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

Altayb, Hisham N.; Elbadawi, Hana S.; Alzahrani, Faisal; Baothman, Othman A.; Kazmi, Imran; Nadeem, Muhammad Shahid; Hosawi, Salman; Chaieb, Kamel

doi:10.3390/ph15081011

Cited by 9 publications

(7 citation statements)

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“…The inclusion of WGS has been reported as a promising tool for estimation of ARB in a one health context (Aslam et al, 2021). In the current review, only four studies included WGS analysis (Adelowo et al, 2020;Le Terrier et al, 2020;Zekar et al, 2020;Altayb et al, 2022), conducted in Nigeria, Algeria and Sudan, respectively. Additionally, a follow-up WGS analysis study for further characterization of isolates previously published was found in South Africa (Richter et al, 2021), however, this study was not included in the current meta-analysis, to avoid duplication of isolate occurrence information.…”

Section: Discussionmentioning

confidence: 99%

Prevalence of extended-spectrum β-lactamase producing Enterobacterales in Africa's water-plant-food interface: A meta-analysis (2010–2022)

Richter

Plessis

Duvenage

et al. 2023

Front. Sustain. Food Syst.

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BackgroundMultidrug-resistant extended-spectrum β-lactamase (ESBL)-producing Enterobacterales is regarded as a critical health issue, yet, surveillance in the water-plant-food interface remains low, especially in Africa.ObjectivesThe objective of the study was to elucidate the distribution and prevalence of antimicrobial resistance in clinically significant members of the Enterobacterales order isolated from the water-plant-food interface in Africa.MethodsA literature search was conducted using six online databases according to the PRISMA guidelines. All available published studies involving phenotypic and genotypic characterization of ESBL-producing Enterobacterales from water, fresh produce or soil in Africa were considered eligible. Identification and characterization methods used as well as a network analysis according to the isolation source and publication year were summarized. Analysis of Escherichia coli, Salmonella spp. and Klebsiella pneumoniae included the calculation of the multiple antibiotic resistance (MAR) index according to isolation sources and statistical analysis was performed using RStudio.ResultsOverall, 51 studies were included for further investigation. Twelve African countries were represented, with environmental AMR surveillance studies predominantly conducted in South Africa. In 76.47% of the studies, occurrence of antimicrobial resistant bacteria was investigated in irrigation water samples, while 50.98% of the studies included fresh produce samples. Analysis of bacterial phenotypic antimicrobial resistance profiles were reported in 94.12% of the studies, with the disk diffusion method predominantly used. When investigating the MAR indexes of the characterized Escherichia coli, Klebsiella pneumoniae and Salmonella spp., from different sources (water, fresh produce or soil), no significant differences were seen across the countries. The only genetic determinant identified using PCR detection in all the studies was the blaCTX − M resistance gene. Only four studies used whole genome sequence analysis for molecular isolate characterization.DiscussionGlobally, AMR surveillance programmes recognize ESBL- and carbapenemase-producing Enterobacterales as vectors of great importance in AMR gene dissemination. However, in low- and middle-income countries, such as those in Africa, challenges to implementing effective and sustainable AMR surveillance programmes remain. This review emphasizes the need for improved surveillance, standardized methods and documentation of resistance gene dissemination across the farm-to-fork continuum in Africa.

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Section: Discussionmentioning

confidence: 99%

Prevalence of extended-spectrum β-lactamase producing Enterobacterales in Africa's water-plant-food interface: A meta-analysis (2010–2022)

Richter

Plessis

Duvenage

et al. 2023

Front. Sustain. Food Syst.

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“…In addition, we found that 12 (50.0%) CTX-M-producing E. coli isolates carried aph(3 ″ )-Ib and aph(6)-Id genes, which encode aminoglycoside adenylyltransferases. These two genes have already been reported as major determinants of sulfonamide and gentamicin resistance in pathogenic E. coli , respectively [ 25 , 26 ]. Although chloramphenicol was banned in food-producing animals in Korea in 1990 because of its suspected carcinogenicity, catB3 and cmlA1 genes, which encode a specific chloramphenicol transporter, were detected in nine (37.5.0%) and five (20.8%) CTX-M-producing E. coli isolates, respectively.…”

Section: Discussionmentioning

confidence: 99%

Comparative Genetic Characterization of CTX-M-Producing Escherichia coli Isolated from Humans and Pigs with Diarrhea in Korea Using Next-Generation Sequencing

Seo

Lee

2023

Microorganisms

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Pathogenic E. coli causes intra- and extraintestinal diseases in humans and pigs and third-generation cephalosporins are the primary option for the treatment of these diseases. The objective of this study was to investigate the characteristics and correlation between CTX-M-producing E. coli from humans and pigs regarding CTX-M-producing E. coli using next-generation sequencing and bioinformatic tools. Among the 24 CTX-M–producing E. coli, three types of CTX-M genes (CTX-M-12, CTX-M-14, and CTX-M-15) were detected in humans and four types of CTX-M genes (CTX-M-14, CTX-M-15, CTX-M-55, and CTX-M-101) were detected in pigs. A total of 24 CTX-M–producing E. coli isolates also showed the following antimicrobial resistance genes: other B-Lactam resistance gene (75.0%); aminoglycoside resistance genes (75.0%); phenicol resistance genes (70.8%); tetracycline resistance genes (70.8%); sulfonamide resistance genes (66.7%); quinolone resistance genes (62.5%); trimethoprim resistance genes (54.2%); and fosfomycin resistance genes (8.3%). FII (92.3%) and FIB (90.9%) were the most common plasmid replicon in humans and pigs, respectively. A total of thirty-eight different genes associated with virulence 24 CTX-M–producing E. coli and all isolates contained at least more than one virulence gene. A total of 24 CTX-M–producing E. coli isolates showed 15 diverse sequence types (STs): thirteen isolates from human belonged to 6 different STs, and 11 isolates from pig belonged to 9 different STs. The presence of virulence genes in E. coli together with antimicrobial resistance genes (including CTX-M genes) emphasizes the necessity of comprehensive surveillance and persistent monitoring of the food chain to avoid all types of bacterial contamination, regardless of human or pig origin.

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“…This may lead to misclassification even by using WGS. In this study, 26% (7/27) of K. quasipneumoniae species were misidentified as K. pneumoniae as a part of a previous study intended to study the genomics of K. pneumoniae and E. coli ( 16 ). This finding is consistent with Long et al who showed that 30% of K. pneumoniae are misidentified by conventional biochemical tests ( 40 ).…”

Section: Discussionmentioning

confidence: 99%

“…Among the K. pneumoniae ( n = 27) 7 were reidentified as K. quasipneumoniae using genomic tools. More details on the rest of K. pneumoniae ( n = 20) isolates, sample collection, and processing have been published elsewhere ( 16 ). The environmental samples were obtained via swabs collected from vegetables and table surfaces in the vegetable market in the Khartoum locality.…”

Section: Methodsmentioning

confidence: 99%

Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes

Altayb

Hosawi²,

Baothman³

et al. 2023

Front. Public Health

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IntroductionThe emergence of bacterial pathogens in environmental hosts represents a major risk to public health. This study aimed at characterizing seven novel environmental strains of K. quasipneumoniae using a genomic approach which was misidentified by phenotypic methods in a previous batch of 27 species thought to be K. pneumoniae.MethodsWhole-genome sequencing was performed using the Illumina platform, and the generated raw reads were de novo assembled. Comparative genomic, resistome, virulome, mobilome, and phylogeny were then investigated using dierent bioinformatics tools.ResultsSix strains were identified as K. quasipneumoniae subsp similipneumoniae and one as K. quasipneumoniae subsp. quasipneumoniae. All isolates were resistant to ampicillin, cephalexin, and amoxicillin-clavulanic acid and harbored the fosA, blaOKP types, oqxB, and oqxA genes. One isolate additionally harbored a gene cassettes consisting of blaSHV−1, blaOXA−1, aac(6′)-Ib-cr, catB genes. The aminoglycoside-modifying enzyme gene aph(3”)-Ia was bracketed by two insertion elements. Plasmid analyses showed that IncFIBK was the most prevalent plasmid, circulating in six isolates, while one isolate exhibited seven different plasmids. The isolates have virulence genes responsible for capsule formation, lipopolysaccharide, iron uptake aerobactin (iutA), salmochelins (iroE, iroN), enterobactin siderophore, adherence, and biofilm formation (mrkA, mrkB, mrkC, mrkD, mrkF, and mrkH).ConclusionOur study highlights the ecology and transmission of K. quasipneumoniae (which have the ability to disseminate to other environmental sources including animals) outside the clinical setting and the contribution of water, vegetables, and table surfaces as potential reservoirs of farm-to-fork transmission of disease via local markets in Khartoum, Sudan.

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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

Cited by 9 publications

References 61 publications

Prevalence of extended-spectrum β-lactamase producing Enterobacterales in Africa's water-plant-food interface: A meta-analysis (2010–2022)

Prevalence of extended-spectrum β-lactamase producing Enterobacterales in Africa's water-plant-food interface: A meta-analysis (2010–2022)

Comparative Genetic Characterization of CTX-M-Producing Escherichia coli Isolated from Humans and Pigs with Diarrhea in Korea Using Next-Generation Sequencing

Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes

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