyomma maculatum Koch sensu lato (s.l.) ticks are the vector of Rickettsia parkeri in Arizona, where nine cases of R. parkeri rickettsiosis have been identified since the initial case in 2014. The current study sought to better define the geographic ranges of the vector and pathogen and to assess the potential public health risk posed by R. parkeri in this region of the southwestern United States. A total of 275 A. maculatum s.l. ticks were collected from 34 locations in four counties in Arizona and one county in New Mexico and screened for DNA of Rickettsia species. Rickettsia parkeri was detected in 20.4% of the ticks, including one specimen collected from New Mexico, the first report of R. parkeri in A. maculatum s.l. from this state. This work demonstrates a broader distribution of A. maculatum s.l. ticks and R. parkeri in the southwestern United States than appreciated previously to suggest that R. parkeri rickettsiosis is underrecognized in this region.

Research paper thumbnail of Rickettsia and Anaplasma species in Dermacentor andersoni ticks from Washington

Ticks and Tick-borne Diseases

Research paper thumbnail of Molecular Confirmation of Rickettsia parkeri in Amblyomma ovale Ticks, Veracruz, Mexico

Emerging Infectious Diseases

Research paper thumbnail of First Report of the Introduction of an Exotic Tick, Amblyomma coelebs (Acari: Ixodidae), Feeding on a Human Traveler Returning to the United States from Central America

Research paper thumbnail of Rickettsia parkeri and “Candidatus Rickettsia andeanae” in Amblyomma maculatum (Acari: Ixodidae) collected from the Atlanta metropolitan area, Georgia, United States

Ticks and Tick-borne Diseases

Research paper thumbnail of Multistate Survey of American Dog Ticks (Dermacentor variabilis) for Rickettsia Species

Vector-Borne and Zoonotic Diseases

Research paper thumbnail of Rickettsia parkeri and Candidatus Rickettsia andeanae in Amblyomma maculatum Ticks, Mexico

Emerging Infectious Diseases

several years after initial infection (1). Issues with primaquine (i.e., CYP2D6-poor metabolizers... more several years after initial infection (1). Issues with primaquine (i.e., CYP2D6-poor metabolizers or hemolysis risk in patients with glucose-6-phosphate dehydrogenase deficiency) complicate treatment of dormant hypnozoites that cause relapse (1). A new treatment, tafenoquine, which still causes hemolysis in glucose-6-phosphate dehydrogenase deficiency, was recently approved in the United States as a single dose for prevention of P. vivax malaria relapse (10), although this medication might not reach at-risk groups in South America. Ecuador and Peru currently follow the Pan American Health Organization guidelines regarding primaquine use (https://www.paho.org/hq/dmdocuments/2011/ TreatmentGuidelines-2nd-ed-2010-eng.pdf). Local ministries of health responded quickly to these cases and implemented case surveillance. However, reductions in resources after elimination of local malaria transmission in 2011-2012 severely limited malaria control efforts in Ecuador and Peru. Imported cases of malaria at the Ecuador-Peru border region pose a serious threat of continued resurgence in local transmission. We urge international solutions for Venezuela's humanitarian crisis and augmentation of infectious disease surveillance and control along migration routes and in surrounding regions.

Research paper thumbnail of Distribution and Establishment of the Lone Star Tick in Connecticut and Implications for Range Expansion and Public Health

Journal of Medical Entomology

Research paper thumbnail of A real-time multiplex PCR assay for detection of Elizabethkingia species, and differentiating between E. anophelis and E. meningoseptica

Journal of Clinical Microbiology

Nosocomial infections of Elizabethkingia species can have fatal outcomes if not identified and tr... more Nosocomial infections of Elizabethkingia species can have fatal outcomes if not identified and treated properly. The current diagnostic tools available require culture and isolation, which can extend the reporting time and delay treatment. Using comparative genomics, we developed an efficient multiplex real-time PCR for the simultaneous detection of all known species of Elizabethkingia, as well as differentiating the two most commonly reported species Elizabethkingia anophelis and Elizabethkingia meningoseptica.

Research paper thumbnail of Prevalence and distribution of seven human pathogens in host-seeking Ixodes scapularis (Acari: Ixodidae) nymphs in Minnesota, USA

Ticks and Tick-borne Diseases

Research paper thumbnail of Whole genome analysis of Fusobacterium nucleatum, Rickettsia typhi and Francisella tularensis

The genomes of Fusobacterium nucleatum subspecies polymorphum strain ATCC 10953, Rickettsia typhi... more The genomes of Fusobacterium nucleatum subspecies polymorphum strain ATCC 10953, Rickettsia typhi strain Wilmington, and Francisella tularensis subspecies holarctica strain OSU18 were sequenced, annotated, and analyzed. Each genome was then compared to the sequenced genomes of closely related bacteria. The genome of F. nucleatum ATCC 10953 was compared to two additional F. nucleatum subspecies, subspecies nucleatum and subspecies vincentii. This

Research paper thumbnail of Colicins produced by the Escherichia fergusonii strains closelyresemble colicins coded by E. coli

Plasmid DNA of six Escherichia fergusonii colicinogenic strains (three producers of colicin E1, t... more Plasmid DNA of six Escherichia fergusonii colicinogenic strains (three producers of colicin E1, two of Ib and one of Ia) was isolated and the colicin-encoding regions of the corresponding Col plasmids were sequenced. Two new variants of colicin E1, one of colicin Ib, and one of colicin Ia were identified as well as new variants of the colicin E1 and colicin Ib immunity proteins and the colicin E1 lysis polypeptide. The recombinant Escherichia coli producer harboring pColE1 from E. fergusonii strain EF36 (pColE1-EF36) was found to be only partially immune to E1 colicins produced by two other E. fergusonii strains suggesting that pColE1-EF36 may represent an ancestor ColE1 plasmid.

Research paper thumbnail of Multi-Locus Sequence Typing of Ehrlichia chaffeensis Reveals Extensive Genotypic Variation across the United States

The American journal of tropical medicine and hygiene, 2021

Ehrlichia chaffeensis causes human monocytic ehrlichiosis, and its principal vector is the Amblyo... more Ehrlichia chaffeensis causes human monocytic ehrlichiosis, and its principal vector is the Amblyomma americanum tick. The most frequently identified cases of ehrlichiosis come from the southeastern and south central states of the United States. In this study, a molecular typing system was developed that allows for the genetic differentiation of E. chaffeensis isolates. This multi-locus typing system included sequencing and analyzing intergenic regions ECH0033-ECH0035 and ECH0217-ECH0218, plus, variable genes variable length PCR target, 28-kDa, 120-kDa, and hemE. We examined a total of 31 unique isolates from humans and white-tailed deer, and eight DNA samples extracted from infected A. americanum collected from multiple states. This is the largest evaluation of E. chaffeensis isolates and their genotypes. Our findings show that when sequences of all six loci were concatenated and compared, the 39 samples could be separated into 23 genotypes and further grouped into six phylogenetic ...

Research paper thumbnail of Complete Genome Sequence of Rickettsia parkeri Strain Black Gap

Microbiology Resource Announcements

A unique genotype of Rickettsia parkeri , designated R. parkeri strain Black Gap, has thus far be... more A unique genotype of Rickettsia parkeri , designated R. parkeri strain Black Gap, has thus far been associated exclusively with the North American tick, Dermacentor parumapertus . The compete genome consists of a single circular chromosome with 1,329,522 bp and a G+C content of 32.5%.

Research paper thumbnail of Phylogenetic Differentiation of Rickettsia parkeri Reveals Broad Dispersal and Distinct Clustering within North American Strains

Microbiology Spectrum

Since 1937, when Rickettsia parkeri was originally identified in Amblyomma maculatum group ticks,... more Since 1937, when Rickettsia parkeri was originally identified in Amblyomma maculatum group ticks, the recognized range and associated vectors for this pathogen have expanded significantly. In recent years, R. parkeri has been identified in 12 tick species from seven countries in the Americas.

Research paper thumbnail of Characterization of a novel transitional group Rickettsia species (Rickettsia tillamookensis sp. nov.) from the western black-legged tick, Ixodes pacificus

International Journal of Systematic and Evolutionary Microbiology

A previously unrecognized Rickettsia species was isolated in 1976 from a pool of Ixodes pacificus... more A previously unrecognized Rickettsia species was isolated in 1976 from a pool of Ixodes pacificus ticks collected in 1967 from Tillamook County, Oregon, USA. The isolate produced low fever and mild scrotal oedema following intraperitoneal injection into male guinea pigs (Cavia porcellus). Subsequent serotyping characterized this isolate as distinct from recognized typhus and spotted fever group Rickettsia species; nonetheless, the isolate remained unevaluated by molecular techniques and was not identified to species level for the subsequent 30 years. Ixodes pacificus is the most frequently identified human-biting tick in the western United States, and as such, formal identification and characterization of this potentially pathogenic Rickettsia species is warranted. Whole-genome sequencing of the Tillamook isolate revealed a genome 1.43 Mbp in size with 32.4 mol% G+C content. Maximum-likelihood phylogeny of core proteins places it in the transitional group of Rickettsia basal to both...

Research paper thumbnail of Performance of Repeat BinaxNOW Severe Acute Respiratory Syndrome Coronavirus 2 Antigen Testing in a Community Setting, Wisconsin, November 2020–December 2020

Clinical Infectious Diseases

Repeating the BinaxNOW antigen test for severe acute respiratory syndrome coronavirus 2 using 2 g... more Repeating the BinaxNOW antigen test for severe acute respiratory syndrome coronavirus 2 using 2 groups of readers within 30 minutes resulted in high concordance (98.9%) in 2110 encounters. Same-day repeat antigen testing did not significantly improve test sensitivity (77.2% to 81.4%) while specificity remained high (99.6%).

Research paper thumbnail of Isolate-Dependent Differences in Clinical, Pathological, and Transcriptional Profiles following In Vitro and In Vivo Infections with Rickettsia rickettsii

Infection and Immunity

Rickettsia rickettsii , the etiological agent of Rocky Mountain spotted fever (RMSF), a life-thre... more Rickettsia rickettsii , the etiological agent of Rocky Mountain spotted fever (RMSF), a life-threatening tick-borne disease that affects humans and various animal species, has been recognized in medicine and science for more than 100 years. Isolate-dependent differences in virulence of R. rickettsii have been documented for many decades; nonetheless, the specific genetic and phenotypic factors responsible for these differences have not been characterized.

Research paper thumbnail of Integrating population genetic structure, microbiome, and pathogens presence data in Dermacentor variabilis

PeerJ

Tick-borne diseases (TBDs) continue to emerge and re-emerge in several regions of the world, high... more Tick-borne diseases (TBDs) continue to emerge and re-emerge in several regions of the world, highlighting the need for novel and effective control strategies. The development of effective strategies requires a better understanding of TBDs ecology, and given the complexity of these systems, interdisciplinary approaches are required. In recent years, the microbiome of vectors has received much attention, mainly because associations between native microbes and pathogens may provide a new promising path towards the disruption of pathogen transmission. However, we still do not fully understand how host genetics and environmental factors interact to shape the microbiome of organisms, or how pathogenic microorganisms affect the microbiome and vice versa. The integration of different lines of evidence may be the key to improve our understanding of TBDs ecology. In that context, we generated microbiome and pathogen presence data for Dermacentor variabilis, and integrated those data sets with...

Research paper thumbnail of COVID-19 Among Workers in Meat and Poultry Processing Facilities ― 19 States, April 2020

MMWR. Morbidity and Mortality Weekly Report

Research paper thumbnail of Distribution and Occurrence of Amblyomma maculatum sensu lato (Acari: Ixodidae) and Rickettsia parkeri (Rickettsiales: Rickettsiaceae), Arizona and New Mexico, 2017–2019

Journal of Medical Entomology

Amblyomma maculatum Koch sensu lato (s.l.) ticks are the vector of Rickettsia parkeri in Arizona,... more Amblyomma maculatum Koch sensu lato (s.l.) ticks are the vector of Rickettsia parkeri in Arizona, where nine cases of R. parkeri rickettsiosis have been identified since the initial case in 2014. The current study sought to better define the geographic ranges of the vector and pathogen and to assess the potential public health risk posed by R. parkeri in this region of the southwestern United States. A total of 275 A. maculatum s.l. ticks were collected from 34 locations in four counties in Arizona and one county in New Mexico and screened for DNA of Rickettsia species. Rickettsia parkeri was detected in 20.4% of the ticks, including one specimen collected from New Mexico, the first report of R. parkeri in A. maculatum s.l. from this state. This work demonstrates a broader distribution of A. maculatum s.l. ticks and R. parkeri in the southwestern United States than appreciated previously to suggest that R. parkeri rickettsiosis is underrecognized in this region.

Research paper thumbnail of Rickettsia and Anaplasma species in Dermacentor andersoni ticks from Washington

Ticks and Tick-borne Diseases

Research paper thumbnail of Molecular Confirmation of Rickettsia parkeri in Amblyomma ovale Ticks, Veracruz, Mexico

Emerging Infectious Diseases

Research paper thumbnail of First Report of the Introduction of an Exotic Tick, Amblyomma coelebs (Acari: Ixodidae), Feeding on a Human Traveler Returning to the United States from Central America

Research paper thumbnail of Rickettsia parkeri and “Candidatus Rickettsia andeanae” in Amblyomma maculatum (Acari: Ixodidae) collected from the Atlanta metropolitan area, Georgia, United States

Ticks and Tick-borne Diseases

Research paper thumbnail of Multistate Survey of American Dog Ticks (Dermacentor variabilis) for Rickettsia Species

Vector-Borne and Zoonotic Diseases

Research paper thumbnail of Rickettsia parkeri and Candidatus Rickettsia andeanae in Amblyomma maculatum Ticks, Mexico

Emerging Infectious Diseases

several years after initial infection (1). Issues with primaquine (i.e., CYP2D6-poor metabolizers... more several years after initial infection (1). Issues with primaquine (i.e., CYP2D6-poor metabolizers or hemolysis risk in patients with glucose-6-phosphate dehydrogenase deficiency) complicate treatment of dormant hypnozoites that cause relapse (1). A new treatment, tafenoquine, which still causes hemolysis in glucose-6-phosphate dehydrogenase deficiency, was recently approved in the United States as a single dose for prevention of P. vivax malaria relapse (10), although this medication might not reach at-risk groups in South America. Ecuador and Peru currently follow the Pan American Health Organization guidelines regarding primaquine use (https://www.paho.org/hq/dmdocuments/2011/ TreatmentGuidelines-2nd-ed-2010-eng.pdf). Local ministries of health responded quickly to these cases and implemented case surveillance. However, reductions in resources after elimination of local malaria transmission in 2011-2012 severely limited malaria control efforts in Ecuador and Peru. Imported cases of malaria at the Ecuador-Peru border region pose a serious threat of continued resurgence in local transmission. We urge international solutions for Venezuela's humanitarian crisis and augmentation of infectious disease surveillance and control along migration routes and in surrounding regions.

Research paper thumbnail of Distribution and Establishment of the Lone Star Tick in Connecticut and Implications for Range Expansion and Public Health

Journal of Medical Entomology

Research paper thumbnail of A real-time multiplex PCR assay for detection of Elizabethkingia species, and differentiating between E. anophelis and E. meningoseptica

Journal of Clinical Microbiology

Nosocomial infections of Elizabethkingia species can have fatal outcomes if not identified and tr... more Nosocomial infections of Elizabethkingia species can have fatal outcomes if not identified and treated properly. The current diagnostic tools available require culture and isolation, which can extend the reporting time and delay treatment. Using comparative genomics, we developed an efficient multiplex real-time PCR for the simultaneous detection of all known species of Elizabethkingia, as well as differentiating the two most commonly reported species Elizabethkingia anophelis and Elizabethkingia meningoseptica.

Research paper thumbnail of Prevalence and distribution of seven human pathogens in host-seeking Ixodes scapularis (Acari: Ixodidae) nymphs in Minnesota, USA

Ticks and Tick-borne Diseases

Research paper thumbnail of Whole genome analysis of Fusobacterium nucleatum, Rickettsia typhi and Francisella tularensis

The genomes of Fusobacterium nucleatum subspecies polymorphum strain ATCC 10953, Rickettsia typhi... more The genomes of Fusobacterium nucleatum subspecies polymorphum strain ATCC 10953, Rickettsia typhi strain Wilmington, and Francisella tularensis subspecies holarctica strain OSU18 were sequenced, annotated, and analyzed. Each genome was then compared to the sequenced genomes of closely related bacteria. The genome of F. nucleatum ATCC 10953 was compared to two additional F. nucleatum subspecies, subspecies nucleatum and subspecies vincentii. This