Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in  Salmonella  Typhi in Lahore, Pakistan

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Abstract

Extensively drug-resistant (XDR) Salmonella Typhi has been reported in Sindh province of Pakistan since 2016. The potential for further spread is of serious concern as remaining treatment options are severely limited. We report the phenotypic and genotypic characterization of 27 XDR S. Typhi isolated from patients attending Jinnah Hospital, Lahore, Pakistan. Isolates were identified by biochemical profiling; antimicrobial susceptibility was determined by a modified Kirby–Bauer method. These findings were confirmed using Illumina whole genome nucleotide sequence data. All sequences were compared to the outbreak strain from Southern Pakistan and typed using the S. Typhi genotyping scheme. All isolates were confirmed by a sequence analysis to harbor an IncY plasmid and the CTX-M-15 ceftriaxone resistance determinant. All isolates were of the same genotypic background as the outbreak strain from Sindh province. We report the first emergence of XDR S. Typhi in Punjab province of Pakistan confirmed by whole genome sequencing.

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis (2014)

Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.

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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

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Prokka: rapid prokaryotic genome annotation.

T Seemann (2014)

The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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Author and article information

Journal

Journal ID (nlm-ta): Microorganisms

Journal ID (iso-abbrev): Microorganisms

Journal ID (publisher-id): microorganisms

Title: Microorganisms

Publisher: MDPI

ISSN (Electronic): 2076-2607

Publication date (Electronic): 01 September 2020

Publication date Collection: September 2020

Volume: 8

Issue: 9

Electronic Location Identifier: 1336

Affiliations

[1 ]Allama Iqbal Medical College & Jinnah Hospital (AIMC&JHL), Lahore 54000, Pakistan; ambereen@ 123456outlook.com

[2 ]Department of Microbiology, Government College University, Faisalabad 38000, Pakistan; mian.muhsaeed@ 123456gmail.com (M.S.); mohsinkhurshid@ 123456gcuf.edu.pk (M.K.); drmhrasool@ 123456gcuf.edu.pk (M.H.R.); drsaqalein@ 123456gcuf.edu.pk (M.S.); matifnisar@ 123456gcuf.edu.pk (M.A.N.)

[3 ]Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; nabil-fareed.alikhan@ 123456quadram.ac.uk (N.-F.A.); david.baker@ 123456quadram.ac.uk (D.B.); emma.ainsworth@ 123456quadram.ac.uk (E.V.A.); keith.turner@ 123456quadram.ac.uk (A.K.T.); john.wain@ 123456quadram.ac.uk (J.W.); gemma.langridge@ 123456quadram.ac.uk (G.C.L.)

[4 ]Department of Chemistry, University of Sargodha, Sargodha 40100, Pakistan; fayyaz9@ 123456gmail.com

[5 ]Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK

[6 ]National Institute of Health, Islamabad 45710, Pakistan; maahin1@ 123456yahoo.com

Author notes

[* ]Correspondence: dr.farhanrasheed@ 123456gmail.com (F.R.); muhammad.yasir@ 123456quadram.ac.uk (M.Y.)

Author information

Farhan Rasheed https://orcid.org/0000-0002-5404-1970

Mohsin Khurshid https://orcid.org/0000-0002-3196-2857

Emma V. Ainsworth https://orcid.org/0000-0002-1534-7838

Muhammad Fayyaz ur Rehman https://orcid.org/0000-0003-2901-7212

Gemma C. Langridge https://orcid.org/0000-0001-8037-2741

Aamer Ikram https://orcid.org/0000-0002-6440-750X

Article

Publisher ID: microorganisms-08-01336

DOI: 10.3390/microorganisms8091336

PMC ID: 7564241

PubMed ID: 32883020

SO-VID: be93beeb-0b0a-4775-a54b-36dd2b7e9591

License:

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan

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Most cited references 39

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Prokka: rapid prokaryotic genome annotation.

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