| 1. |
- Legese, Melese Hailu, et al.
(författare)
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Genomic Epidemiology of Carbapenemase-Producing and Colistin-Resistant Enterobacteriaceae among Sepsis Patients in Ethiopia : a Whole-Genome Analysis
- 2022
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Ingår i: Antimicrobial Agents and Chemotherapy. - : American Society for Microbiology. - 0066-4804 .- 1098-6596. ; 66:8
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Tidskriftsartikel (refereegranskat)abstract
- Sepsis due to carbapenemase-producing and colistin-resistant Enterobacteriaceae is a global health threat. A multicenter study was conducted between October 2019 and September 2020 at four hospitals located in different parts of Ethiopia. From a total of 1,416 sepsis patients, blood culture was performed. Enterobacteriaceae were confirmed using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Carbapenem and colistin susceptibility testing was performed using disk diffusion, broth microdilution, and Etest strip. Enterobacteriaceae isolates (n = 301) were subjected to whole-genome sequencing using Illumina HiSeq 2500. SPAdes version 3.9 was used for genome assembly. Carbapenem and colistin resistance genes, chromosomal point mutations, sequence types, and plasmid replicons were identified using tools at the Center for Genomic Epidemiology. Phylogeny structure was constructed using CSI Phylogeny 1.4. Visualization of trees and metadata was done using iTOL v6.5.2. Among 301 Enterobacteriaceae, 22 Klebsiella pneumoniae, 2 Klebsiella variicola, and 3 Enterobacter cloacae isolates showed reduced susceptibility to meropenem (7% of tested isolates). bla(NDM-1), bla(NDM-5), and bla(OXA-181) were variants of carbapenemase genes detected. Co-occurrence of bla(NDM-5) and bla(OXA-181) was detected with 4 K. pneumoniae strains. K. pneumoniae and K. variicola showed chromosomal alterations of ompK36 and ompk37. Plasmid incompatibility (Inc) groups Col, IncC, IncHI, IncF, IncFII, IncR, and IncX3 were identified among carbapenem-resistant K. pneumoniae and E. cloacae isolates. Two mcr-9 genes were detected from Salmonella species and K. pneumoniae. The dissemination of carbapenemase-producing Enterobacteriaceae in all hospitals is worrying. Multiple carbapenemase genes were detected, with bla(NDM) variants the most frequent. The occurrence of colistin-resistant Enterobacteriaceae among sepsis patients is critical. Implementation of effective antimicrobial stewardship is urgently needed.
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| 2. |
- Legese, Melese Hailu, et al.
(författare)
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Molecular Epidemiology of Extended-Spectrum Beta-Lactamase and AmpC Producing Enterobacteriaceae among Sepsis Patients in Ethiopia : A Prospective Multicenter Study
- 2022
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Ingår i: Antibiotics. - : MDPI AG. - 2079-6382. ; 11:2
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Tidskriftsartikel (refereegranskat)abstract
- Extended-spectrum beta-lactamases (ESBLs) and AmpC producing Enterobacteriaceae are public health threats. This study aims to characterize ESBL and AmpC producing Enterobacteriaceae isolated from sepsis patients. A multicenter study was conducted at four hospitals located in central (Tikur Anbessa and Yekatit 12), southern (Hawassa) and northern (Dessie) parts of Ethiopia. Blood culture was performed among 1416 sepsis patients. Enterobacteriaceae (n = 301) were confirmed using MALDI-TOF and subjected for whole genome sequencing using the Illumina (HiSeq 2500) system. The overall genotypic frequencies of ESBL and AmpC producing Enterobacteriaceae were 75.5% and 14%, respectively. The detection of ESBL producing Enterobacteriaceae at Hawassa, Yekatit 12, Tikur Anbessa and Dessie was 95%, 90%, 82% and 55.8%, respectively. The detection frequency of bla(CTX-M), bla(TEM) and bla(SHV) genes was 73%, 63% and 33%, respectively. The most frequently detected ESBL gene was bla(CTX-M-15) (70.4%). The common AmpC genes were bla(ACT) (n = 22) and bla(CMY) (n = 13). Of Enterobacteriaceae that harbored AmpC (n = 42), 71% were ESBL co-producers. Both bla(TEM-1B) (61.5%) and bla(SHV-187) (27.6%) were the most frequently detected variants of bla(TEM) and bla(SHV), respectively. The molecular epidemiology of ESBL producing Enterobacteriaceae showed high frequencies and several variants of ESBL and AmpC genes. Good antimicrobial stewardship and standard bacteriological laboratory services are necessary for the effective treatment of ESBL producing Enterobacteriaceae.
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| 3. |
- Legese, Melese Hailu, et al.
(författare)
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Sepsis : emerging pathogens and antimicrobial resistance in Ethiopian referral hospitals
- 2022
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Ingår i: Antimicrobial Resistance and Infection Control. - : BioMed Central (BMC). - 2047-2994. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundSepsis due to multidrug resistant (MDR) bacteria is a growing public health problem mainly in low-income countries.MethodsA multicenter study was conducted between October 2019 and September 2020 at four hospitals located in central (Tikur Anbessa and Yekatit 12), southern (Hawassa) and northern (Dessie) parts of Ethiopia. A total of 1416 patients clinically investigated for sepsis were enrolled. The number of patients from Tikur Anbessa, Yekatit 12, Dessie and Hawassa hospital was 501, 298, 301 and 316, respectively. At each study site, blood culture was performed from all patients and positive cultures were characterized by their colony characteristics, gram stain and conventional biochemical tests. Each bacterial species was confirmed using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI TOF). Antimicrobial resistance pattern of bacteria was determined by disc diffusion. Logistic regression analysis was used to assess associations of dependent and independent variables. A p-value < 0.05 was considered as statistically significant. The data was analyzed using SPSS version 25.ResultsAmong 1416 blood cultures performed, 40.6% yielded growth. Among these, 27.2%, 0.3% and 13.1%, were positive for pathogenic bacteria, yeast cells and possible contaminants respectively. Klebsiella pneumoniae (26.1%), Klebsiella variicola (18.1%) and E. coli (12.4%) were the most frequent. Most K. variicola were detected at Dessie (61%) and Hawassa (36.4%). Almost all Pantoea dispersa (95.2%) were isolated at Dessie. Rare isolates (0.5% or 0.2% each) included Leclercia adecarboxylata, Raoultella ornithinolytica, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Burkholderia cepacia, Kosakonia cowanii and Lelliottia amnigena. Enterobacteriaceae most often showed resistance to ampicillin (96.2%), ceftriaxone (78.3%), cefotaxime (78%), cefuroxime (78%) and ceftazidime (76.4%). MDR frequency of Enterobacteriaceae at Hawassa, Tikur Anbessa, Yekatit 12 and Dessie hospital was 95.1%, 93.2%, 87.3% and 67.7%, respectively. Carbapenem resistance was detected in 17.1% of K. pneumoniae (n = 111), 27.7% of E. cloacae (n = 22) and 58.8% of Acinetobacter baumannii (n = 34).ConclusionDiverse and emerging gram-negative bacterial etiologies of sepsis were identified. High multidrug resistance frequency was detected. Both on sepsis etiology types and MDR frequencies, substantial variation between hospitals was determined. Strategies to control MDR should be adapted to specific hospitals. Standard bacteriological services capable of monitoring emerging drug-resistant sepsis etiologies are essential for effective antimicrobial stewardship.
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