TY - JOUR
T1 - Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch
AU - Argimón, Silvia
AU - David, Sophia
AU - Underwood, Anthony
AU - Abrudan, Monica
AU - Wheeler, Nicole E
AU - Kekre, Mihir
AU - Abudahab, Khalil
AU - Yeats, Corin A
AU - Goater, Richard
AU - Taylor, Ben
AU - Harste, Harry
AU - Muddyman, Dawn
AU - Feil, Edward J
AU - Brisse, Sylvain
AU - Holt, Kathryn
AU - Donado-Godoy, Pilar
AU - Ravikumar, K L
AU - Okeke, Iruka N
AU - Carlos, Celia
AU - Aanensen, David M
AU - Fabian bernal, Johan
AU - Arevalo, Alejandra
AU - Fernanda valencia, Maria
AU - Osma castro, Erik C D
AU - Nagaraj, Geetha
AU - Shamanna, Varun
AU - Govindan, Vandana
AU - Prabhu, Akshata
AU - Sravani, D
AU - Shincy, M R
AU - Rose, Steffimole
AU - Ravishankar, K N
AU - Oaikhena, Anderson O
AU - Afolayan, Ayorinde O
AU - Ajiboye, Jolaade J
AU - Ewomazino odih, Erkison
AU - Lagrada, Marietta L
AU - Macaranas, Polle Krystle V
AU - Olorosa, Agnettah M
AU - Gayeta, June M
AU - Masim, Melissa Ana L
AU - Herrera, Elmer M
AU - Molloy, Ali
AU - Stelling, John
PY - 2021/12/1
Y1 - 2021/12/1
N2 - Background: Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting.Methods: We developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR.Results: Using Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1–O3) represented 88.9% of all genomes, whereas capsule types were much more diverse.Conclusions: Pathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance.
AB - Background: Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting.Methods: We developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR.Results: Using Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1–O3) represented 88.9% of all genomes, whereas capsule types were much more diverse.Conclusions: Pathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance.
KW - antimicrobial resistance
KW - epidemiology
KW - genomic surveillance
KW - Klebsiella
KW - Pathogenwatch
U2 - 10.1093/cid/ciab784
DO - 10.1093/cid/ciab784
M3 - Article
SN - 1058-4838
VL - 73
SP - S325–S335
JO - Clinical Infectious Diseases
JF - Clinical Infectious Diseases
IS - Supplement_4
ER -