5 On War, Loyalty, and Reconciliation

Seemann, Anika

doi:10.1515/9783110682120-009

Cited by 2 publications

(2 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…First, the quality was assessed using QUAST [ 34 ]. Then, the draft assemblies were queried using the ABRicate v1.0.1 [ 35 ] pipeline against CARD [ 36 ] to identify AMR genes, VFDB [ 37 ] to identify virulence factors, and PlasmidFinder [ 38 ] to identify plasmids. The assemblies were queried against the Klebsiella MLST database using the command line mlst v2.19 [ 39 ] pipeline to determine the sequence types, while the capsule (K) and O types were determined using the Kleborate pipeline [ 40 ] against the Kaptive database [ 41 ].…”

Section: Methodsmentioning

confidence: 99%

Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing

et al. 2022

View full text Add to dashboard Cite

Klebsiella pneumoniae is a globally significant opportunistic pathogen causing healthcare-associated and community-acquired infections. This study examined the epidemiology and the distribution of resistance and virulence genes in clinical K. pneumoniae strains in Kenya. A total of 89 K. pneumoniae isolates were collected over six years from five counties in Kenya and were analyzed using whole-genome sequencing and bioinformatics. These isolates were obtained from community-acquired (62/89) and healthcare-associated infections (21/89), and from the hospital environment (6/89). Genetic analysis revealed the presence of blaNDM-1 and blaOXA-181 carbapenemase genes and the armA and rmtF genes known to confer pan-aminoglycoside resistance. The most abundant extended-spectrum beta-lactamase genes identified were blaCTX-M-15 (36/89), blaTEM (35/89), and blaOXA (18/89). In addition, one isolate had a mobile colistin resistance gene (mcr-8). Fluoroquinolone resistance-conferring mutations in gyrA and parC genes were also observed. The most notable virulence factors were those associated with hyper-virulence (rmpA/A2 and magA), yersiniabactin (ybt), salmochelin (iro), and aerobactin (iuc and iutA). A total of 38 distinct sequence types were identified, including known global lineages ST14, ST15, ST147, and ST307, and a regional clone ST17 implicated in regional outbreaks. In addition, this study genetically characterized two potential hypervirulent isolates and two community-acquired ST147 high-risk clones that contained carbapenemase genes, yersiniabactin, and other multidrug resistance genes. These results demonstrate that the resistome and virulome of Kenyan clinical and hospital environmental K. pneumoniae isolates are diverse. The reservoir of high-risk clones capable of spreading resistance, and virulence factors have the potential to cause unmanageable infection outbreaks with high morbidity and mortality.

show abstract

Section: Methodsmentioning

confidence: 99%

Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Short reads for lab-adapted VISA strains, clinical VISA strains selected based on the stated MIC criteria, or all strains in the Staphopia database were aligned against the Staph_ASR reference with bwa. Mutations were called against the Staph_ASR reference (classes 1 and 2 described previously) with snippy (version 4.6.0) (36), selected from the Staphopia database (27), or simulated in the Staph_ASR reference (class 4) with the syntheticVCF tool compiled in C (37). Mutations called per strain in classes 1-3 were then merged into a nonredundant set per class with bcftools (version 1.11) merge.…”

Section: Methodsmentioning

confidence: 99%

Development of an amplicon nanopore sequencing strategy for detection of mutations conferring intermediate resistance to vancomycin in Staphylococcus aureus strains

Moller

Petit

Davis

et al. 2022

Preprint

View full text Add to dashboard Cite

Staphylococcus aureus is a major cause of bacteremia and other hospital-acquired infections. The cell-wall active antibiotic vancomycin is commonly used to treat both methicillin-resistant (MRSA) and sensitive (MSSA) infections, but vancomycin intermediate S. aureus (VISA) variants can arise through de novo mutations. Here we performed pilot experiments to develop a combined PCR/long-read sequencing-based method for detection of previously known VISA-causing mutations. We amplified 16 genes (walR, walK, rpoB, graR, graS, vraF, vraG, stpI, vraR, vraS, agrA, sarA, clpP, ccpA, prsA, and yvqF) known from prior studies to be associated with mutations responsible for VISA as 10 amplicons and sequenced amplicon pools as long-reads with Oxford Nanopore adapter ligation on Flongle flow cells. We then detected mutations by mapping reads against a parental consensus or known reference sequence and comparing called variants against a database of known VISA mutations from laboratory selection. There was high (>1000x) coverage of each amplicon in the pool, no relationship between amplicon length and coverage, and the ability to detect the causative mutation (walK 646C>G) in a VISA mutant derived from the USA300 strain (N384-3 from parental strain N384). Mixing mutant (N384-3) and parental (N384) DNA at various ratios from 0 to 1 mutant suggested a mutation detection threshold of roughly the average minor allele frequency of 6.5% at 95% confidence (two standard errors above mean mutation frequency). The study lays the groundwork for direct S. aureus antibiotic phenotype inference using rapid nanopore sequencing from clinical samples.

show abstract

5 On War, Loyalty, and Reconciliation

Cited by 2 publications

References 0 publications

Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing

Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing

Development of an amplicon nanopore sequencing strategy for detection of mutations conferring intermediate resistance to vancomycin in Staphylococcus aureus strains

Contact Info

Product

Resources

About