Global diversity and antimicrobial resistance of typhoid fever pathogens : insights from a meta-analysis of 13,000 Salmonella Typhi genomes
- Carey, Megan, Dyson, Zoe, Ingle, Danielle, Amir, Afreenish, Aworh, Mabel, Chattaway, Marie, Chew, Ka, Crump, John, Feasey, Nicholas, Howden, Benjamin, Keddy, Karen, Maes, Mailis, Parry, Christopher, Van Puyvelde, Sandra, Webb, Hattie, Afolayan, Ayorinde, Alexander, Anna, Anandan, Shalini, Andrews, Jason, Ashton, Philip, Basnyat, Buddha, Bavdekar, Ashish, Bogoch, Isaac, Clemens, John, da Silva, Kesia, De, Anuradha, de Ligt, Joep, Diaz Guevara, Paula, Dolecek, Christiane, Greenhill, Andrew
- Authors: Carey, Megan , Dyson, Zoe , Ingle, Danielle , Amir, Afreenish , Aworh, Mabel , Chattaway, Marie , Chew, Ka , Crump, John , Feasey, Nicholas , Howden, Benjamin , Keddy, Karen , Maes, Mailis , Parry, Christopher , Van Puyvelde, Sandra , Webb, Hattie , Afolayan, Ayorinde , Alexander, Anna , Anandan, Shalini , Andrews, Jason , Ashton, Philip , Basnyat, Buddha , Bavdekar, Ashish , Bogoch, Isaac , Clemens, John , da Silva, Kesia , De, Anuradha , de Ligt, Joep , Diaz Guevara, Paula , Dolecek, Christiane , Greenhill, Andrew
- Date: 2023
- Type: Text , Journal article
- Relation: eLife Vol. 12, no. (2023), p.
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- Description: Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal ‘sentinel’ surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (=3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has becomedominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions: The consortium’s aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. © Carey et al. **Please note that there are multiple authors for this article therefore only the name of the first 30 including Federation University Australia affiliate “Andrew Greenhill” is provided in this record**
- Authors: Carey, Megan , Dyson, Zoe , Ingle, Danielle , Amir, Afreenish , Aworh, Mabel , Chattaway, Marie , Chew, Ka , Crump, John , Feasey, Nicholas , Howden, Benjamin , Keddy, Karen , Maes, Mailis , Parry, Christopher , Van Puyvelde, Sandra , Webb, Hattie , Afolayan, Ayorinde , Alexander, Anna , Anandan, Shalini , Andrews, Jason , Ashton, Philip , Basnyat, Buddha , Bavdekar, Ashish , Bogoch, Isaac , Clemens, John , da Silva, Kesia , De, Anuradha , de Ligt, Joep , Diaz Guevara, Paula , Dolecek, Christiane , Greenhill, Andrew
- Date: 2023
- Type: Text , Journal article
- Relation: eLife Vol. 12, no. (2023), p.
- Full Text:
- Reviewed:
- Description: Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal ‘sentinel’ surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (=3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has becomedominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions: The consortium’s aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. © Carey et al. **Please note that there are multiple authors for this article therefore only the name of the first 30 including Federation University Australia affiliate “Andrew Greenhill” is provided in this record**
A survey of early-career researchers in Australia
- Christian, Katherine, Johnstone, Carolyn, Larkins, Jo-ann, Wright, Wendy, Doran, Michael
- Authors: Christian, Katherine , Johnstone, Carolyn , Larkins, Jo-ann , Wright, Wendy , Doran, Michael
- Date: 2021
- Type: Text , Journal article
- Relation: eLife Vol. 10, no. (2021), p. 1-19
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- Description: Early-career researchers (ECRs) make up a large portion of the academic workforce and their experiences often reflect the wider culture of the research system. Here we surveyed 658 ECRs working in Australia to better understand the needs and challenges faced by this community. Although most respondents indicated a ‘love of science’, many also expressed an intention to leave their research position. The responses highlight how job insecurity, workplace culture, mentorship and ‘questionable research practices’ are impacting the job satisfaction of ECRs and potentially compromising science in Australia. We also make recommendations for addressing some of these concerns. © Christian et al.
- Authors: Christian, Katherine , Johnstone, Carolyn , Larkins, Jo-ann , Wright, Wendy , Doran, Michael
- Date: 2021
- Type: Text , Journal article
- Relation: eLife Vol. 10, no. (2021), p. 1-19
- Full Text:
- Reviewed:
- Description: Early-career researchers (ECRs) make up a large portion of the academic workforce and their experiences often reflect the wider culture of the research system. Here we surveyed 658 ECRs working in Australia to better understand the needs and challenges faced by this community. Although most respondents indicated a ‘love of science’, many also expressed an intention to leave their research position. The responses highlight how job insecurity, workplace culture, mentorship and ‘questionable research practices’ are impacting the job satisfaction of ECRs and potentially compromising science in Australia. We also make recommendations for addressing some of these concerns. © Christian et al.
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