scholarly journals Using the NCBI AMRFinder Tool to Determine Antimicrobial Resistance Genotype-Phenotype Correlations Within a Collection of NARMS Isolates

2019 ◽  
Author(s):  
Michael Feldgarden ◽  
Vyacheslav Brover ◽  
Daniel H. Haft ◽  
Arjun B. Prasad ◽  
Douglas J. Slotta ◽  
...  
Keyword(s):  
Public Health ◽  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Monitoring System ◽  
Resistance Genes ◽  
Health Problem ◽  
Public Health Problem ◽  
Gene Symbol ◽  
Major Public Health Problem ◽  
Gene Database

AbstractAntimicrobial resistance (AMR) is a major public health problem that requires publicly available tools for rapid analysis. To identify acquired AMR genes in whole genome sequences, the National Center for Biotechnology Information (NCBI) has produced a high-quality, curated, AMR gene reference database consisting of up-to-date protein and gene nomenclature, a set of hidden Markov models (HMMs), and a curated protein family hierarchy. Currently, the Bacterial Antimicrobial Resistance Reference Gene Database contains 4,579 antimicrobial resistance gene proteins and more than 560 HMMs.Here, we describe AMRFinder, a tool that uses this reference dataset to identify AMR genes. To assess the predictive ability of AMRFinder, we measured the consistency between predicted AMR genotypes from AMRFinder against resistance phenotypes of 6,242 isolates from the National Antimicrobial Resistance Monitoring System (NARMS). This included 5,425Salmonella enterica, 770Campylobacterspp., and 47Escherichia coliphenotypically tested against various antimicrobial agents. Of 87,679 susceptibility tests performed, 98.4% were consistent with predictions.To assess the accuracy of AMRFinder, we compared its gene symbol output with that of a 2017 version of ResFinder, another publicly available resistance gene database. Most gene calls were identical, but there were 1,229 gene symbol differences between them, with differences due to both algorithmic differences and database composition. AMRFinder missed 16 loci that Resfinder found, while Resfinder missed 1,147 loci AMRFinder identified. Two missing drug classes from the 2017 version of ResFinder contributed 81% of missed loci. Based on these results, AMRFinder appears to be a highly accurate AMR gene detection system.ImportanceAntimicrobial resistance is a major public health problem. Traditionally, antimicrobial resistance has been identified using phenotypic assays. With the advent of genome sequencing, we now can identify resistance genes and deduce if an isolate could be resistant to antibiotics. We describe a database of 4,579 acquired antimicrobial resistance genes, the largest publicly available, and a software tool to identify genes in bacterial genomes, AMRFinder. Unlike other tools, AMRFinder uses a gene hierarchy to prevent overpredicting what the correct gene call should be, enabling more accurate assessment. To assess these resources, we determined the resistance gene content of over 6,200 bacterial isolates from the National Antimicrobial Resistance Monitoring System that have been assayed using traditional methods and that also have had their genomes sequenced. We also compared our gene assessments to those of a popularly used tool. We found that AMRFinder has a high overall consistency between genotypes and phenotypes.

scholarly journals Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates

2019 ◽  
Vol 63 (11) ◽  
Author(s):  
Michael Feldgarden ◽  
Vyacheslav Brover ◽  
Daniel H. Haft ◽  
Arjun B. Prasad ◽  
Douglas J. Slotta ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Detection System ◽  
Public Health Problem ◽  
Gene Symbol ◽  
Reference Database ◽  
Major Public Health Problem ◽  
Gene Detection ◽  
Content Type ◽  
Gene Database

ABSTRACT Antimicrobial resistance (AMR) is a major public health problem that requires publicly available tools for rapid analysis. To identify AMR genes in whole-genome sequences, the National Center for Biotechnology Information (NCBI) has produced AMRFinder, a tool that identifies AMR genes using a high-quality curated AMR gene reference database. The Bacterial Antimicrobial Resistance Reference Gene Database consists of up-to-date gene nomenclature, a set of hidden Markov models (HMMs), and a curated protein family hierarchy. Currently, it contains 4,579 antimicrobial resistance proteins and more than 560 HMMs. Here, we describe AMRFinder and its associated database. To assess the predictive ability of AMRFinder, we measured the consistency between predicted AMR genotypes from AMRFinder and resistance phenotypes of 6,242 isolates from the National Antimicrobial Resistance Monitoring System (NARMS). This included 5,425 Salmonella enterica, 770 Campylobacter spp., and 47 Escherichia coli isolates phenotypically tested against various antimicrobial agents. Of 87,679 susceptibility tests performed, 98.4% were consistent with predictions. To assess the accuracy of AMRFinder, we compared its gene symbol output with that of a 2017 version of ResFinder, another publicly available resistance gene detection system. Most gene calls were identical, but there were 1,229 gene symbol differences (8.8%) between them, with differences due to both algorithmic differences and database composition. AMRFinder missed 16 loci that ResFinder found, while ResFinder missed 216 loci that AMRFinder identified. Based on these results, AMRFinder appears to be a highly accurate AMR gene detection system.

scholarly journals NEW WORLD LEISHMANIOSIS IN RUSSIAN TOURISTS WHO VISITED SOUTH AMERICAN COUNTRIES AND THE FIRST EXPERIENCE OF THE TREATMENT WITH PERU BALSAM

2017 ◽  
Vol 22 (2) ◽  
pp. 106-112
Author(s):  
A. M Bronshteyn ◽  
N. G Kochergin ◽  
N. A Malyshev ◽  
V. Ya Lashin ◽  
S. V Burova ◽  
...  
Keyword(s):  
Public Health ◽  
Cutaneous Leishmaniasis ◽  
Health Problem ◽  
New World ◽  
Folk Medicine ◽  
Public Health Problem ◽  
Major Public Health Problem ◽  
South American ◽  
Parasite Resistance ◽  
Local Species

Two cases of New World cutaneous leishmaniasis acquired by Russian tourists in Peru and possibly in Bolivia are presented. L. viannia ( L.braziliensis complex) was identified in Liverpool School of Tropical medicine in the patient travelled to Bolivia. The present study aimed to investigate Balsamum peruvianum one of the product of folk medicine of Indians of Amazon region against local species of Leishmania resulted in healing the ulcers. Leishmaniasis is a major public health problem, and the alarming spread of parasite resistance has increased the importance of discovering new therapeutic products.

Development of new dinuclear Fe(III) coordination compounds with in vitro nanomolar antitrypanosomal activity

2021 ◽  
Author(s):  
Felipe Figuerôa Moreira ◽  
Juliana de Araujo Portes ◽  
Nathalia Florencia Barros Azeredo ◽  
Christiane Fernandes ◽  
Adolfo Horn ◽  
...  
Keyword(s):  
Public Health ◽  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Health Problem ◽  
Coordination Compounds ◽  
Public Health Problem ◽  
Neglected Tropical Disease ◽  
Major Public Health Problem ◽  
Protozoan Pathogen

Chagas disease is a neglected tropical disease caused by the protozoan pathogen Trypanosoma cruzi. The disease is the major public health problem affecting about 6 to 7 million people worldwide,...

scholarly journals Smoking in Latin America: a major public health problem

1998 ◽  
Vol 14 (suppl 3) ◽  
pp. S109-S115 ◽  
Author(s):  
Vera Luiza da Costa e Silva ◽  
Sergio Koifman
Keyword(s):  
Public Health ◽  
Latin America ◽  
Latin American ◽  
Health Problem ◽  
Public Health Problem ◽  
Lung Cancer Mortality ◽  
Developed Countries ◽  
Major Public Health Problem ◽  
Tobacco Epidemic ◽  
Latin American Countries

Smoking has become a major public health problem in Latin America, and its scope varies from country to country. Despite difficulties in obtaining methodologically consistent data for the region, we analyzed the results from prevalence surveys in 14 Latin American countries. Smoking prevalence among men varied from 24.1% (Paraguay) to 66.3% (Dominican Republic) and among women from 5.5% (Paraguay) to 26,6% (Uruguay). By applying point prevalence data to the stage model of the tobacco epidemic in developed countries, we concluded that the Latin American countries are in stage 2, i.e., with a clearly rising prevalence among men, a prevalence for women that is beginning to increase, and mortality attributable to smoking among men still not reflecting peak prevalence. None of the countries analyzed appeared to have reached stage 3, in which one observes a downward trend in prevalence of smoking among men and peak prevalence among women, with broad impact on tobacco-related mortality. The only exception appears to be Paraguay, which is still emerging from stage 1, i.e., with low prevalence rates among men, too. Nevertheless, high lung cancer mortality rates in Uruguay and Argentina are comparable to those of the developed countries.

scholarly journals Cerebral Cystic Echinococcosis

2020 ◽  
Vol 2020 ◽  
pp. 1-5
Author(s):  
Abolghasem Siyadatpanah ◽  
Enrico Brunetti ◽  
Amir Emami Zeydi ◽  
Yousef Dadi Moghadam ◽  
Nelson Iván Agudelo Higuita
Keyword(s):  
Public Health ◽  
Health Problem ◽  
Larval Stage ◽  
Cystic Echinococcosis ◽  
Public Health Problem ◽  
Major Public Health Problem ◽  
Cestode Species ◽  
Iranian Patient ◽  
The World ◽  
The Brain

Cystic echinococcosis (CE) is a neglected helminthic disease and major public health problem in several regions of the world. The zoonosis is caused by the larval stage of different cestode species belonging to the genus Echinococcus. CE can affect any organ with the liver and lungs being most commonly involved. The brain is involved in less than 2% of the cases. We report a case of a CE1 echinococcal cyst of the brain in an Iranian patient.

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