Transmission patterns of hyper-endemic multi-drug resistant Klebsiella pneumoniae in a Cambodian neonatal unit: a longitudinal study with whole genome sequencing

AbstractBackgroundKlebsiella pneumoniae is an important and increasing cause of life-threatening disease in hospitalised neonates. Third generation cephalosporin resistance (3GC-R) is frequently a marker of multi-drug resistance, and can complicate management of infections. 3GC-R K. pneumoniae is hyper-endemic in many developing country settings, but its epidemiology is poorly understood and prospective studies of endemic transmission are lacking. We aimed to determine the transmission dynamics of 3GC-R K. pneumoniae in a newly opened neonatal unit (NU) in Cambodia.MethodsWe performed a prospective longitudinal study between September and November 2013. Rectal swabs from 37 consented patients were collected upon NU admission and every three days thereafter. Morphologically different colonies from swabs growing cefpodoxime-resistant K. pneumoniae were selected for whole-genome sequencing (WGS).Results32/37 (86%) patients screened positive for 3GC-R K. pneumoniae and 93 colonies from 119 swabs were sequenced. Isolates were resistant to a median of six (range 3-9) antimicrobials. WGS revealed high diversity; pairwise distances between isolates from the same patient were either 0-1 SNV or >1,000 SNVs; 19/32 colonized patients harboured K. pneumoniae colonies differing by >1000 SNVs. Diverse lineages accounted for 18 probable importations to the NU and nine probable transmission clusters involving 19/37 (51%) of screened patients. Median cluster size was 5 patients (range 3-9).ConclusionsThe epidemiology of 3GC-R K. pneumoniae was characterised by multiple introductions and a dense network of cross-infection, with half of screened neonates part of a transmission cluster. Efforts to reduce the 3GC-R K. pneumoniae disease burden should consider targeting both processes.

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Transmission Dynamics of Hyper-Endemic Multi-Drug Resistant Klebsiella pneumoniae in a Southeast Asian Neonatal Unit: A Longitudinal Study With Whole Genome Sequencing

Frontiers in Microbiology ◽

10.3389/fmicb.2018.01197 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 13

Author(s):

Pieter W. Smit ◽

Nicole Stoesser ◽

Sreymom Pol ◽

Esther van Kleef ◽

Mathupanee Oonsivilai ◽

...

Keyword(s):

Longitudinal Study ◽

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Southeast Asian ◽

Neonatal Unit ◽

Transmission Dynamics ◽

Whole Genome ◽

Drug Resistant

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Whole Genome Sequencing of Pediatric Klebsiella pneumoniae Strains Reveals Important Insights Into Their Virulence-Associated Traits

Frontiers in Microbiology ◽

10.3389/fmicb.2021.711577 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mauricio Flores-Valdez ◽

Miguel A. Ares ◽

Roberto Rosales-Reyes ◽

Javier Torres ◽

Jorge A. Girón ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Outer Membrane Proteins ◽

Multi Drug Resistance ◽

Phylogenomic Analysis ◽

Whole Genome ◽

Clustering Methods ◽

Genes Encoding ◽

Tract Infections

Klebsiella pneumoniae is recognized as a common cause of nosocomial infections and outbreaks causing pneumonia, septicemia, and urinary tract infections. This opportunistic bacterium shows an increasing acquisition of antibiotic-resistance genes, which complicates treatment of infections. Hence, fast reliable strain typing methods are paramount for the study of this opportunistic pathogen’s multi-drug resistance genetic profiles. In this study, thirty-eight strains of K. pneumoniae isolated from the blood of pediatric patients were characterized by whole-genome sequencing and genomic clustering methods. Genes encoding β-lactamase were found in all the bacterial isolates, among which the blaSHV variant was the most prevalent (53%). Moreover, genes encoding virulence factors such as fimbriae, capsule, outer membrane proteins, T4SS and siderophores were investigated. Additionally, a multi-locus sequence typing (MLST) analysis revealed 24 distinct sequence types identified within the isolates, among which the most frequently represented were ST76 (16%) and ST70 (11%). Based on LPS structure, serotypes O1 and O3 were the most prevalent, accounting for approximately 63% of all infections. The virulence capsular types K10, K136, and K2 were present in 16, 13, and 8% of the isolates, respectively. Phylogenomic analysis based on virtual genome fingerprints correlated with the MLST data. The phylogenomic reconstruction also denoted association between strains with a higher abundance of virulence genes and virulent serotypes compared to strains that do not possess these traits. This study highlights the value of whole-genomic sequencing in the surveillance of virulence attributes among clinical K. pneumoniae strains.

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Whole-genome sequencing supports the delineation of the multidrug-resistant CG14 and CG15 Klebsiella pneumoniae clones

10.26226/morressier.56d5ba2cd462b80296c9697a ◽

2016 ◽

Author(s):

Angela Novais

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Multidrug Resistant ◽

Whole Genome

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Whole Genome Sequencing and Antimicrobial Resistance of Staphylococcus aureus from Surgical Site Infections in Ghana

Pathogens ◽

10.3390/pathogens10020196 ◽

2021 ◽

Vol 10 (2) ◽

pp. 196

Author(s):

Beverly Egyir ◽

Jeannette Bentum ◽

Naiki Attram ◽

Anne Fox ◽

Noah Obeng-Nkrumah ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Meca Gene ◽

Surgical Site Infections ◽

Illumina Miseq ◽

Multi Drug Resistance ◽

Toxin Gene ◽

Whole Genome ◽

Flight Mass Spectrometry

Staphylococcus aureus (S. aureus) is a common cause of surgical site infections (SSIs) globally. Data on the occurrence of methicillin-susceptible S. aureus (MSSA) as well as methicillin-resistant S. aureus (MRSA) among patients with surgical site infections (SSIs) in sub-Saharan African are scarce. We characterized S. aureus from SSIs in Ghana using molecular methods and antimicrobial susceptibility testing (AST). Wound swabs or aspirate samples were collected from subjects with SSIs. S. aureus was identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF-MS); AST was performed by Kirby-Bauer disk diffusion, and results were interpreted according to the Clinical and Laboratory Standards Institute (CLSI) guideline. Detection of spa, mecA, and pvl genes was performed by polymerase chain reaction (PCR). Whole-genome sequencing (WGS) was done using the Illumina MiSeq platform. Samples were collected from 112 subjects, with 13 S. aureus isolates recovered. Of these, 92% were sensitive to co-trimoxazole, 77% to clindamycin, and 54% to erythromycin. Multi-drug resistance was detected in 5 (38%) isolates. The four mecA gene-positive MRSA isolates detected belonged to ST152 (n = 3) and ST5 (n = 1). In total, 62% of the isolates were positive for the Panton-Valentine leukocidin (pvl) toxin gene. This study reports, for the first time, a pvl-positive ST152-t355 MRSA clone from SSIs in Ghana. The occurrence of multi-drug-resistant S. aureus epidemic clones suggests that continuous surveillance is required to monitor the spread and resistance trends of S. aureus in hospital settings in the country.

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