High prevalence of blaCTX-M-15 and nosocomial transmission of hypervirulent epidemic clones of Klebsiella pneumoniae at a tertiary hospital in Ethiopia

Abstract

Background Genomic epidemiology of antibiotic resistance is not sufficiently studied in low-income countries. Objectives To determine prevalence of ESBL production, and resistome and virulome profiles, of Klebsiella pneumoniae isolated at Jimma Medical Center, Ethiopia. Methods Strains isolated from patients with suspected infections between June and November 2016 were characterized by MALDI-TOF for species identification and disc diffusion for antimicrobial susceptibility testing. All K. pneumoniae isolates were characterized by double disc diffusion for ESBL production and all ESBL-producing strains (ESBL-KP) were subjected to WGS on the Illumina (HiSeq 2500) platform. DNA was extracted by automated systems (MagNA Pure 96). Genome assembly was performed using SPAdes (v. 3.9) and draft genomes were used for analysing molecular features of the strains. Maximum likelihood trees were generated using FastTree/2.1.8 based on SNPs in shared genomic regions to identify transmission clusters. Results Of the 146 K. pneumoniae strains isolated, 76% were ESBL-KP; 93% of the ESBL-KP strains showed resistance to multiple antimicrobial classes. blaCTX-M-15 (84.4%) was the most prevalent ESBL gene. Resistance genes for aminoglycosides and/or fluoroquinolones [aac(6′)-Ib-cr (65.1%)], phenicols [catB3 (28.4%)], sulphonamides [sul1 (61.2%) and sul2 (60.5%)], trimethoprim [dfrA27 (32.1%)], macrolides [mph(A) (12.8%)] and rifampicin [arr2/arr3 (39.4%)] were prevalent. Plasmids of the IncF and IncR families were prevalent among ST218, ST147, ST15 and ST39. KL64 and KL57 capsular types and O1 and O2 LPSs were prevalent. A high-risk clone, ST218-KL57 encoding rmpA1/rmpA2 and iutA, was detected. Phylogenetic analysis showed a cluster of clonally related strains from different units of the hospital. Conclusions Prevalence of ESBL-KP was high and blaCTX-M-15 was the predominant ESBL gene. ESBL genes had spread through both clonal and polyclonal expansion of high-risk and hypervirulent clones. Nosocomial transmission of MDR strains between different units of the hospital was observed.

Prevalence and risk factors for antimicrobial resistance among newborns with gram-negative sepsis

“…Community outbreak and vertical transmission seemed more plausible for ST218 cases, which occurred within a month and mostly among newborns that were outborn, delivered vaginally, and had EOS. With the extreme case fatality rate of 80% observed with ST218 cases, all having the KL57 serotype, it is more likely that the newborns in this study were infected with the hypervirulent type of ST218/KL57, which has been reported among patients at a tertiary hospital about 350km from Addis Ababa in Jimma, Ethiopia, likewise other countries [ 63 , 64 ]. While there was no difference in the incidence of ST35 between inborn and outborn, the higher incidence of ST35 and ST218 among newborns delivered vaginally may necessitate the screening of pregnant women for colonization by these strains when community outbreaks are suspected.…”

Whole genome sequencing of OXA-232-producing wzi93-KL112-O1 carbapenem-resistant Klebsiella pneumoniae in human bloodstream infection co-harboring chromosomal ISEcp1-based blaCTX-M-15 and one rmpA2-associated virulence plasmid

“…More importantly, BSIs caused by CRKP present critical problems in terms of clinical therapy ( Xiao et al., 2020 ). Hypervirulent K. pneumoniae strains could also cause serious infections among healthy individuals ( Sewunet et al., 2021 ). These hypervirulent K. pneumoniae strains are usually resistant to antimicrobials agents and become high-risk clones in the hospital ( Sewunet et al., 2021 ).…”

An Arsenal of Multiple Antimicrobial Resistance, Toxins, and Virulence Factors in Gram-Negative Bacterial Isolates from Food – A Formidable Combination!

“…These authors also described that 50% of Gram-negative clinical isolates tested positive for ESBL of CTX-M ( bla CTX-M ). 24 Another group 25 reported the finding of more than three-quarters of Klebsiella pneumonia isolates being ESBL producers in the same study area with bla CTX-M and bla TEM genes being the most prevalent. Resistance to other classes of antibiotics (aminoglycosides, ciprofloxacin, and sulfamethoxazole) was also found to be high (ranging from 63% to 95%).…”