Integrating Whole-Genome Sequencing Within the National Antimicrobial Resistance Surveillance Program in the Philippines.

Argimón S., Masim M.A.L., Gayeta J.M., Lagrada M.L., Macaranas P.K.V., Cohen V., et al.

Nature Communications 2020; 11:2719.

Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread.

David S, Reuter S, Harris SR, Glasner C, Feltwell T et al.

Nature microbiology 2019; 4; 11;1919-1929

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.

A McNally, T Kallonen, C Connor, K Abudahab, DM Aanensen, C Horner, SJ Peacock, J Parkhill, J Croucher, J Corander.

mBio 2019; 10 (2), e00644-19

Genomic sequence investigation Streptococcus pyogenes clusters in England (2010-2015).

Coelho JM, Kapatai G, Jironkin A, Al-Shahib A, Daniel R, Dhami C, Laranjeira AM, Chambers T, Phillips S, Tewolde R, Underwood A, Chalker VJ.

Clin Microbiol Infect. 2019; 25(1):96‐101. doi:10.1016/j.cmi.2018.04.011

PANINI: Pangenome Neighbour Identification for Bacterial Populations

K Abudahab, JM Prada, Z Yang, SD Bentley, NJ Croucher, J Corander, DM Aanensen.

Microb Genom. 2019; 5(4):e000220. doi:10.1099/mgen.0.000220

Phandango: an interactive viewer for bacterial population genomics.

J Hadfield, NJ Croucher, RJ Goater, K Abudahab, DM Aanensen, SR Harris.

Bioinformatics 2018; 34 (2), 292-293.

Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey

SR Harris, MJ Cole, G Spiteri, L Sánchez-Busó, D Golparian, et al.

The Lancet Infectious Diseases 2018; 18(7): 758-768

Sustained transmission of high-level azithromycin-resistant Neisseria gonorrhoeae in England: an observational study.

Fifer H, Cole M, Hughes G, Padfield S, Smolarchuk C, Woodford N, Wensley A, Mustafa N, Schaefer U, Myers R, Templeton K, Shepherd J, Underwood A.

Lancet Infect Dis. 2018;18(5):573‐581. doi:10.1016/S1473-3099

Gene exchange drives the ecological success of a multi-host bacterial pathogen.

Richardson EJ, Bacigalupe R, Harrison EM, …..Aanensen DM et al.

Nat Ecol Evol. 2018; 2(9):1468‐1478. doi:10.1038/s41559-018-0617-0

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

Park SE, Pham DT, Boinett C, …. Aanensen DM et al.

Nat Commun. 2018; 9(1):5094. Published 2018 Nov 30. doi:10.1038/s41467-018-07370-z

Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective multinational study.

Grundmann H, Glasner C, Albiger B, Aanensen DM et al.

Lancet Ifect Dis. 2017; 17(2):153‐163. doi:10.1016/S1473-3099(16)30257-2

Scarlet Fever Incident Management Team. Genome analysis following a national increase in Scarlet Fever in England 2014

Chalker V, Jironkin A, Coelho J, Al-Shahib A, Platt S, Kapatai G, Daniel R, Dhami C, Laranjeira M, Chambers T, Guy R, Lamagni T, Harrison T, Chand M, Johnson AP, Underwood A.

BMC Genomics. 2017; 18(1):224. doi:10.1186/s12864-017-3603-z

The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens.

Bayliss SC, Verner-Jeffreys DW, Bartie KL, Aanensen DM et al.

Front Microbiol. 2017; 8:121. doi:10.3389/fmicb.2017.00121

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe.

Aanensen DM, Feil EJ, Holden MT, … Yeats CA, et al.

mBio. 2016;7(3):e00444-16. doi:10.1128/mBio.00444-16

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography.

Argimón S., Abudahab K., Goater R.J.E., Fedosejev A., Bhai J., Glasner C., Feil E.J., Holden M.T.G., Yeats C.A., Grundmann H., Spratt B.G., Aanensen D.M.

Microbial Genomics 2016; 2(11):000093.

Genomic Analysis and Comparison of Two Gonorrhea Outbreaks.

Didelot X, Dordel J, Whittles LK, … Aanensen DM et al.

mBio. 2016;7(3):e00525-16. doi:10.1128/mBio.00525-16

Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently.

David S, Rusniok C, Mentasti M, Gomez-Valero L, Harris SR, Lechat P, Lees J, Ginevra C, Glaser P, Ma L, Bouchier C, Underwood A, Jarraud S, Harrison TG, Parkhill J, Buchrieser C.

Genome Res. 2016; 26(11):1555‐1564. doi:10.1101/gr.209536.116

Species Mash-up.

Argimón S, Aanensen DM.

Nat Rev Microbiol. 2016; 14(12):730. doi:10.1038/nrmicro.2016.175

Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline.

Kapatai G, Sheppard CL, Al-Shahib A, Litt DJ, Underwood AP, Harrison TG, Fry NK. PeerJ.

2016;4:e2477. Published 2016 Sep 14. doi:10.7717/peerj.2477

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.

Sun Z., Harris H.M.B., McCann A., Yang X., Argimón S., et al.

Nature Biotechnology 2015; 6:8322.

Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries.

Argimón S., Konganti K., Chen H., Alekseyenko A.V., Brown S., and Caufield P.W.

Infection Genetics and Evolution 2014; 21:269-278.

Phylogenetic Analysis of Glucosyltransferases and Implications for the Coevolution of Mutans Streptococci with their Mammalian Hosts.

Argimón S., Alekseyenko A.V., DeSalle R., and Caufield P.W.

PLoS One. 2013; 8(2):e56305.

The NIHR Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance (2020). Whole-Genome Sequencing as Part of National and International Surveillance Programmes for Antimicrobial Resistance: A Roadmap.

BMJ Global Health. 5 e002244.

WHO Technical Note (2020): GLASS whole-genome sequencing for surveillance of antimicrobial resistance

WHO Technical Note (2019): Molecular methods for antimicrobial resistance (AMR) diagnostics to enhance the Global Antimicrobial Resistance Surveillance System

Integrating Whole-Genome Sequencing Within the National Antimicrobial Resistance Surveillance Program in the Philippines

Argimón S., Masim M.A.L., Gayeta J.M., Lagrada M.L., Macaranas P.K.V., Cohen V., et al.

Nature Communications 2020; 11:2719.

Phage cocktail SalmoFREE® reduces Salmonella on a commercial broiler farm

V Clavijo, D Baquero, S Hernandez, J C Farfan, J Arias, A Arévalo, P Donado-Godoy, M Vives-Flores.

Poultry Science 2019; 98:5054-5063.

doi: 10.3382/ps/pez251

Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring bla CMY-2 and bla SHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries

Luis Ricardo Castellanos, Linda van der Graaf-van Bloois, Pilar Donado-Godoy, Dik J Mevius, Jaap A Wagenaar, Joost Hordijk, Aldert L Zomer

Antimicrobial Agents Chemotherapy 2019; 63:e02546-18 doi: 10.1128/AAC.02546-18

Antimicrobial Resistance in Salmonella enterica Serovar Paratyphi B Variant Java in Poultry from Europe and Latin America

L Ricardo Castellanos, Linda van der Graaf-van Bloois, Pilar Donado-Godoy, Kees Veldman, Francisco Duarte, María T Acuña, Claudia Jarquín, François-Xavier Weill, Dik J Mevius, Jaap A Wagenaar, Joost Hordijk, Aldert L Zomer

Emerg Infect Dis 2020; 26:1164-1173.

doi: 10.3201/eid2606.191121.

Genomic Characterization of Extended-Spectrum Cephalosporin-Resistant Salmonella enterica in the Colombian Poultry Chain

Luis Ricardo Castellanos, Linda van der Graaf-van Bloois, Pilar Donado-Godoy, et al.

Front Microbiol 2018;9:2431.

doi: 10.3389/fmicb.2018.02431

Impact of Hajj on the S. pneumoniae carriage among Indian pilgrims during 2016- a longitudinal molecular surveillance study.

Ganaie F, Nagaraj G, Govindan V, Ravikumar KL et al.

Travel medicine and infectious disease. 2018; 23; 64-71

Nasopharyngeal Pneumococcal Colonization and Impact of a Single Dose of 13-Valent Pneumococcal Conjugate Vaccine in Indian Children with HIV and Their Unvaccinated Parents.

BK Arya, SD Bhattacharya, Ravikumar KL, et al.

  1. Pediatr Infect Dis J. 2018 May;37(5):451-458.

A Novel approach for serotyping S. pneumoniae using an automated microarray assay with augmented utility.

Govindan V, Shaik AH, Ravikumar KL.

  1. 7(7) 32-34.

Bacterial Profile of Middle Ear Fluid with Recurrent Acute Otitis Media Infection Using Culture Independent 16S rDNA Gene Sequencing.

Nagaraj G, Girdhar A, Chinnappa J, Ganaie F, Govindan V, Ravikumar KL.

J Pediatr Infect Dis. 2018: DOI: 10.1055/s-0038-1675786.

Serotyping and Multiple Carriage Detection of S. pneumoniae in Nasopharyngeal Samples-Multiplex PCR Fluorescent Assisted Fragment Analysis Typing.

Geetha Nagaraj, Ganaie F, Govindan V, Ravikumar KL et al.

EC Microbiology 15.1 (2019): 61-76

One Assay for All: A Microarray technology for identification and Serotyping of Streptococcus pneumoniae in Culture Negative qmPCR Positive Serum Specimens.

Avid Hussain, Ravikumar KL.

Indian Journal of Research, 8 (2019): 168-171.

Molecular surveillance of regional S. pneumoniae serotype distribution in invasive pneumococcal disease among children across

Geetha Nagaraj, Vandana Govindan, Venkatesha. VT, Feroze Ganaie, Ravikumar Kadahalli Lingegowda.

India, Journal of Infectious Diseases and Research (Accepted for publication)

Detection of Meningitis pathogens prevalent in culture negative pediatric CSF samples collected across India with Real-time Multiplex PCR

Geetha Nagaraj, Venkatesha. VT, Vandana Govindan, Feroze Ganaie, Ravikumar Kadahalli Lingegowda.

Frontiers in neurology (Under Review)

Indian population genomic datasets describing the pre-vaccine evolutionary epidemiology of Streptococcus pneumoniae using a Whole Genome Sequencing approach.

Geetha N, Stephanie W. Lo, Vandana G, Feroze G, Venkatesha VT, Ravikumar KL, Stephen D. Bentley, Rebecca A. Gladstone, Robert F. Breiman, Lesley McGee and the Globa Pneumococcal Sequencing Consortium

Microbial Genomics (Under Peer review)

High-resolution genomic profiling of carbapenem-resistant Klebsiella pneumoniae isolates: A multicentric retrospective Indian study

Geetha N, Varun S, Vandana G, Steffimole R, Akshatha KP, Sravani D, Shincy MR, Venkatesha VT, Ravikumar KL.

(Under peer review)

ZMPB allelic variation in Streptococcus pneumoniae isolates causing meningitis in Indian population.

Geetha N, Vandana G, Varun S, Sowmya PR, Venkatesha VT, Ravikumar KL.

Pneumonia (Under review)

Special edition articles under review and delivered on behalf of the NIHR GHRU on AMR

Publication April 2020

Empowering microbiology laboratories in emerging economies with scalable genome sequencing for routine pathogen surveillance

Overcoming data bottlenecks in pathogen genomic surveillance

Good Financial Grant Practice (GFGP): A tool for developing & demonstrating institutional financial & grant management capacity in Global Health

Train the trainer as an effective approach to building global networks of experts in genomic surveillance of AMR

Complexity of genomic epidemiology of carbapenem-resistant Klebsiella pneumoniae isolates in Colombia urges the reinforcement of whole genome sequencing based surveillance programs

High-resolution genomic profiling of carbapenem-resistant Klebsiella pneumoniae isolates: A multicentric retrospective Indian study

Clones and clusters of antimicrobial-resistant Klebsiella from southwestern Nigeria

Rapid genomic characterisation and global surveillance of Klebsiella using Pathogenwatch

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