Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019

Tapfumanei Mashe; Pimlapas Leekitcharoenphon; Sekesai Mtapuri-Zinyowera; Robert A Kingsley; V Robertson; Andrew Tarupiwa; Marleen M Kock; Evidence P Makombe; Blessmore V Chaibva; Portia Manangazira; Isaac Phiri; Simon Nyadundu; Chriswell T Chigwena; Last P Mufoya; Gaetan Thilliez; Stanely Midzi; Lusubilo W Mwamakamba; Esther L Hamblion; Jorge Matheu; Jacob Dyring Jensen; Frank Møller Aarestrup; Rene S. Hendriksen; Marthie M Ehlers

doi:10.1093/jac/dkaa519

Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019

Tapfumanei Mashe^*, Pimlapas Leekitcharoenphon, Sekesai Mtapuri-Zinyowera, Robert A Kingsley, V Robertson, Andrew Tarupiwa, Marleen M Kock, Evidence P Makombe, Blessmore V Chaibva, Portia Manangazira, Isaac Phiri, Simon Nyadundu, Chriswell T Chigwena, Last P Mufoya, Gaetan Thilliez, Stanely Midzi, Lusubilo W Mwamakamba, Esther L Hamblion, Jorge Matheu, Jacob Dyring JensenFrank Møller Aarestrup, Rene S. Hendriksen, Marthie M Ehlers

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › Research › peer-review

Abstract

BACKGROUND: Typhoid fever, caused by S. enterica ser. Typhi, continues to be a substantial health burden in developing countries. Little is known of the genotypic diversity of S. enterica ser. Typhi in Zimbabwe, but this is key for understanding the emergence and spread of this pathogen and devising interventions for its control.

OBJECTIVES: To report the molecular epidemiology of S. enterica ser. Typhi outbreak strains circulating from 2012 to 2019 in Zimbabwe, using comparative genomics.

METHODS: : A review of typhoid cases records from 2012 to 2019 in Zimbabwe was performed. The phylogenetic relationship of outbreak isolates from 2012 to 2019 and emergence of antibiotic resistance was investigated by whole-genome sequence analysis.

RESULTS: A total 22 479 suspected typhoid cases, 760 confirmed cases were reported from 2012 to 2019 and 29 isolates were sequenced. The majority of the sequenced isolates were predicted to confer resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracycline and fluoroquinolones (including qnrS detection). The qnrS1 gene was associated with an IncN (subtype PST3) plasmid in 79% of the isolates. Whole-genome SNP analysis, SNP-based haplotyping and resistance determinant analysis showed that 93% of the isolates belonged to a single clade represented by multidrug-resistant H58 lineage I (4.3.1.1), with a maximum pair-wise distance of 22 SNPs.

CONCLUSIONS: This study has provided detailed genotypic characterization of the outbreak strain, identified as S. Typhi 4.3.1.1 (H58). The strain has reduced susceptibility to ciprofloxacin due to qnrS carried by an IncN (subtype PST3) plasmid resulting from ongoing evolution to full resistance.

Original language	English
Journal	Journal of Antimicrobial Chemotherapy
Volume	76
Issue number	5
Pages (from-to)	1160–1167
ISSN	0305-7453
DOIs	https://doi.org/10.1093/jac/dkaa519
Publication status	Published - 2021

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Mashe, T., Leekitcharoenphon, P., Mtapuri-Zinyowera, S., Kingsley, R. A., Robertson, V., Tarupiwa, A., Kock, M. M., Makombe, E. P., Chaibva, B. V., Manangazira, P., Phiri, I., Nyadundu, S., Chigwena, C. T., Mufoya, L. P., Thilliez, G., Midzi, S., Mwamakamba, L. W., Hamblion, E. L., Matheu, J., ... Ehlers, M. M. (2021). Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019. Journal of Antimicrobial Chemotherapy, 76(5), 1160–1167. https://doi.org/10.1093/jac/dkaa519

@article{e2275c5850fb4d018596c3085e61af80,

title = "Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019",

abstract = "BACKGROUND: Typhoid fever, caused by S. enterica ser. Typhi, continues to be a substantial health burden in developing countries. Little is known of the genotypic diversity of S. enterica ser. Typhi in Zimbabwe, but this is key for understanding the emergence and spread of this pathogen and devising interventions for its control.OBJECTIVES: To report the molecular epidemiology of S. enterica ser. Typhi outbreak strains circulating from 2012 to 2019 in Zimbabwe, using comparative genomics.METHODS: : A review of typhoid cases records from 2012 to 2019 in Zimbabwe was performed. The phylogenetic relationship of outbreak isolates from 2012 to 2019 and emergence of antibiotic resistance was investigated by whole-genome sequence analysis.RESULTS: A total 22 479 suspected typhoid cases, 760 confirmed cases were reported from 2012 to 2019 and 29 isolates were sequenced. The majority of the sequenced isolates were predicted to confer resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracycline and fluoroquinolones (including qnrS detection). The qnrS1 gene was associated with an IncN (subtype PST3) plasmid in 79% of the isolates. Whole-genome SNP analysis, SNP-based haplotyping and resistance determinant analysis showed that 93% of the isolates belonged to a single clade represented by multidrug-resistant H58 lineage I (4.3.1.1), with a maximum pair-wise distance of 22 SNPs.CONCLUSIONS: This study has provided detailed genotypic characterization of the outbreak strain, identified as S. Typhi 4.3.1.1 (H58). The strain has reduced susceptibility to ciprofloxacin due to qnrS carried by an IncN (subtype PST3) plasmid resulting from ongoing evolution to full resistance.",

author = "Tapfumanei Mashe and Pimlapas Leekitcharoenphon and Sekesai Mtapuri-Zinyowera and Kingsley, {Robert A} and V Robertson and Andrew Tarupiwa and Kock, {Marleen M} and Makombe, {Evidence P} and Chaibva, {Blessmore V} and Portia Manangazira and Isaac Phiri and Simon Nyadundu and Chigwena, {Chriswell T} and Mufoya, {Last P} and Gaetan Thilliez and Stanely Midzi and Mwamakamba, {Lusubilo W} and Hamblion, {Esther L} and Jorge Matheu and Jensen, {Jacob Dyring} and Aarestrup, {Frank M{\o}ller} and Hendriksen, {Rene S.} and Ehlers, {Marthie M}",

note = "{\textcopyright} The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: [email protected].",

year = "2021",

doi = "10.1093/jac/dkaa519",

language = "English",

volume = "76",

pages = "1160–1167",

journal = "Journal of Antimicrobial Chemotherapy",

issn = "0305-7453",

publisher = "Oxford University Press",

number = "5",

}

Mashe, T, Leekitcharoenphon, P, Mtapuri-Zinyowera, S, Kingsley, RA, Robertson, V, Tarupiwa, A, Kock, MM, Makombe, EP, Chaibva, BV, Manangazira, P, Phiri, I, Nyadundu, S, Chigwena, CT, Mufoya, LP, Thilliez, G, Midzi, S, Mwamakamba, LW, Hamblion, EL, Matheu, J, Jensen, JD , Aarestrup, FM , Hendriksen, RS & Ehlers, MM 2021, 'Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019', Journal of Antimicrobial Chemotherapy, vol. 76, no. 5, pp. 1160–1167. https://doi.org/10.1093/jac/dkaa519

TY - JOUR

T1 - Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019

AU - Mashe, Tapfumanei

AU - Leekitcharoenphon, Pimlapas

AU - Mtapuri-Zinyowera, Sekesai

AU - Kingsley, Robert A

AU - Robertson, V

AU - Tarupiwa, Andrew

AU - Kock, Marleen M

AU - Makombe, Evidence P

AU - Chaibva, Blessmore V

AU - Manangazira, Portia

AU - Phiri, Isaac

AU - Nyadundu, Simon

AU - Chigwena, Chriswell T

AU - Mufoya, Last P

AU - Thilliez, Gaetan

AU - Midzi, Stanely

AU - Mwamakamba, Lusubilo W

AU - Hamblion, Esther L

AU - Matheu, Jorge

AU - Jensen, Jacob Dyring

AU - Aarestrup, Frank Møller

AU - Hendriksen, Rene S.

AU - Ehlers, Marthie M

PY - 2021

Y1 - 2021

N2 - BACKGROUND: Typhoid fever, caused by S. enterica ser. Typhi, continues to be a substantial health burden in developing countries. Little is known of the genotypic diversity of S. enterica ser. Typhi in Zimbabwe, but this is key for understanding the emergence and spread of this pathogen and devising interventions for its control.OBJECTIVES: To report the molecular epidemiology of S. enterica ser. Typhi outbreak strains circulating from 2012 to 2019 in Zimbabwe, using comparative genomics.METHODS: : A review of typhoid cases records from 2012 to 2019 in Zimbabwe was performed. The phylogenetic relationship of outbreak isolates from 2012 to 2019 and emergence of antibiotic resistance was investigated by whole-genome sequence analysis.RESULTS: A total 22 479 suspected typhoid cases, 760 confirmed cases were reported from 2012 to 2019 and 29 isolates were sequenced. The majority of the sequenced isolates were predicted to confer resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracycline and fluoroquinolones (including qnrS detection). The qnrS1 gene was associated with an IncN (subtype PST3) plasmid in 79% of the isolates. Whole-genome SNP analysis, SNP-based haplotyping and resistance determinant analysis showed that 93% of the isolates belonged to a single clade represented by multidrug-resistant H58 lineage I (4.3.1.1), with a maximum pair-wise distance of 22 SNPs.CONCLUSIONS: This study has provided detailed genotypic characterization of the outbreak strain, identified as S. Typhi 4.3.1.1 (H58). The strain has reduced susceptibility to ciprofloxacin due to qnrS carried by an IncN (subtype PST3) plasmid resulting from ongoing evolution to full resistance.

AB - BACKGROUND: Typhoid fever, caused by S. enterica ser. Typhi, continues to be a substantial health burden in developing countries. Little is known of the genotypic diversity of S. enterica ser. Typhi in Zimbabwe, but this is key for understanding the emergence and spread of this pathogen and devising interventions for its control.OBJECTIVES: To report the molecular epidemiology of S. enterica ser. Typhi outbreak strains circulating from 2012 to 2019 in Zimbabwe, using comparative genomics.METHODS: : A review of typhoid cases records from 2012 to 2019 in Zimbabwe was performed. The phylogenetic relationship of outbreak isolates from 2012 to 2019 and emergence of antibiotic resistance was investigated by whole-genome sequence analysis.RESULTS: A total 22 479 suspected typhoid cases, 760 confirmed cases were reported from 2012 to 2019 and 29 isolates were sequenced. The majority of the sequenced isolates were predicted to confer resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracycline and fluoroquinolones (including qnrS detection). The qnrS1 gene was associated with an IncN (subtype PST3) plasmid in 79% of the isolates. Whole-genome SNP analysis, SNP-based haplotyping and resistance determinant analysis showed that 93% of the isolates belonged to a single clade represented by multidrug-resistant H58 lineage I (4.3.1.1), with a maximum pair-wise distance of 22 SNPs.CONCLUSIONS: This study has provided detailed genotypic characterization of the outbreak strain, identified as S. Typhi 4.3.1.1 (H58). The strain has reduced susceptibility to ciprofloxacin due to qnrS carried by an IncN (subtype PST3) plasmid resulting from ongoing evolution to full resistance.

U2 - 10.1093/jac/dkaa519

DO - 10.1093/jac/dkaa519

M3 - Journal article

C2 - 33347558

SN - 0305-7453

VL - 76

SP - 1160

EP - 1167

JO - Journal of Antimicrobial Chemotherapy

JF - Journal of Antimicrobial Chemotherapy

IS - 5

ER -

Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019

Abstract

Bibliographical note

UN SDGs

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