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

2020 ◽  
Vol 8 (9) ◽  
pp. 1336
Author(s):  
Farhan Rasheed ◽  
Muhammad Saeed ◽  
Nabil-Fareed Alikhan ◽  
David Baker ◽  
Mohsin Khurshid ◽  
...  
Keyword(s):  
Sequence Data ◽  
Treatment Options ◽  
Salmonella Typhi ◽  
Whole Genome ◽  
Outbreak Strain ◽  
Nucleotide Sequence Data ◽  
Sindh Province ◽  
Genome Nucleotide Sequence ◽  
Emergence Of Resistance

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.

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

2020 ◽  
Author(s):  
Farhan Rasheed ◽  
Muhammad Saeed ◽  
Nabil-Fareed Alikhan ◽  
David Baker ◽  
Mohsin Khurshid ◽  
...  
Keyword(s):  
Typhoid Fever ◽  
Food Chain ◽  
Sequence Data ◽  
Treatment Options ◽  
Added Value ◽  
Future Research ◽  
Whole Genome ◽  
Outbreak Strain ◽  
Nucleotide Sequence Data ◽  
Sindh Province

AbstractBackgroundExtensively 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 characterisation of 27 XDR S. Typhi isolated from patients attending Jinnah Hospital, Lahore, Pakistan.MethodsIsolates 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.FindingsTwenty-seven XDR S. Typhi isolates were identified from patients at Jinnah Hospital in Lahore between January and April 2019. All isolates were confirmed by sequence analysis to harbour 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.SummaryWe report the first emergence of XDR S. Typhi in Punjab province of Pakistan confirmed by whole genome sequencing.FundingThis work was supported by the BBSRC-funded QIB Institute Strategic Programme “Microbes in the Food Chain” BB/R012504/1 and its constituent projects Microbial Survival in the Food Chain (BBS/E/F/000PR10349) and Research Infrastructure (BBS/E/F/000PR10352), and the BBSRC funded Core Capability Grant (project number BB/CCG1860/1).Research in contextEvidence before this studyTyphoid fever is endemic in Pakistan, with widespread resistance to first line drugs: ampicillin, co-trimoxazole, and chloramphenicol, and to fluoroquinolones. In 2017 the first report of additional resistance to ceftriaxone was published as XDR typhoid fever from southern Pakistan. Treatment of XDR typhoid fever has been a clinical challenge; options are scarce, and the level of chronic carriage is unknown. Current treatment is dependent upon azithromycin and this represents a major threat for the community as resistance has been reported from Bangladesh.Added value of this studyThis study is the first genomic report of XDR typhoid fever in a central part of Pakistan, describing the same genetic background as strains responsible for XDR typhoid in Sindh province. We have confirmed that the outbreak strain of XDR S. Typhi is now present in the most populated province and second largest city of Pakistan.Implications of all the available evidenceThe present study highlights the gravity of the situation - the spread of this strain is of serious concern. The clinical situation remains unchanged since this study was performed; we believe it is imperative that future research focuses upon the biology, transmission and control of this strain.

scholarly journals Sequencing and Computational Approaches to Identification and Characterization of Microbial Organisms

2013 ◽  
Vol 5 ◽  
pp. BECB.S10886 ◽  
Author(s):  
Brijesh Singh Yadav ◽  
Venkateswarlu Ronda ◽  
Dinesh P. Vashista ◽  
Bhaskar Sharma
Keyword(s):  
Sequence Data ◽  
Microbial Interactions ◽  
Microbial Pathogens ◽  
Nucleotide Sequence Data ◽  
Computational Approaches ◽  
Microbial Detection ◽  
Sequencing Technologies ◽  
Sequencing Platforms ◽  
Identification And Characterization

The recent advances in sequencing technologies and computational approaches are propelling scientists ever closer towards complete understanding of human-microbial interactions. The powerful sequencing platforms are rapidly producing huge amounts of nucleotide sequence data which are compiled into huge databases. This sequence data can be retrieved, assembled, and analyzed for identification of microbial pathogens and diagnosis of diseases. In this article, we present a commentary on how the metagenomics incorporated with microarray and new sequencing techniques are helping microbial detection and characterization.

scholarly journals An Assessment of the Molecular Diversity of Ticks and Tick-Borne Microorganisms of Small Ruminants in Pakistan

2020 ◽  
Vol 8 (9) ◽  
pp. 1428 ◽  
Author(s):  
Abdul Ghafar ◽  
Adil Khan ◽  
Alejandro Cabezas-Cruz ◽  
Charles G. Gauci ◽  
Sadaf Niaz ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Small Ruminants ◽  
Ixodid Ticks ◽  
Nucleotide Sequence Data ◽  
Health Significance ◽  
Second Internal Transcribed Spacer ◽  
Theileria Spp

This study investigated ticks and tick-borne microorganisms of small ruminants from five districts of the Federally Administered Tribal Area (FATA) of Pakistan. Morphological (n = 104) and molecular (n = 54) characterization of the ticks revealed the presence of six ixodid ticks: Rhipicephalus (Rh.) haemaphysaloides, Rh. microplus, Rh. turanicus, Haemaphysalis (Hs.) punctata, Hs. sulcata and Hyalomma anatolicum. Phylogenetic analyses of nucleotide sequence data for two mitochondrial (16S and cytochrome c oxidase 1) and one nuclear (second internal transcribed spacer) DNA regions provided strong support for the grouping of the six tick species identified in this study. Microfluidic real-time PCR, employing multiple pre-validated nuclear and mitochondrial genetic markers, detected 11 potential pathogens and endosymbionts in 72.2% of the ticks (n = 54) tested. Rickettsia (R.) massiliae was the most common pathogen found (42.6% of ticks) followed by Theileria spp. (33.3%), Anaplasma (A.) ovis and R. slovaca (25.9% each). Anaplasma centrale, A. marginale, Ehrlichia spp., R. aeschlimannii, R. conorii and endosymbionts (Francisella- and Coxiella-like) were detected at much lower rates (1.9–22.2%) in ticks. Ticks from goats (83.9%) carried significantly higher microorganisms than those from sheep (56.5%). This study demonstrates that ticks of small ruminants from the FATA are carrying multiple microorganisms of veterinary and medical health significance and provides the basis for future investigations of ticks and tick-borne diseases of animals and humans in this and neighboring regions.

scholarly journals Characterization of a pigeon paramyxovirus (PPMV-1) isolated from chickens in South Africa : research communication

2004 ◽  
Vol 71 (2) ◽  
Author(s):  
C. Abolnik ◽  
R.F. Horner ◽  
R. Maharaj ◽  
G.J. Viljoen
Keyword(s):  
South Africa ◽  
Nucleotide Sequence ◽  
Newcastle Disease ◽  
Sequence Data ◽  
Far East ◽  
Nucleotide Sequence Data ◽  
Sequence Identity ◽  
Death Time ◽  
The Far East

A paramyxovirus with a thermostability of 60 min (typical of velogenic viruses) and a mean death time of > 90 h (typical of lentogenic viruses) was isolated from layers near Mooi River, South Africa. Our results, based on comparative nucleotide sequence data indicated that the virus is pigeon paramyxovirus 1 (PPMV-1), a variant of Newcastle disease virus. The F0 cleavage site contains a 112RRKKRF117 motif, and the virus had 98 % sequence identity with PPMV-1 strains from the Far East. PPMV-1 was last reported in South Africa during the 1980s, with this being the first report of PPMV-1 isolated from chickens in South Africa.

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