First Whole-Genome Sequence of a Highly Resistant Klebsiella pneumoniae Sequence Type 14 Strain Isolated from Sudan

Mohamed, Sofia B.; Kambal, Sumaya; Munir, Abdalla; Abdalla, Nusiba I.; Hassan, Mohamed M.; Hamad, Ahmed; Mohammed, Sara E.; Ahmed, Fatima E.; Hamid, Omnia; Ismail, Arshad; Allam, Mushal

doi:10.1128/mra.00552-19

Cited by 3 publications

(2 citation statements)

References 7 publications

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“…The observed similarities and difference with the local, regional, and international studies highlights the diversity and dynamic nature of the representative local population of K. pneumoniae as well as the potential for regional dissemination of clones in different countries, and the need to support local capacity in robust epidemiological surveillance. The first WGS study on a single ST14 K. pneumoniae from Sudan was conducted in 2019 [27]. To the best of our knowledge, this is the first WGS-based study of a large collection of K. pneumoniae from Sudan.…”

Section: Discussionmentioning

confidence: 99%

Klebsiella pneumonia in Sudan: Multidrug Resistance, Polyclonal Dissemination, and Virulence

Osman¹,

Yokoyama

Altayb

et al. 2023

Antibiotics

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The emergence and global expansion of hyper-virulent and multidrug resistant (MDR) Klebsiella pneumoniae is an increasing healthcare threat worldwide. The epidemiology of MDR K. pneumoniae is under-characterized in many parts of the world, particularly Africa. In this study, K. pneumoniae isolates from hospitals in Khartoum, Sudan, have been whole-genome sequenced to investigate their molecular epidemiology, virulence, and resistome profiles. Eighty-six K. pneumoniae were recovered from patients in five hospitals in Khartoum between 2016 and 2020. Antimicrobial susceptibility was performed by disk-diffusion and broth microdilution. All isolates underwent whole genome sequencing using Illumina MiSeq; cgMLST was determined using Ridom SeqSphere+, and 7-loci MLST virulence genes and resistomes were identified. MDR was observed at 80%, with 35 isolates (41%) confirmed carbapenem-resistant. Thirty-seven sequence types were identified, and 14 transmission clusters (TC). Five of these TCs involved more than one hospital. Ybt9 was the most common virulence gene detected, in addition to some isolates harbouring iuc and rmp1. There is a diverse population of K. pneumoniae in Khartoum hospitals, harbouring multiple resistance genes, including genes coding for ESBLs, carbapenemases, and aminoglycoside-modifying enzymes, across multiple ST’s. The majority of isolates were singletons and transmissions were rare.

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Section: Discussionmentioning

confidence: 99%

Klebsiella pneumonia in Sudan: Multidrug Resistance, Polyclonal Dissemination, and Virulence

Osman¹,

Yokoyama

Altayb

et al. 2023

Antibiotics

View full text Add to dashboard Cite

show abstract

“…These projects include studies that have analyzed the full genome sequence of Dromedary camels to evaluate the genomic diversity and signatures of positive selection [ 27 ], the phylogenetic tree analysis of Streptomyces isolates from soil [ 28 ], and anti-hepatitis B virus activity isolated from Guiera senegalensis leaves [ 29 ]. The studies also included articles that investigated the prediction of the appropriate Middle East Respiratory Syndrome Coronavirus (MERS-CoV) epitope vaccine [ 30 ], identification of mutations in the Theileria annulata prolyl isomerase I gene ( TaPIN1 ) [ 31 ], malaria drug resistance molecular markers [ 32 ], whole genome sequencing of Klebsiella pneumoniae [ 33 ] and Acinetobacter baumannii [ 34 ], and the function of EIL/EIN3 transcription factor genes in cotton fiber development [ 35 ].…”

Section: Challenges To the Growth Of Bioinformatics In Sudanmentioning

confidence: 99%

Bioinformatics in Sudan: Status and challenges case study: The National University-Sudan

et al. 2021

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The ever increasing applications of bioinformatics in providing effective interpretation of large and complex biological data require expertise in the use of sophisticated computational tools and advanced statistical tests, skills that are mostly lacking in the Sudanese research community. This can be attributed to paucity in the development and promotion of bioinformatics, lack of senior bioinformaticians, and the general status quo of inadequate research funding in Sudan. In this paper, we describe the challenges that have encountered the development of bioinformatics as a discipline in Sudan. Additionally, we highlight on specific actions that may help develop and promote its education and training. The paper takes the National University Biomedical Research Institute (NUBRI) as an example of an institute that has tackled many of these challenges and strives to drive powerful efforts in the development of bioinformatics in the country.

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Co-Occurrence of β-Lactam and Aminoglycoside Resistance Determinants among Clinical and Environmental Isolates of Klebsiella pneumoniae and Escherichia coli: A Genomic Approach

et al. 2022

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The presence of antimicrobial-resistance genes (ARGs) in mobile genetic elements (MGEs) facilitates the rapid development and dissemination of multidrug-resistant bacteria, which represents a serious problem for human health. This is a One Health study which aims to investigate the co-occurrence of antimicrobial resistance determinants among clinical and environmental isolates of K. pneumoniae and E. coli. Various bioinformatics tools were used to elucidate the bacterial strains’ ID, resistome, virulome, MGEs, and phylogeny for 42 isolates obtained from hospitalized patients (n = 20) and environmental sites (including fresh vegetables, fruits, and drinking water) (n = 22). The multilocus sequence typing (MLST) showed that K. pneumoniae belonged to ten sequence types (STs) while the E. coli belonged to seventeen STs. Multidrug-resistant isolates harbored β-lactam, aminoglycoside resistance determinants, and MGE were detected circulating in the environment (drinking water, fresh vegetables, and fruits) and in patients hospitalized with postoperative infections, neonatal sepsis, and urinary tract infection. Four K. pneumoniae environmental isolates (7E, 16EE, 1KE, and 19KE) were multidrug-resistant and were positive for different beta-lactam and aminoglycoside resistance determinants. blaCTX-M-15 in brackets of ISEc 9 and Tn 3 transposases was detected in isolates circulating in the pediatrics unit of Soba hospital and the environment. This study documented the presence of bacterial isolates harboring a similar pattern of antimicrobial resistance determinants circulating in hospitals and environments. A rapid response is needed from stakeholders to initiate a program for infection prevention and control measures to detect such clones disseminated in the communities and hospitals.

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First Whole-Genome Sequence of a Highly Resistant Klebsiella pneumoniae Sequence Type 14 Strain Isolated from Sudan

Cited by 3 publications

References 7 publications

Klebsiella pneumonia in Sudan: Multidrug Resistance, Polyclonal Dissemination, and Virulence

Klebsiella pneumonia in Sudan: Multidrug Resistance, Polyclonal Dissemination, and Virulence

Bioinformatics in Sudan: Status and challenges case study: The National University-Sudan

Co-Occurrence of β-Lactam and Aminoglycoside Resistance Determinants among Clinical and Environmental Isolates of Klebsiella pneumoniae and Escherichia coli: A Genomic Approach

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