scholarly journals Using next generation sequencing to tackle non-typhoidal Salmonella infections

2013 ◽  
Vol 7 (01) ◽  
pp. 001-005 ◽  
Author(s):  
John Wain ◽  
Karen H Keddy ◽  
Rene S Hendriksen ◽  
Salvatore Rubino
Keyword(s):  
Next Generation Sequencing ◽  
Invasive Disease ◽  
Multidrug Resistant ◽  
Sub Saharan Africa ◽  
Next Generation ◽  
Salmonella Infections ◽  
Large Numbers ◽  
Sub Saharan ◽  
Generation Sequencing ◽  
Epidemiology And Public Health

The publication of studies using next generation sequencing to analyse large numbers of bacterial isolates from global epidemics is transforming microbiology, epidemiology and public health. The emergence of multidrug resistant Salmonella Typhimurium ST313 is one example. While the epidemiology in Africa appears to be human-to-human spread and the association with invasive disease almost absolute, more needs to be done to exclude the possibility of animal reservoirs and to transfer the ability to track all Salmonella infections to the laboratories in the front line. In this mini-review we summarise what is currently known about non-typhoidal Salmonella in sub-Saharan Africa and discuss some of the issues which remain.

scholarly journals Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Sofonias K. Tessema ◽  
Jaishree Raman ◽  
Craig W. Duffy ◽  
Deus S. Ishengoma ◽  
Alfred Amambua-Ngwa ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Falciparum Malaria ◽  
Sub Saharan Africa ◽  
Next Generation ◽  
Sub Saharan ◽  
Generation Sequencing

scholarly journals Clinical Integration of Next Generation Sequencing: Coverage and Reimbursement Challenges

2014 ◽  
Vol 42 (S1) ◽  
pp. 22-41 ◽  
Author(s):  
Patricia A. Deverka ◽  
Jennifer C. Dreyfus
Keyword(s):  
Next Generation Sequencing ◽  
Information Needs ◽  
Market Demand ◽  
Next Generation ◽  
Clinical Integration ◽  
Public And Private ◽  
Regulatory Decision ◽  
Large Numbers ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Clinical next generation sequencing (NGS) is a term that refers to a variety of technologies that permit rapid sequencing of large numbers of DNA segments, up to and including entire genomes. As an approach that is playing an increasingly important role in obtaining genetic information from patients, it may be viewed by public and private payers either positively, as an enabler of the promised benefits of personalized medicine, or as “the perfect storm” resulting from the confluence of high market demand, an uproven technology, and an unprepared delivery system. A number of recent studies have noted that coverage and reimbursement will be critical for clinical integration of NGS, yet the evidentiary pathway for payer decision-making is unclear. Although there are multiple reasons for this uncertain reimbursement environment, the situation stems in large part from a long-standing lack of alignment between the information needs of regulators and post-regulatory decision-makers such as payers.

scholarly journals Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center

2015 ◽  
Vol 60 (3) ◽  
pp. 1249-1257 ◽  
Author(s):  
Hajime Kanamori ◽  
Christian M. Parobek ◽  
David J. Weber ◽  
David van Duin ◽  
William A. Rutala ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Acinetobacter Baumannii ◽  
Resistance Genes ◽  
Reference Genome ◽  
Index Case ◽  
Multidrug Resistant ◽  
Next Generation ◽  
The Third ◽  
Burn Center ◽  
Generation Sequencing

Next-generation sequencing (NGS) analysis has emerged as a promising molecular epidemiological method for investigating health care-associated outbreaks. Here, we used NGS to investigate a 3-year outbreak of multidrug-resistantAcinetobacter baumannii(MDRAB) at a large academic burn center. A reference genome from the index case was generated usingde novoassembly of PacBio reads. Forty-six MDRAB isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and sequenced using an Illumina platform. After mapping to the index case reference genome, four samples were excluded due to low coverage, leaving 42 samples for further analysis. Multilocus sequence types (MLST) and the presence of acquired resistance genes were also determined from the sequencing data. A transmission network was inferred from genomic and epidemiological data using a Bayesian framework. Based on single-nucleotide variant (SNV) differences, this MDRAB outbreak represented three sequential outbreaks caused by distinct clones. The first and second outbreaks were caused by sequence type 2 (ST2), while the third outbreak was caused by ST79. For the second outbreak, the MLST and PFGE results were discordant. However, NGS-based SNV typing detected a recombination event and consequently enabled a more accurate phylogenetic analysis. The distribution of resistance genes varied among the three outbreaks. The first- and second-outbreak strains possessed ablaOXA-23-likegroup, while the third-outbreak strains harbored ablaOXA-40-likegroup. NGS-based analysis demonstrated the superior resolution of outbreak transmission networks for MDRAB and provided insight into the mechanisms of strain diversification between sequential outbreaks through recombination.

scholarly journals Fecal Microbiome and Resistome Profiling of Healthy and Diseased Pakistani Individuals Using Next-Generation Sequencing

2021 ◽  
Vol 9 (3) ◽  
pp. 616
Author(s):  
Ome Kalsoom Afridi ◽  
Johar Ali ◽  
Jeong Ho Chang
Keyword(s):  
Next Generation Sequencing ◽  
Multidrug Resistant ◽  
Next Generation ◽  
Initial Screening ◽  
Antibiotic Resistant ◽  
Fecal Microbiome ◽  
Microbial Dysbiosis ◽  
Resistant Genes ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

In this paper, we aimed to characterize the fecal microbiome and its resistomes of healthy and diseased subjects infected with multidrug-resistant Escherichia coli using next-generation sequencing (NGS). After initial screening, 26 stools samples belonging to healthy (n = 13) and diseased subjects (n = 13) were selected and subjected to NGS. A total of 23 and 42 antibiotic-resistant genes (ARGs) conferring resistance to 6 and 9 classes of antibiotics were identified in the resistomes of healthy and diseased subjects, respectively. Bacteroidetes were found to be the major phylum in both healthy and diseased subjects; however, Proteobacteria was predominantly present in the diseased subjects only. Microbial dysbiosis and predominance of various ARGs in the resistome of diseased subjects reflect the excessive usage of antibiotics in Pakistan and warrants immediate attention to regulate the use of various antimicrobials.

scholarly journals New Variant of Multidrug-Resistant Salmonella enterica Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Alison E. Mather ◽  
Tu Le Thi Phuong ◽  
Yunfeng Gao ◽  
Simon Clare ◽  
Subhankar Mukhopadhyay ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Invasive Disease ◽  
Multidrug Resistant ◽  
Sub Saharan Africa ◽  
Whole Genome ◽  
Phase 2 ◽  
Serovar Typhimurium ◽  
Sub Saharan

ABSTRACT Nontyphoidal Salmonella (NTS), particularly Salmonella enterica serovar Typhimurium, is among the leading etiologic agents of bacterial enterocolitis globally and a well-characterized cause of invasive disease (iNTS) in sub-Saharan Africa. In contrast, S. Typhimurium is poorly defined in Southeast Asia, a known hot spot for zoonotic disease with a recently described burden of iNTS disease. Here, we aimed to add insight into the epidemiology and potential impact of zoonotic transfer and antimicrobial resistance (AMR) in S. Typhimurium associated with iNTS and enterocolitis in Vietnam. We performed whole-genome sequencing and phylogenetic reconstruction on 85 human (enterocolitis, carriage, and iNTS) and 113 animal S. Typhimurium isolates isolated in Vietnam. We found limited evidence for the zoonotic transmission of S. Typhimurium. However, we describe a chain of events where a pandemic monophasic variant of S. Typhimurium (serovar I:4,[5],12:i:− sequence type 34 [ST34]) has been introduced into Vietnam, reacquired a phase 2 flagellum, and acquired an IncHI2 multidrug-resistant plasmid. Notably, these novel biphasic ST34 S. Typhimurium variants were significantly associated with iNTS in Vietnamese HIV-infected patients. Our study represents the first characterization of novel iNTS organisms isolated outside sub-Saharan Africa and outlines a new pathway for the emergence of alternative Salmonella variants into susceptible human populations. IMPORTANCE Salmonella Typhimurium is a major diarrheal pathogen and associated with invasive nontyphoid Salmonella (iNTS) disease in vulnerable populations. We present the first characterization of iNTS organisms in Southeast Asia and describe a different evolutionary trajectory from that of organisms causing iNTS in sub-Saharan Africa. In Vietnam, the globally distributed monophasic variant of Salmonella Typhimurium, the serovar I:4,[5],12:i:− ST34 clone, has reacquired a phase 2 flagellum and gained a multidrug-resistant plasmid to become associated with iNTS disease in HIV-infected patients. We document distinct communities of S. Typhimurium and I:4,[5],12:i:− in animals and humans in Vietnam, despite the greater mixing of these host populations here. These data highlight the importance of whole-genome sequencing surveillance in a One Health context in understanding the evolution and spread of resistant bacterial infections.

scholarly journals Prevalence and extent of heteroresistance by next generation sequencing of multidrug-resistant tuberculosis

PLoS ONE ◽  
2017 ◽  
Vol 12 (5) ◽  
pp. e0176522 ◽  
Author(s):  
Darwin J. Operario ◽  
Alexander F. Koeppel ◽  
Stephen D. Turner ◽  
Yongde Bao ◽  
Suporn Pholwat ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Multidrug Resistant ◽  
Next Generation ◽  
Resistant Tuberculosis ◽  
Multidrug Resistant Tuberculosis ◽  
Generation Sequencing

scholarly journals Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant Escherichia coli

Animals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2350
Author(s):  
Ome Kalsoom Afridi ◽  
Johar Ali ◽  
Jeong Ho Chang
Keyword(s):  
Escherichia Coli ◽  
Next Generation Sequencing ◽  
Broiler Chickens ◽  
Multidrug Resistant ◽  
Next Generation ◽  
Pump System ◽  
Fecal Microbiome ◽  
Khyber Pakhtunkhwa ◽  
E Coli ◽  
Generation Sequencing

The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) Escherichia coli (E. coli). Fecal samples (n = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR E. coli. Upon initial screening, thirteen (13) MDR E. coli isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were iroN, iutA, iss, and iucA. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as E. coli, Salmonella enterica, Klebsiella pneumoniae, and Shigella flexneri belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR E. coli of Khyber Pakhtunkhwa for the first time using NGS.

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