scholarly journals Serotyping of sub-Saharan Africa Salmonella strains isolated from poultry feces using multiplex PCR and whole genome sequencing

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Assèta Kagambèga ◽  
Lari M. Hiott ◽  
David S. Boyle ◽  
Elizabeth A. McMillan ◽  
Poonam Sharma ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
The United States ◽  
Sub Saharan Africa ◽  
Whole Genome ◽  
Chain Reaction ◽  
Food Borne ◽  
Polymerase Chain ◽  
Sub Saharan

Abstract Background Salmonella enterica remains a leading cause of food-borne diseases worldwide. Serotype information is important in food safety and public health activities to reduce the burden of salmonellosis. In the current study, two methods were used to determine serotypes of 111 strains of Salmonella isolated from poultry feces in Burkina Faso. First, Salmonella Multiplex Assay for Rapid Typing (SMART) Polymerase Chain Reaction (PCR) was used to determine the serovars of the S. enterica isolates. Second, serovar prediction based on whole genome sequencing (WGS) data was performed using SeqSero 2.0. Results Among the 111 Salmonella isolates, serotypes for 17 (15.31%) isolates were identified based on comparison to a panel of representative SMART codes previously determined for the 50 most common serovars in the United States. Forty-four (44) new SMART codes were developed for common and uncommon serotypes. A total of 105 (94.59%) isolates were serotyped using SeqSero 2.0 for serovar prediction based on WGS data. Conclusion We determined that SeqSero 2.0 was more comprehensive for identifying Salmonella serotypes from Burkina Faso than SMART PCR.

scholarly journals Serotyping of sub-Saharan Africa Salmonella Strains Isolated from Different Sources Using Multiplex PCR and Capillary Electrophoresis Analysis and whole Genome Sequencing

2020 ◽  
Author(s):  
Assèta Kagambèga ◽  
Lari M. Hiott ◽  
David S. Boyle ◽  
Elizabeth A. McMillan ◽  
Kaisa Haukka ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
The United States ◽  
Sub Saharan Africa ◽  
Whole Genome ◽  
Food Borne ◽  
Polymerase Chain ◽  
Sub Saharan ◽  
Different Sources

Abstract BackgroundSalmonella enterica remains a leading cause of food-borne diseases worldwide. Serotype information is important in food safety and public health activities to reduce the burden of salmonellosis. In the current study, two methods were used to determine serotypes of 225 clinical, environmental, food and veterinary isolates of Salmonella from Burkina Faso. First, Salmonella Multiplex Assay for Rapid Typing (SMART) Polymerase Chain Reaction (PCR) was used to determine the serovars of the S. enterica isolates. Second, serovar prediction based on whole genome sequencing (WGS) data was performed using SeqSero 2.0.ResultsAmong the 225 Salmonella isolates, serotypes for 48 (21.33%) isolates were identified based on comparison to a panel of representative SMART codes previously determined for the 50 most common serovars in the United States. One hundred and seventy-six new SMART codes were developed for common and uncommon serotypes. Serotypes for a total of 205 (91.1%) isolates were identified using SeqSero 2.0 for serovar prediction based on WGS data.ConclusionWe determined that SeqSero 2.0 was more comprehensive for identifying Salmonella serotypes from Burkina Faso than SMART PCR.

scholarly journals SARS-CoV-2 R.1 lineage variants prevailed in Tokyo in March 2021

2021 ◽  
Author(s):  
Katsutoshi Nagano ◽  
Chihiro Tani-Sassa ◽  
Yumi Iwasaki ◽  
Yuna Takatsuki ◽  
Sonoka Yuasa ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Disease Severity ◽  
Genome Sequencing ◽  
Melting Curve ◽  
Melting Curve Analysis ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Crucial Issue ◽  
Chain Reaction ◽  
Polymerase Chain

Background: The spread of SARS-CoV-2 variants, such as B.1.1.7 and B.1.351, has become a crucial issue worldwide. Therefore, we began testing all patients with COVID-19 for the N501Y and E484K mutations associated with SARS-CoV-2. Study design: Nasopharyngeal swab samples from 108 patients who visited our hospital between February and April 2021 were analyzed. The samples were analyzed using reverse transcription-polymerase chain reaction with melting curve analysis to detect the N501Y and E484K mutations. A part of the samples were also subjected to whole genome sequencing. Clinical parameters such as mortality and admission to the intensive care unit were analyzed to examine the association between increased disease severity and the E484K mutation. Results: The ratio of cases showing the 501N+484K mutation rapidly increased from 8% in February to 46% in March. Whole genome sequencing revealed that the viruses with 501N+484K mutation are R.1 lineage variants. Evidence of increased disease severity related to the R.1 variants were not found. Conclusions: We found that the R.1 lineage variants rapidly prevailed in Tokyo in March 2021.

scholarly journals Genomic investigation of a suspected multi-drug resistant Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa

2020 ◽  
Author(s):  
Jennifer Cornick ◽  
Patrick Musicha ◽  
Chikondi Peno ◽  
Ezgi Saeger ◽  
Pui-ying Iroh Toh ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Sub Saharan Africa ◽  
Whole Genome ◽  
Drug Resistant ◽  
Sub Saharan ◽  
Neonatal Care Unit ◽  
Suspected Outbreak

ABSTRACTA suspected outbreak of multi-drug resistant (MDR) Klebsiella pneumoniae in a Malawian neonatal unit was investigated using whole-genome sequencing. Strain-types, virulence and resistance genes of K. pneumoniae isolated from patients from the hospital over a four-year period were identified. A MDR ST340 clone was implicated as the likely outbreak cause.

scholarly journals Serotyping of sub-Saharan Africa Salmonella Strains Isolated from Different Sources Using Multiplex PCR and Capillary Electrophoresis Analysis and whole Genome Sequencing

2020 ◽  
Author(s):  
Assèta Kagambèga ◽  
Lari M. Hiott ◽  
David S. Boyle ◽  
Elizabeth A. McMillan ◽  
Kaisa Haukka ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Whole Genome Sequencing ◽  
Multiplex Pcr ◽  
Genome Sequencing ◽  
Sub Saharan Africa ◽  
Whole Genome ◽  
Sub Saharan ◽  
Different Sources

Abstract The authors have withdrawn this preprint due to author disagreement.

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 PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

2017 ◽  
Vol 22 (23) ◽  
Author(s):  
Celine Nadon ◽  
Ivo Van Walle ◽  
Peter Gerner-Smidt ◽  
Josefina Campos ◽  
Isabel Chinen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Real Time ◽  
Genome Sequencing ◽  
Disease Surveillance ◽  
The United States ◽  
Global Network ◽  
Asia Pacific ◽  
Whole Genome ◽  
Source Attribution ◽  
Food Borne

PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies. WGS data are suitable for surveillance and outbreak purposes and for answering scientific questions pertaining to source attribution, antimicrobial resistance, transmission patterns, and virulence, which will further enable the protection and improvement of public health with respect to food-borne disease.

scholarly journals Whole-Genome Sequencing of Kaposi's Sarcoma-Associated Herpesvirus from Zambian Kaposi's Sarcoma Biopsy Specimens Reveals Unique Viral Diversity

2015 ◽  
Vol 89 (24) ◽  
pp. 12299-12308 ◽  
Author(s):  
Landon N. Olp ◽  
Adrien Jeanniard ◽  
Clemence Marimo ◽  
John T. West ◽  
Charles Wood
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Kaposi's Sarcoma ◽  
Sequence Data ◽  
Kaposi’S Sarcoma ◽  
Sub Saharan Africa ◽  
Whole Genome ◽  
Phylogenetic Clustering ◽  
Western Countries ◽  
Sub Saharan

ABSTRACTKaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent for Kaposi's sarcoma (KS). Both KSHV and KS are endemic in sub-Saharan Africa where approximately 84% of global KS cases occur. Nevertheless, whole-genome sequencing of KSHV has only been completed using isolates from Western countries—where KS is not endemic. The lack of whole-genome KSHV sequence data from the most clinically important geographical region, sub-Saharan Africa, represents an important gap since it remains unclear whether genomic diversity has a role on KSHV pathogenesis. We hypothesized that distinct KSHV genotypes might be present in sub-Saharan Africa compared to Western countries. Using a KSHV-targeted enrichment protocol followed by Illumina deep-sequencing, we generated and analyzed 16 unique Zambian, KS-derived, KSHV genomes. We enriched KSHV DNA over cellular DNA 1,851 to 18,235-fold. Enrichment provided coverage levels up to 24,740-fold; therefore, supporting highly confident polymorphism analysis. Multiple alignment of the 16 newly sequenced KSHV genomes showed low level variability across the entire central conserved region. This variability resulted in distinct phylogenetic clustering between Zambian KSHV genomic sequences and those derived from Western countries. Importantly, the phylogenetic segregation of Zambian from Western sequences occurred irrespective of inclusion of the highly variable genes K1 and K15. We also show that four genes within the more conserved region of the KSHV genome contained polymorphisms that partially, but not fully, contributed to the unique Zambian KSHV whole-genome phylogenetic structure. Taken together, our data suggest that the whole KSHV genome should be taken into consideration for accurate viral characterization.IMPORTANCEOur results represent the largest number of KSHV whole-genomic sequences published to date and the first time that multiple genomes have been sequenced from sub-Saharan Africa, a geographic area where KS is highly endemic. Based on our new sequence data, it is apparent that whole-genome KSHV diversity is greater than previously appreciated and differential phylogenetic clustering exists between viral genomes of Zambia and Western countries. Furthermore, individual genes may be insufficient for KSHV genetic characterization. Continued investigation of the KSHV genetic landscape is necessary in order to effectively understand the role of viral evolution and sequence diversity on KSHV gene functions and pathogenesis.

scholarly journals Molecular typing of bacteria of the genus Asaia in malaria vector Anopheles arabiensis Patton, 1905

2012 ◽  
Vol 44 (2) ◽  
pp. 7 ◽  
Author(s):  
S. Epis ◽  
M. Montagna ◽  
F. Comandatore ◽  
C. Damiani ◽  
A. Diabaté ◽  
...  
Keyword(s):  
Molecular Typing ◽  
Internal Transcribed Spacer ◽  
Anopheles Arabiensis ◽  
Acetic Acid Bacterium ◽  
Sub Saharan Africa ◽  
Randomly Amplified Polymorphic Dna ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Sub Saharan ◽  
Dna Pcr

The acetic acid bacterium <em>Asaia</em> spp. was successfully detected in <em>Anopheles arabiensis</em> Patton, 1905, one of the major vector of human malaria in Sub-Saharan Africa. A collection of 45 <em>Asaia</em> isolates in cellfree media was established from 20 individuals collected from the field in Burkina Faso. 16S rRNA universal polymerase chain reaction (PCR) and specific qPCR, for the detection of <em>Asaia</em> spp. were performed in order to reveal the presence of different bacterial taxa associated with this insect. The isolates were typed by internal transcribed spacer-PCR, BOX-PCR, and randomly amplified polymorphic DNA-PCR, proved the presence of different <em>Asaia</em> in <em>A. arabiensis</em>.

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