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Evaluation of gut bacterial community composition and antimicrobial resistome in pregnant and non-pregnant women from Saudi population

Authors Khan I, Yasir M, Farman M, Kumosani T, AlBasri SF, Bajouh OS, Azhar EI

Received 9 January 2019

Accepted for publication 1 May 2019

Published 21 June 2019 Volume 2019:12 Pages 1749—1761

DOI https://doi.org/10.2147/IDR.S200213

Checked for plagiarism Yes

Review by Single-blind

Peer reviewers approved by Dr Amy Norman

Peer reviewer comments 2

Editor who approved publication: Dr Sahil Khanna


Imran Khan,1–3,* Muhammad Yasir,1,4,* Muhammad Farman,1,5 Taha Kumosani,6 Samera F AlBasri,7 Osama S Bajouh,7 Esam I Azhar1,4

1Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; 2Biochemistry Department, Faculty of Science; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; 3State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology Taipa, Macau, People’s Republic of China; 4Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; 5Department of Biology, King Abdulaziz University, Jeddah, Saudi Arabia; 6Biochemistry Department, Faculty of Science; Production of Bio-products for Industrial Applications Research Group, and Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; 7Department of Obstetrics & Gynecology, King Abdul Aziz University Hospital, Jeddah, Saudi Arabia

*These authors contributed equally to this work

Background: Gut microbiota (GM) has recently been described as a functional reservoir of antimicrobial resistant genes (ARGs). However, the ARG-carrying bacterial species in the human gut has been poorly studied. This study, for the first time, is reporting bacterial communities’ composition and antimicrobial resistome in the stool samples of pregnant and non-pregnant (NP) Saudi females.
Methods: Gut bacterial community composition was analyzed by 16S amplicon sequencing and culturomics. High throughput MALDI-TOF technique was used for identification of the isolates from stool samples and evaluated for resistance against 13 antibiotics using the agar dilution method. Clinically important ARGs were PCR amplified from genomic DNA of the stool samples using gene-specific primers.
Results: 16S amplicon sequencing revealed that GM of pregnant and NP women were predominantly comprised of phyla Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Bacterial diversity decreased in pregnant groups, whereas phylum Bacteroidetes declined significantly (p<0.05) in the first trimester. We noticed a relatively high abundance of butyrate-producing bacteria (eg, Faecalibacterium spp. and Eubacterium spp.) in the gut of pregnant women, whereas Prevotella copri was found at significantly (p<0.01) higher abundance in NP women. Moreover, about 14,694 isolates were identified and classified into 132 distinct species. The majority of the species belonged to phyla Firmicutes and Proteobacteria. About 8,125 isolates exhibited resistance against antibiotics. Out of 73 resistant-species, Enterococcus was the most diverse genus and Escherichia coli was the highly prevalent bacterium. The majority of the isolates were resistant to antibiotics; trimethoprim/sulfamethoxazole, cycloserine, and cefixime. ARGs encoding resistance against aminoglycoside, macrolide, quinolone, β-lactam, and tetracycline antibiotics were predominantly found in genomic DNA of the stool samples.
Conclusion: We conclude that pregnancy-associated GM modulations may help to sustain a healthy pregnancy, but a higher proportion of antibiotic resistance could be deleterious for both maternal and fetal health.

Keywords: gut microbiota, antimicrobial resistance, metagenomics, culturomics, pregnancy, Saudi Arabia
 

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