Multidrug-resistant enteric bacteria in Nigeria and potential use of bacteriophages as biocontrol

Oyejobi, Greater Kayode; Sule, Waidi Folorunso; Akinde, Sunday B.; Khan, Fazal Mehmood; Ogolla, Faith

doi:10.1016/j.scitotenv.2022.153842

Cited by 9 publications

(7 citation statements)

References 117 publications

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“…The presence of these pathogens and, importantly, the carriage of AMR genes, plasmids, and virulence genes conferring pathogenicity and resistant phenotypes in these healthy children are of great concern to public health. The occurrence of these pathogenic enteric bacteria in febrile individuals is well documented across the country [ 22 , 35 , 41 , 42 ]; however, there is limited information on healthy individuals in Sub-Saharan Africa as far as the authors know, which makes this study one of the very few studies with a genomic surveillance report on healthy children in Nigeria.…”

Section: Discussionmentioning

confidence: 99%

Genomic Characterization of Multidrug-Resistant Pathogenic Enteric Bacteria from Healthy Children in Osun State, Nigeria

Uwanibe,

Olawoye,

Happi

et al. 2024

Microorganisms

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Antimicrobial resistance (AMR) is responsible for the spread and persistence of bacterial infections. Surveillance of AMR in healthy individuals is usually not considered, though these individuals serve as reservoirs for continuous disease transmission. Therefore, it is essential to conduct epidemiological surveillance of AMR in healthy individuals to fully understand the dynamics of AMR transmission in Nigeria. Thirteen multidrug-resistant Citrobacter spp., Enterobacter spp., Klebsiella pneumoniae, and Escherichia coli isolated from stool samples of healthy children were subjected to whole genome sequencing (WGS) using Illumina and Oxford nanopore sequencing platforms. A bioinformatics analysis revealed antimicrobial resistance genes such as the pmrB_Y358N gene responsible for colistin resistance detected in E. coli ST219, virulence genes such as senB, and ybtP&Q, and plasmids in the isolates sequenced. All isolates harbored more than three plasmid replicons of either the Col and/or Inc type. Plasmid reconstruction revealed an integrated tetA gene, a toxin production caa gene in two E. coli isolates, and a cusC gene in K. quasivariicola ST3879, which induces neonatal meningitis. The global spread of AMR pathogenic enteric bacteria is of concern, and surveillance should be extended to healthy individuals, especially children. WGS for epidemiological surveillance will improve the detection of AMR pathogens for management and control.

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Section: Discussionmentioning

confidence: 99%

Genomic Characterization of Multidrug-Resistant Pathogenic Enteric Bacteria from Healthy Children in Osun State, Nigeria

Uwanibe,

Olawoye,

Happi

et al. 2024

Microorganisms

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“…In this study, we recovered enteric pathogens of public health interest, such as Klebsiella quasivariicola, Enterobacter hormaechei, and Escherichia coli. The occurrence of these pathogenic enteric bacteria in febrile individuals is well-documented across the country (17,32,33); however, little or no information on healthy individuals.…”

Section: Discussionmentioning

confidence: 99%

Genomic Characterisation of Multidrug-Resistant Pathogenic Enteric Bacteria from healthy children in Osun State, Nigeria

Uwanibe

Olawoye

Happi

et al. 2023

Preprint

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Antimicrobial resistance (AMR) has been established to be a significant driver for the persistence and spread of bacterial infections. It is, therefore, essential to conduct epidemiological surveillance of AMR in healthy individuals to understand the actual dynamics of AMR in Nigeria. Multi-drug resistant Klebsiella quasivariicola (n=1), Enterobacter hormaechei (n=1), and Escherichia coli (n=3) from stool samples of healthy children were subjected to whole genome sequencing using Illumina Nextseq1000/2000 and Oxford nanopore. Bioinformatics analysis reveals antimicrobial resistance, virulence genes, and plasmids. This pathogenic enteric bacteria harbored more than three plasmid replicons of either Col and/or Inc type associated with outbreaks and AMR resistant gene pmrB responsible for colistin resistance. Plasmid reconstruction revealed an integrated tetA gene responsible for tetracycline resistance, and caa gene responsible for toxin production in two of the E.coli isolates, and a cusC gene known to induce neonatal meningitis in the K. quasivariicola ST3879. The global spread of MDR pathogenic enteric bacteria is a worrying phenomenon, and close surveillance of healthy individuals, especially children, is strongly recommended to prevent the continuous spread and achieve the elimination and eradication of these infections. Molecular epidemiological surveillance using whole genome sequencing (WGS) will improve the detection of MDR pathogens in Nigeria.

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“…Thermobaculum spp. is well-known to exist in temperatures as high as 90 degrees Celsius 25 , and it is documented to contain antibacterial or antimicrobial-resistant genes 26,27 . Similarly, the two Actinobacteria genera, Geodermatophilus and Rubrobacter, are also known to be antibacterial-resistant genera.…”

Section: Illustration: Soil Microbiome and Ariditymentioning

confidence: 99%

Multi-group Analysis of Compositions of Microbiomes with Covariate Adjustments and Repeated Measures

Peddada

Hua

2023

Preprint

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Microbiome differential abundance analysis methods for a pair of groups are well established in the literature. However, many microbiome studies involve multiple groups, sometimes even ordered groups, such as stages of a disease, and require different types of comparisons. Standard pairwise comparisons are not only inefficient in terms of power and false discovery rates, but they may not address the scientific question of interest. In this paper, we propose a general framework for performing a wide range of multi-group analyses with covariate adjustments and repeated measures. We demonstrate the effectiveness of our methodology through two real data sets. The first example explores the effects of aridity on the soil microbiome, and the second example investigates the effects of surgical interventions on the microbiome of IBD patients.

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Multidrug-resistant enteric bacteria in Nigeria and potential use of bacteriophages as biocontrol

Cited by 9 publications

References 117 publications

Genomic Characterization of Multidrug-Resistant Pathogenic Enteric Bacteria from Healthy Children in Osun State, Nigeria

Genomic Characterization of Multidrug-Resistant Pathogenic Enteric Bacteria from Healthy Children in Osun State, Nigeria

Genomic Characterisation of Multidrug-Resistant Pathogenic Enteric Bacteria from healthy children in Osun State, Nigeria

Multi-group Analysis of Compositions of Microbiomes with Covariate Adjustments and Repeated Measures

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