OzFoodNet into the future: the rapid evolution of foodborne disease surveillance in Australia

2017 ◽  
Vol 38 (4) ◽  
pp. 179
Author(s):  
Ben Polkinghorne ◽  
Anthony Draper ◽  
Michelle Harlock ◽  
Robyn Leader
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Diagnostic Tests ◽  
Disease Surveillance ◽  
Rapid Evolution ◽  
Enteric Pathogens ◽  
Whole Genome ◽  
Foodborne Disease ◽  
Surveillance Network ◽  
Culture Independent

OzFoodNet is Australia's national enhanced foodborne disease surveillance network. OzFoodNet is currently evolving in order to meet the most significant challenges faced since it commenced in 2000: the transition to culture independent diagnostic tests and the introduction of whole genome sequencing for typing of enteric pathogens. This has changed the nature of foodborne disease surveillance and outbreak investigation in Australia.

scholarly journals Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016–2017 Season

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 108 ◽  
Author(s):  
Bruno Simon ◽  
Maxime Pichon ◽  
Martine Valette ◽  
Gwendolyne Burfin ◽  
Mathilde Richard ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Influenza Viruses ◽  
Influenza Surveillance ◽  
Whole Genome ◽  
University Hospitals ◽  
Surveillance Network ◽  
Genetic Traits ◽  
H3n2 Influenza ◽  
The Impact

Influenza viruses cause a remarkable disease burden and significant morbidity and mortality worldwide, and these impacts vary between seasons. To understand the mechanisms associated with these differences, a comprehensive approach is needed to characterize the impact of influenza genomic traits on the burden of disease. During 2016–2017, a year with severe A(H3N2), we sequenced 176 A(H3N2) influenza genomes using next generation sequencing (NGS) for routine surveillance of circulating influenza viruses collected via the French national influenza community-based surveillance network or from patients hospitalized in the intensive care units of the University Hospitals of Lyon, France. Taking into account confounding factors, sequencing and clinical data were used to identify genomic variants and quasispecies associated with influenza severity or vaccine failure. Several amino acid substitutions significantly associated with clinical traits were found, including NA V263I and NS1 K196E which were associated with severity and co-occurred only in viruses from the 3c.2a1 clade. Additionally, we observed that intra-host diversity as a whole and on a specific set of gene segments increased with severity. These results support the use of whole genome sequencing as a tool for the identification of genetic traits associated with severe influenza in the context of influenza surveillance.

scholarly journals Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets

2020 ◽  
Vol 14 (11) ◽  
pp. e0008796 ◽  
Author(s):  
Catherine N. Wilson ◽  
Caisey V. Pulford ◽  
James Akoko ◽  
Blanca Perez Sepulveda ◽  
Alexander V. Predeus ◽  
...  
Keyword(s):  
Lymph Node ◽  
Whole Genome Sequencing ◽  
Bloodstream Infection ◽  
Genome Sequencing ◽  
Mesenteric Lymph Node ◽  
Zoonotic Transmission ◽  
Whole Genome ◽  
Foodborne Disease ◽  
Mesenteric Lymph ◽  
The Uk

Salmonella is a major cause of foodborne disease globally. Pigs can carry and shed non-typhoidal Salmonella (NTS) asymptomatically, representing a significant reservoir for these pathogens. To investigate Salmonella carriage by African domestic pigs, faecal and mesenteric lymph node samples were taken at slaughter in Nairobi, Busia (Kenya) and Chikwawa (Malawi) between October 2016 and May 2017. Selective culture, antisera testing and whole genome sequencing were performed on samples from 647 pigs; the prevalence of NTS carriage was 12.7% in Busia, 9.1% in Nairobi and 24.6% in Chikwawa. Two isolates of S. Typhimurium ST313 were isolated, but were more closely related to ST313 isolates associated with gastroenteritis in the UK than bloodstream infection in Africa. The discovery of porcine NTS carriage in Kenya and Malawi reveals potential for zoonotic transmission of diarrhoeal strains to humans in these countries, but not for transmission of clades specifically associated with invasive NTS disease in Africa.

scholarly journals Analysis of false-negative rapid diagnostic tests for symptomatic malaria in the Democratic Republic of the Congo

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jonathan B. Parr ◽  
Eddy Kieto ◽  
Fernandine Phanzu ◽  
Paul Mansiangi ◽  
Kashamuka Mwandagalirwa ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Diagnostic Tests ◽  
Democratic Republic ◽  
False Negative ◽  
Rapid Diagnostic Tests ◽  
Whole Genome ◽  
Symptomatic Malaria ◽  
Asymptomatic Children ◽  
Republic Of The Congo

AbstractThe majority of Plasmodium falciparum malaria diagnoses in Africa are made using rapid diagnostic tests (RDTs) that detect histidine-rich protein 2. Increasing reports of false-negative RDT results due to parasites with deletions of the pfhrp2 and/or pfhrp3 genes (pfhrp2/3) raise concern about existing malaria diagnostic strategies. We previously identified pfhrp2-negative parasites among asymptomatic children in the Democratic Republic of the Congo (DRC), but their impact on diagnosis of symptomatic malaria is unknown. We performed a cross-sectional study of false-negative RDTs in symptomatic subjects in 2017. Parasites were characterized by microscopy; RDT; pfhrp2/3 genotyping and species-specific PCR assays; a bead-based immunoassay for Plasmodium antigens; and/or whole-genome sequencing. Among 3627 symptomatic subjects, 427 (11.8%) had RDT-/microscopy + results. Parasites from eight (0.2%) samples were initially classified as putative pfhrp2/3 deletions by PCR, but antigen testing and whole-genome sequencing confirmed the presence of intact genes. 56.8% of subjects had PCR-confirmed malaria. Non-falciparum co-infection with P. falciparum was common (13.2%). Agreement between PCR and HRP2-based RDTs was satisfactory (Cohen’s kappa = 0.66) and superior to microscopy (0.33). Symptomatic malaria due to pfhrp2/3-deleted P. falciparum was not observed. Ongoing HRP2-based RDT use is appropriate for the detection of falciparum malaria in the DRC.

scholarly journals Causes of false-negative rapid diagnostic tests for symptomatic malaria in the DRC

2020 ◽  
Author(s):  
Jonathan B Parr ◽  
Eddy Kieto ◽  
Fernandine Phanzu ◽  
Paul Masiangi ◽  
Kashamuka Mwandagalirwa ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Falciparum Malaria ◽  
Genome Sequencing ◽  
Diagnostic Tests ◽  
False Negative ◽  
Rapid Diagnostic Tests ◽  
Whole Genome ◽  
Cross Sectional ◽  
Symptomatic Malaria ◽  
Asymptomatic Children

Background The majority of Plasmodium falciparum malaria diagnoses in Africa are made using rapid diagnostic tests (RDTs) that detect histidine-rich protein 2. Increasing reports of false-negative RDT results due to parasites with deletions of the pfhrp2 and/or pfhrp3 genes (pfhrp2/3) raise concern about existing malaria diagnostic strategies. We previously identified pfhrp2-negative parasites among asymptomatic children in the Democratic Republic of the Congo (DRC), but their impact on diagnosis of symptomatic malaria is unknown. Methods We performed a cross-sectional study of false-negative RDTs in symptomatic subjects in 2017. Parasites were characterized by microscopy; RDT; pfhrp2/3 genotyping and species-specific PCR assays; a multiplex bead-based immunoassay; and/or whole-genome sequencing. Results Among 3,627 symptomatic subjects, we identified 427 (11.8%) RDT-/microscopy+ cases. Parasites from eight (0.2%) samples were initially classified as putative pfhrp2/3 deletions by PCR, but antigen testing and whole-genome sequencing confirmed the presence of intact genes. Malaria prevalence was high (57%) and non-falciparum co-infection common (15%). HRP2-based RDT performance was satisfactory and superior to microscopy. Conclusions Symptomatic malaria due to pfhrp2/3-deleted P. falciparum was not observed in the DRC. Ongoing HRP2-based RDT use is appropriate for the detection of falciparum malaria in the DRC.

scholarly journals The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage in Maintaining a Long-Term Hospital Outbreak of ST228 Methicillin-Resistant Staphylococcus aureus

mBio ◽  
2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Laurence Senn ◽  
Olivier Clerc ◽  
Giorgio Zanetti ◽  
Patrick Basset ◽  
Guy Prod’hom ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tertiary Care ◽  
Enteric Pathogens ◽  
Hospital Environment ◽  
Whole Genome ◽  
Care Hospital ◽  
Methicillin Resistant

ABSTRACT Whole-genome sequencing (WGS) of 228 isolates was used to elucidate the origin and dynamics of a long-term outbreak of methicillin-resistant Staphylococcus aureus (MRSA) sequence type 228 (ST228) SCC mec I that involved 1,600 patients in a tertiary care hospital between 2008 and 2012. Combining of the sequence data with detailed metadata on patient admission and movement confirmed that the outbreak was due to the transmission of a single clonal variant of ST228, rather than repeated introductions of this clone into the hospital. We note that this clone is significantly more frequently recovered from groin and rectal swabs than other clones ( P < 0.0001) and is also significantly more transmissible between roommates ( P < 0.01). Unrecognized MRSA carriers, together with movements of patients within the hospital, also seem to have played a major role. These atypical colonization and transmission dynamics can help explain how the outbreak was maintained over the long term. This “stealthy” asymptomatic colonization of the gut, combined with heightened transmissibility (potentially reflecting a role for environmental reservoirs), means the dynamics of this outbreak share some properties with enteric pathogens such as vancomycin-resistant enterococci or Clostridium difficile . IMPORTANCE Using whole-genome sequencing, we showed that a large and prolonged outbreak of methicillin-resistant Staphylococcus aureus was due to the clonal spread of a specific strain with genetic elements adapted to the hospital environment. Unrecognized MRSA carriers, the movement of patients within the hospital, and the low detection with clinical specimens were also factors that played a role in this occurrence. The atypical colonization of the gut means the dynamics of this outbreak may share some properties with enteric pathogens.

scholarly journals Whole-Genome Sequencing Reveals the Origin and Rapid Evolution of an Emerging Outbreak Strain ofStreptococcus pneumoniae12F

2016 ◽  
Vol 62 (9) ◽  
pp. 1126-1132 ◽  
Author(s):  
Xianding Deng ◽  
Gisele Peirano ◽  
Erin Schillberg ◽  
Tony Mazzulli ◽  
Scott D. Gray-Owen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rapid Evolution ◽  
Whole Genome ◽  
Outbreak Strain

scholarly journals Whole-Genome Sequence of the Mycoplasma mucosicanis Type Strain

2019 ◽  
Vol 8 (41) ◽  
Author(s):  
Rebecca L. Tallmadge ◽  
Patrick K. Mitchell ◽  
Renee Anderson ◽  
Rebecca Franklin-Guild ◽  
Laura B. Goodman
Keyword(s):  
Whole Genome Sequencing ◽  
Clinical Significance ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Diagnostic Tests ◽  
Type Strain ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type

Whole-genome sequencing of Mycoplasma mucosicanis type strain 1642 was performed to support efforts to better understand the clinical significance of Mycoplasma infection in canine health. The availability of this sequence will also further the development of highly specific diagnostic tests.

scholarly journals Interpretation of Whole-Genome Sequencing for Enteric Disease Surveillance and Outbreak Investigation

2019 ◽  
Vol 16 (7) ◽  
pp. 504-512 ◽  
Author(s):  
John M. Besser ◽  
Heather A. Carleton ◽  
Eija Trees ◽  
Steven G. Stroika ◽  
Kelley Hise ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Disease Surveillance ◽  
Outbreak Investigation ◽  
Whole Genome ◽  
Enteric Disease
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