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Article ; Online: Reducing risks from respiratory pathogens at the 2024 Hajj.

Memish, Ziad A / Alshamrani, Majid M / Kattan, Rana F / Azhar, Esam I / Farahat, Fayssal M / Albarrak, Ali M / Zumla, Alimuddin

The Lancet. Infectious diseases

2024

Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2061641-7
ISSN	1474-4457 ; 1473-3099
ISSN (online)	1474-4457
ISSN	1473-3099
DOI	10.1016/S1473-3099(24)00260-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Retraction Note: Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota.

Hamad, Ibrahim / Ranque, Stéphane / Azhar, Esam I / Yasir, Muhammad / Jiman-Fatani, Asif A / Tissot-Dupont, Hervé / Raoult, Didier / Bittar, Fadi

Scientific reports

2024 Volume 14, Issue 1, Page(s) 7771

Language	English
Publishing date	2024-04-02
Publishing country	England
Document type	Retraction of Publication
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-58471-3
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Article: Meningitis and Bacteremia by Unusual Serotype of

Brek, Thamer / Gohal, Gassem A / Yasir, Muhammad / Azhar, Esam I / Al-Zahrani, Ibrahim A

Interdisciplinary perspectives on infectious diseases

2024 Volume 2024, Page(s) 3554734

Abstract: Background: Although meningitis caused by : Objectives: We conducted an investigation into the first reported case of neonatal meningitis caused by nontyphoidal : Methods: CSF and blood culture were collected from a female neonate patient to ... ...

Abstract	Background: Although meningitis caused by Objectives: We conducted an investigation into the first reported case of neonatal meningitis caused by nontyphoidal Methods: CSF and blood culture were collected from a female neonate patient to confirm the presence of bacterial meningitis. WGS was conducted to find out the comprehensive genomic characterization of Results: A 3-week-old infant was admitted to a local hospital with fever, poor feeding, and hypoactivity. She was diagnosed with Salmonella meningitis and bacteremia caused by Conclusions: We presented a genomic report of rare case of NTS meningitis in an infant who is living in a rural town in Jazan region, Saudi Arabia. Further research is required to understand the impact of host genetic factors on invasive nontyphoidal Salmonella infection.
Language	English
Publishing date	2024-03-22
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	2478373-0
ISSN	1687-7098 ; 1687-708X
ISSN (online)	1687-7098
ISSN	1687-708X
DOI	10.1155/2024/3554734
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Article: Microbiological risk assessment and resistome analysis from shotgun metagenomics of bovine colostrum microbiome.

Yasir, Muhammad / Al-Zahrani, Ibrahim A / Khan, Raees / Soliman, Samah Abdullah / Turkistani, Safaa A / Alawi, Maha / Azhar, Esam I

Saudi journal of biological sciences

2024 Volume 31, Issue 4, Page(s) 103957

Abstract: Colostrum is known for its nutraceutical qualities, probiotic attributes, and health benefits. The aim of this study was to profile colostrum microbiome from bovine in rural sites of a developing country. The focus was on microbiological safety ... ...

Abstract	Colostrum is known for its nutraceutical qualities, probiotic attributes, and health benefits. The aim of this study was to profile colostrum microbiome from bovine in rural sites of a developing country. The focus was on microbiological safety assessments and antimicrobial resistance, taking into account the risks linked with the consumption of raw colostrum. Shotgun sequencing was employed to analyze microbiome in raw buffalo and cow colostrum. Alpha and beta diversity analyses revealed increased inter and intra-variability within colostrum samples' microbiome from both livestock species. The colostrum microbiome was mainly comprised of bacteria, with over 90% abundance, whereas fungi and viruses were found in minor abundance. Known probiotic species, such as
Language	English
Publishing date	2024-02-16
Publishing country	Saudi Arabia
Document type	Journal Article
ZDB-ID	2515206-3
ISSN	2213-7106 ; 1319-562X
ISSN (online)	2213-7106
ISSN	1319-562X
DOI	10.1016/j.sjbs.2024.103957
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Article: Metagenomic Insights into the Microbiome and Resistance Genes of Traditional Fermented Foods in Arabia.

Yasir, Muhammad / Alkhaldy, Areej A / Soliman, Samah Abdullah / Turkistani, Safaa A / Azhar, Esam I

Foods (Basel, Switzerland)

2023 Volume 12, Issue 18

Abstract: This study uncovered microbial communities and evaluated the microbiological safety of traditional fermented foods consumed in the Arab region. Samples of dairy and non-dairy fermented foods-mish, jibneh, zabadi, and pickles-were collected from local ... ...

Abstract	This study uncovered microbial communities and evaluated the microbiological safety of traditional fermented foods consumed in the Arab region. Samples of dairy and non-dairy fermented foods-mish, jibneh, zabadi, and pickles-were collected from local markets in Saudi Arabia. Using the MiSeq system, samples were sequenced using 16S amplicons and shotgun metagenomics. Alpha and beta diversity indicated inter- and intra-variation in the studied fermented foods' bacterial communities. In the case of mish, the replicates were clustered. Twenty-one genera were found to be significantly different (FDR < 0.05) in abundance in pairwise comparison of fermented foods. Five high-quality, metagenome-assembled genomes (MAGs) of
Language	English
Publishing date	2023-09-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704223-6
ISSN	2304-8158
ISSN	2304-8158
DOI	10.3390/foods12183342
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Article ; Online: Genomic analysis of extensively drug resistant (XDR) Klebsiella pneumoniae high-risk clone ST14 co-harboring bla

Al-Zahrani, Ibrahim A / Aljabri, Ahmed / Alhazmi, Wafaa A / Yasir, Muhammad / Abujamel, Turki / Alghamdi, Ahmed K / Azhar, Esam I

Journal of infection and public health

2024 Volume 17, Issue 4, Page(s) 669–675

Abstract: Background: This study presents a comprehensive genomic analysis of NDM and OXA-48-producing Klebsiella pneumoniae in the Western region of Saudi Arabia, traversed by tens of millions of Muslims from various countries annually. This significant influx ... ...

Abstract	Background: This study presents a comprehensive genomic analysis of NDM and OXA-48-producing Klebsiella pneumoniae in the Western region of Saudi Arabia, traversed by tens of millions of Muslims from various countries annually. This significant influx of visitors invariably leads to the spread and diversity of MDR bacteria. Methods: Genome sequencing was performed using MiSeq system of 29 CPKP isolates that were NDM and OXA-48-positive isolated from nosocomial infections and demonstrated resistance to most antibiotics, including carbapenems. Results: WGS analysis showed that 12 (41.3%) isolates co-harbored bla Conclusion: this study provides insights into the spread and prevalence of high-risk clones of CPKP in the Western region of Saudi Arabia. The ST14 high-risk clone appears to be the predominant CPKP clone in this region, posing a significant threat to public health. This study also reports the presence of two globally disseminated hypervirulent K. pneumoniae (hvKp) clones, namely ST2096 and ST383. Therefore, it is essential to improve surveillance and implement strict infection control measures in this region, which receives a substantial number of visitors to effectively monitor and reduce the spread of high-risk clones of antimicrobial-resistant bacteria, including CPKP.
MeSH term(s)	Humans ; Klebsiella pneumoniae ; Klebsiella Infections/epidemiology ; Klebsiella Infections/microbiology ; Saudi Arabia/epidemiology ; beta-Lactamases/genetics ; beta-Lactamases/pharmacology ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Genomics ; Microbial Sensitivity Tests ; Hydroxamic Acids
Chemical Substances	aerobactin (26198-65-2) ; beta-Lactamases (EC 3.5.2.6) ; Anti-Bacterial Agents ; Virulence Factors ; Hydroxamic Acids
Language	English
Publishing date	2024-02-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2467587-8
ISSN	1876-035X ; 1876-0341
ISSN (online)	1876-035X
ISSN	1876-0341
DOI	10.1016/j.jiph.2024.02.011
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Article ; Online: Prevalence of permethrin-resistant kdr mutation in head lice (

Alsaady, Isra M / Altwaim, Sarah / Gattan, Hattan S / Alghanmi, Maimonah / Zawawi, Ayat / Ahmedah, Hanadi / Wakid, Majed H / Azhar, Esam I

PeerJ

2023 Volume 11, Page(s) e16273

Abstract: ... Head ... ...

Abstract	Head lice
MeSH term(s)	Animals ; Humans ; Child ; Permethrin/pharmacology ; Pediculus/genetics ; Saudi Arabia/epidemiology ; Insecticides/pharmacology ; Prevalence ; Lice Infestations/epidemiology ; Mutation/genetics ; Students
Chemical Substances	Permethrin (509F88P9SZ) ; Insecticides
Language	English
Publishing date	2023-10-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359 ; 2167-8359
ISSN (online)	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.16273
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Article ; Online: Repurposing of antibacterial compounds for suppression of

Kumar, Geethu S / Dubey, Amit / Panda, Siva Prasad / Alawi, Maha M / Sindi, Anees A / Azhar, Esam I / Dwivedi, Vivek Dhar / Agrawal, Sharad

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–13

Abstract: Tuberculosis infection has always been a global concern for public health, and the mortality rate has increased tremendously every year. The ability of the ... ...

Abstract	Tuberculosis infection has always been a global concern for public health, and the mortality rate has increased tremendously every year. The ability of the resuscitation
Language	English
Publishing date	2023-08-07
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2245059
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Zs.A 2093: Show issues

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Article: 16S amplicon sequencing of microbial communities in enriched and non-enriched sediments of non-volcanic hot spring with temperature gradients.

Yasir, Muhammad / Qureshi, Arooj K / Azhar, Esam I

PeerJ

2021 Volume 9, Page(s) e10995

Abstract: Microorganisms in geothermal springs can offer insights into the fundamental and applied study of extremophiles. However, low microbial abundance and culturing requirements limit the ability to analyze microbial diversity in these ecosystems. In this ... ...

Abstract	Microorganisms in geothermal springs can offer insights into the fundamental and applied study of extremophiles. However, low microbial abundance and culturing requirements limit the ability to analyze microbial diversity in these ecosystems. In this study, culture-dependent and culture-independent techniques were used to analyze sediment samples from the non-volcanic Tatta Pani hot springs in district Poonch of Azad Kashmir. Microbial composition, temperature gradient, and enrichment effects on rare taxa were evaluated. In total, 31 distinct bacterial phyla and 725 genera were identified from the non-enriched Tatta Pani hot spring sediment samples, and 33 distinct bacterial phyla and 890 genera from the enriched sediment samples. Unique phyla specimens from the enriched samples included Candidatus Cloacimonetes, Caldiserica, and Korarchaeota archaea. The enriched samples yielded specific microbiota including 805 bacteria and 42 archaea operational taxonomic units with 97% similarity, though decreased thermophilic microbiota were observed in the enriched samples. Microbial diversity increased as temperature decreased. Candidate novel species were isolated from the culture-dependent screening, along with several genera that were not found in the 16S amplicon sequencing data. Overall, the enriched sediments showed high microbial diversity but with adverse changes in the composition of relatively dominant bacteria. Metagenomic analyses are needed to study the diversity, phylogeny, and functional investigation of hot spring microbiota.
Language	English
Publishing date	2021-04-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.10995
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Article ; Online: 16S amplicon sequencing of microbial communities in enriched and non-enriched sediments of non-volcanic hot spring with temperature gradients

Muhammad Yasir / Arooj K. Qureshi / Esam I. Azhar

PeerJ, Vol 9, p e

2021 Volume 10995

Abstract	Microorganisms in geothermal springs can offer insights into the fundamental and applied study of extremophiles. However, low microbial abundance and culturing requirements limit the ability to analyze microbial diversity in these ecosystems. In this study, culture-dependent and culture-independent techniques were used to analyze sediment samples from the non-volcanic Tatta Pani hot springs in district Poonch of Azad Kashmir. Microbial composition, temperature gradient, and enrichment effects on rare taxa were evaluated. In total, 31 distinct bacterial phyla and 725 genera were identified from the non-enriched Tatta Pani hot spring sediment samples, and 33 distinct bacterial phyla and 890 genera from the enriched sediment samples. Unique phyla specimens from the enriched samples included Candidatus Cloacimonetes, Caldiserica, and Korarchaeota archaea. The enriched samples yielded specific microbiota including 805 bacteria and 42 archaea operational taxonomic units with 97% similarity, though decreased thermophilic microbiota were observed in the enriched samples. Microbial diversity increased as temperature decreased. Candidate novel species were isolated from the culture-dependent screening, along with several genera that were not found in the 16S amplicon sequencing data. Overall, the enriched sediments showed high microbial diversity but with adverse changes in the composition of relatively dominant bacteria. Metagenomic analyses are needed to study the diversity, phylogeny, and functional investigation of hot spring microbiota.
Keywords	Hot spring ; 16S amplicon sequencing ; Thermophile ; Tatta Pani ; Culture-dependent ; Enrichment ; Medicine ; R
Subject code	550
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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