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Antimicrobial Resistance: Genes, Genomes and Emerging Technologies

Guest Editors:
Abd El-Latif Hesham: Beni-Suef University, Egypt
Youxiong Que: Fujian Agriculture and Forestry University, China 
Divakar Sharma: Lady Hardinge Medical College, India


BMC Genomics and BMC Microbiology were calling for submissions to our Collection on Antimicrobial Resistance: Genes, Genomes and Emerging Technologies. Antimicrobial resistance (AMR) has developed into a silent pandemic ever expanding in the background, disrupting lives and responsible for multiple deaths across the globe. As more of the research community joins in the fight against antimicrobial resistance to combat this ever-present threat to society, it has become clear that combining forces across disciplines is the way forward. A large part of the effort in combating AMR still comes from studying its genes and genomes, gathering surveillance and understanding cellular mechanisms to target. In recognition of this important, and growing area of research BMC Microbiology together with BMC Genomics welcomed submissions to this cross-journal collection on antimicrobial Resistance: Genes, Genomes, and Emerging Technologies.

Meet the Guest Editors

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Abd El-Latif Hesham: Beni-Suef University, Egypt

Abd El-Latif Hesham is a full Professor of Microbial Genetics and Environmental Meta-Genome Biotechnology, and presently working as Head of Genetics Department at the Faculty of Agriculture, Beni-Suef University (BSU), Egypt. He is one of the leading experts in the area of microbial genetics,  environmental meta-genome biotechnology, anti-microbial activates, and multi-drug resistant bacteria. Prof. Hesham has been elected as member of the Egyptian National Biotechnology Network of Expertise (NBNE); Member of the National Committee for Genetic Sciences and has been appointed as the Country Representative for Egypt and the Arab Counties by International Biodeterioration & Biodegradation Society (IBBS) UK, which belongs to the Federation of European Microbiological Societies. Prof. Hesham serves as an editorial board member for BMC Microbiology.

Youxiong Que: Fujian Agriculture and Forestry University, China 

Youxiong Que is a full Professor in the College of Agriculture at the Fujian Agriculture and Forestry University (FAFU). He was employed as an assistant professor in 2008, promoted to be an associate professor in 2010 and a professor in 2015. He has been a visiting scientist at USDA-ARS during 2010-2011. He is now the director of Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs / FAFU, China. His research interests are in the fields of crop genetics and biotechnology especially sugarcane biotechnology, including but not limited to the following three aspects, molecular interaction between crop and pathogen, gene mining and function identification, and molecular breeding. 

Divakar Sharma: Lady Hardinge Medical College, India

Dr. Sharma has a PhD in Biotechnology from Jiwaji University, Gwalior and National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India, with a special interest in drug resistant tuberculosis, antimicrobial resistance, bacterial infections, biofilms etc. After his PhD, he continued the post doctoral research work on the exploration of drug resistance in microbes by genomics, proteomic, and bioinformatics approaches in the National JALMA Institute for Leprosy and Other Mycobacterial Diseases and Aligarh Muslim University, India as an ICMR-PDF and SERB-N-PDF. After that Dr. Sharma served as a research scientist in IIT Delhi and Maulana Azad Medical College, Delhi, India. Currently he is working as a Scientist at Lady Hardinge Medical College, Delhi, India and exploring therenostics and alternative therapeutic drug target to combat antibiotic resistance.  


About the collection

BMC Genomics and BMC Microbiology called for submissions to our Collection on Antimicrobial Resistance: Genes, Genomes and Emerging Technologies. 

Antimicrobial resistance (AMR) has developed into a silent pandemic ever expanding in the background, disrupting lives and responsible for multiple deaths across the globe. As more of the research community joins in the fight against antimicrobial resistance to combat this ever-present threat to society, it has become clear that combining forces across disciplines is the way forward. A large part of the effort in combating AMR still comes from studying its genes and genomes, gathering surveillance and understanding cellular mechanisms to target. In recognition of this important, and growing area of research BMC Microbiology together with BMC Genomics published this cross-journal collection on antimicrobial Resistance – Genes, genomes, and emerging technologies.

The collection broadly covers the following areas of research:

  • Genomic surveillance
  • Antimicrobial discovery
  • Machine learning and GWAS approaches
  • Genetic basis of AMR and AMR diagnostics
  • Global trends in AMR
  • AMR and big data
  • Tackling AMR
  • Emerging approaches to combat AMR
  • New technologies and methods in AMR research
  • Bacterial sequencing in clinical practice
  • Biosensors and artificial intelligence to support antimicrobial optimization
  • AMR modelling research
  • Exploring the targets to be used as theranostics

 Image credit: © vrx123 / stock.adobe.com

  1. Bacteroides fragilis group (BFG) species are the most significant anaerobic pathogens and are also the most antibiotic-resistant anaerobic species. Therefore, surveying their antimicrobial resistance levels and i...

    Authors: József Sóki, Ingrid Wybo, Zain Baaity, Glória Stefán, Samo Jeverica, Nurver Ulger, Catalina-Suzana Stingu, Bakhtiyar Mahmood, Katalin Burián and Elisabeth Nagy
    Citation: BMC Microbiology 2024 24:202
  2. People living with HIV (PLWH) are at increased risk of acquisition of multidrug resistant organisms due to higher rates of predisposing factors. The gut microbiome is the main reservoir of the collection of an...

    Authors: Elisa Rubio Garcia, Maria Casadellà, Mariona Parera, Jordi Vila, Roger Paredes and Marc Noguera-Julian
    Citation: BMC Microbiology 2024 24:201
  3. The dramatic increase of antimicrobial resistance in the healthcare realm has become inexorably linked to the abuse of antibiotics over the years. Therefore, this study seeks to identify potential postbiotic m...

    Authors: Sharleen Livina Isaac, Ahmad Zuhairi Abdul Malek, Nurul Syafika Hazif, Farah Syahrain Roslan, Amalia Mohd Hashim, Adelene Ai-Lian Song, Raha Abdul Rahim and Wan Ahmad Kamil Wan Nur Ismah
    Citation: BMC Genomics 2024 25:571
  4. Klebsiella pneumoniae, a notorious pathogen for causing nosocomial infections has become a major cause of neonatal septicemia, leading to high morbidity and mortality worldwide. This opportunistic bacterium has ...

    Authors: Sidra Rahmat Ullah, Sidra Irum, Iqra Mahnoor, Humaira Ismatullah, Mariam Mumtaz, Saadia Andleeb, Abdur Rahman and Muhsin Jamal
    Citation: BMC Genomics 2024 25:408
  5. Non-coding RNA is a key epigenetic regulation factor during skeletal muscle development and postnatal growth, and miR-542-3p was reported to be conserved and highly expressed in the skeletal muscle among diffe...

    Authors: Dandan Li, Yongqi Yue, Xinxin Feng, Weibing Lv, Yilin Fan, Peiran Sha, Te Zhao, Yaqiu Lin, Xianrong Xiong, Jian Li and Yan Xiong
    Citation: BMC Genomics 2024 25:325
  6. Congenital infection caused by vertical transmission of microsporidia N. bombycis can result in severe economic losses in the silkworm-rearing industry. Whole-transcriptome analyses have revealed non-coding RNAs ...

    Authors: Zigang Shen, Zhuojun Ke, Qiong Yang, Samson Teweldeberhan Ghebremichael, Tangxin Li, Tian Li, Jie Chen, Xianzhi Meng, Heng Xiang, Chunfeng Li, Zeyang Zhou, Guoqing Pan and Ping Chen
    Citation: BMC Genomics 2024 25:321
  7. Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Ente...

    Authors: David Hourigan, Ewelina Stefanovic, Colin Hill and R. Paul Ross
    Citation: BMC Microbiology 2024 24:103
  8. Antimicrobial resistance (AMR) remains a significant global health threat particularly impacting low- and middle-income countries (LMICs). These regions often grapple with limited healthcare resources and acce...

    Authors: Mike Nsubuga, Ronald Galiwango, Daudi Jjingo and Gerald Mboowa
    Citation: BMC Genomics 2024 25:287
  9. Polymorphisms of Plasmodium falciparum chloroquine resistance transporter (pfcrt), Plasmodium falciparum multi-drug resistance 1 (pfmdr1) and Plasmodium falciparum kelch 13-propeller (pfk13) genes are accepted as...

    Authors: Phunuch Muhamad, Papichaya Phompradit, Wanna Chaijaroenkul and Kesara Na-Bangchang
    Citation: BMC Genomics 2024 25:269
  10. Escherichia coli, a ubiquitous inhabitant of the gut microbiota, has been recognized as an indicator of fecal contamination and a potential reservoir for antibiotic resistance genes. Its prevalence in drinking wa...

    Authors: Oluwaseyi Samuel Olanrewaju, Lesego G Molale-Tom, Rinaldo K Kritzinger and Cornelius Carlos Bezuidenhout
    Citation: BMC Genomics 2024 25:263
  11. The intrinsic concentration of RpoS, the second most abundant sigma factor, varies widely across the E. coli species. Bacterial isolates that express high levels of RpoS display high resistance to environmental s...

    Authors: Estela Ynés Valencia, Felipe de Moraes Gomes, Katia Ospino and Beny Spira
    Citation: BMC Microbiology 2024 24:72
  12. Antimicrobial resistance poses a huge risk to human health worldwide, while Bangladesh is confronting the most severe challenge between the food supply and the huge consumption of antibiotics annually. More im...

    Authors: Md Atiqul Haque, Huilong Hu, Jiaqi Liu, Md Aminul Islam, Foysal Hossen, Md Arifur Rahman, Firoz Ahmed and Cheng He
    Citation: BMC Microbiology 2024 24:61
  13. The most widely practiced strategy for constructing the deep learning (DL) prediction model for drug resistance of Mycobacterium tuberculosis (MTB) involves the adoption of ready-made and state-of-the-art archite...

    Authors: Yu Wang, Zhonghua Jiang, Pengkuan Liang, Zhuochong Liu, Haoyang Cai and Qun Sun
    Citation: BMC Genomics 2024 25:167
  14. Streptococcus iniae is an important fish pathogen that cause significant economic losses to the global aquaculture industry every year. Although there have some reports on the genotype of S.iniae and its relation...

    Authors: Xiangying Xiong, Ruifang Chen and Junxiang Lai
    Citation: BMC Genomics 2023 24:775
  15. The prevalence of Acinetobacter baumannii in nosocomial infections and its remarkable ability to develop antimicrobial resistance have been a critical issue in hospital settings. Here, we examined the genomic fea...

    Authors: Made Rai Dwitya Wiradiputra, Krit Thirapanmethee, Piyatip Khuntayaporn, Pagakrong Wanapaisan and Mullika Traidej Chomnawang
    Citation: BMC Genomics 2023 24:689
  16. Candida glabrata is an important cause of invasive candidiasis. Echinocandins are the first-line treatment of invasive candidiasis caused by C. glabrata. The epidemiological echinocandin sensitivity requires long...

    Authors: Yi Li, Xin Hou, Ruoyu Li, Kang Liao, Ling Ma, Xiaoming Wang, Ping Ji, Haishen Kong, Yun Xia, Hui Ding, Wei Kang, Ge Zhang, Jin Li, Meng Xiao, Yingxing Li and Yingchun Xu
    Citation: BMC Microbiology 2023 23:341

    The Correction to this article has been published in BMC Microbiology 2023 23:375

  17. With the promotion of “One Health,” the health of animals and their impact on the environment have become major concerns recently. Widely distributed in China, the whooper swans (Cygnus cygnus) and black swans (C...

    Authors: Yin Fu, Kaihui Zhang, Fa Shan, Junqiang Li, Yilin Wang, Xiaoying Li, Huiyan Xu, Ziyang Qin and Longxian Zhang
    Citation: BMC Genomics 2023 24:635
  18. The emergence and wide spread of carbapenemase-producing Enterobacteriaceae (CPE) poses a growing threat to global public health. However, clinically derived carbapenemase-producing Citrobacter causing multiple i...

    Authors: Jianzhong Ye, Lulu Jin, Yaling Li, Hao Xu, Yishuai Lin, Tieli Zhou, Beiwen Zheng, Maofeng Wang and Zhongyong Wang
    Citation: BMC Genomics 2023 24:506
  19. As substitutes for antibiotics, probiotic bacteria protect against digestive infections caused by pathogenic bacteria. Ligilactobacillus salivarius is a species of native lactobacillus found in both humans and an...

    Authors: Jiajun Yang, Peng Shang, Bo Zhang, Jing Wang, Zhenyu Du, Shanfeng Wang, Jun Xing and Hao Zhang
    Citation: BMC Microbiology 2023 23:242
  20. The Acinetobacter baumannii genomic resistance islands (AbGRIs), which were characterized in the genome of the global clone 2 (GC2) A. baumannii contain resistance genes. Here, we aimed to determine the occurrenc...

    Authors: Ghazal Naderi, Mahla Asadian, Pegah Afarinesh Khaki, Mohammadreza Salehi, Alireza Abdollahi and Masoumeh Douraghi
    Citation: BMC Microbiology 2023 23:234
  21. Whole genome sequencing (WGS) of bacterial isolates can be used to identify antimicrobial resistance (AMR) genes. Previous studies have shown that genotype-based AMR has variable accuracy for predicting carbap...

    Authors: Rebecca Rose, David J. Nolan, Deborah Ashcraft, Amy K. Feehan, Leonor Velez-Climent, Christopher Huston, Benjamin Lain, Simon Rosenthal, Lucio Miele, Gary B. Fogel, George Pankey, Julia Garcia-Diaz and Susanna L. Lamers
    Citation: BMC Microbiology 2023 23:225
  22. Antimicrobial resistance (AMR) is a major public health challenge, particularly in sub-Saharan Africa (SSA). This study aimed to investigate the evolution and predict the future outlook of AMR in SSA over a 12...

    Authors: Dickson Aruhomukama and Hellen Nakabuye
    Citation: BMC Microbiology 2023 23:214
  23. Preterm labor syndrome is associated with high perinatal morbidity and mortality, and intra-amniotic infection is a cause of preterm labor. The standard identification of causative microorganisms is based on t...

    Authors: Pisut Pongchaikul, Roberto Romero, Paninee Mongkolsuk, Pornpun Vivithanaporn, Thidathip Wongsurawat, Piroon Jenjaroenpun, Perapon Nitayanon, Iyarit Thaipisuttikul, Threebhorn Kamlungkuea, Arunee Singsaneh, Pitak Santanirand and Piya Chaemsaithong
    Citation: BMC Genomics 2023 24:405
  24. Non-typeable Haemophilus influenzae (NTHi) has become the major cause of invasive H. influenzae diseases in the post-H. influenzae type b vaccine era. The emergence of multidrug-resistant (MDR) NTHi is a growing ...

    Authors: Pei-Yi Su, Wei-Hung Cheng and Cheng-Hsun Ho
    Citation: BMC Microbiology 2023 23:178
  25. The emergence of different viral infections calls for the development of new, effective, and safe antiviral drugs. Glycyrrhiza glabra is a well-known herbal remedy possessing antiviral properties.

    Authors: Dalia Elebeedy, Aml Ghanem, Shaza H. Aly, Mohamed A. Ali, Ahmed H. I. Faraag, Mohamed K. El-Ashrey, Aya M. salem, Mahmoud A. El Hassab and Ahmed I. Abd El Maksoud
    Citation: BMC Microbiology 2023 23:173
  26. Identifying clarithromycin resistance is essential for eradicating Helicobacter pylori (HP). Therefore, we evaluated the performance of Allplex™ H.pylori & ClariR Assay (Allplex™) for diagnosing and detecting cla...

    Authors: Ilsoo Kim, Lee-So Maeng, Joon Sung Kim, Byung-Wook Kim, Dae Young Cheung, Jin Il Kim and Soo-heon Park
    Citation: BMC Microbiology 2023 23:155

    The Correction to this article has been published in BMC Microbiology 2023 23:188

  27. Antimicrobial resistant infections continue to be a leading global public health crisis. Mobile genetic elements, such as plasmids, have been shown to play a major role in the dissemination of antimicrobial re...

    Authors: Nikolina Walas, Samuel Slown, Heather K. Amato, Tyler Lloyd, Monica Bender, Vici Varghese, Mark Pandori and Jay P. Graham
    Citation: BMC Microbiology 2023 23:147
  28. Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen, that is transmitted from a variety of animals, especially cattle to humans via contaminated food, water, feaces or contact with infected envir...

    Authors: Hanady G. Nada, Amera Saeed El-Tahan, Gamal El-Didamony and Ahmed Askora
    Citation: BMC Microbiology 2023 23:127
  29. The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) attracted extensive attention. Information on CRKP from hospital wastewater (HWW) is limited. The aims of this study were to investigate the geno...

    Authors: Zhiqiang Xie, Jiangqing Huang, Shengcen zhang, BinBin Xu, Qianwen Zhang and Bin Li
    Citation: BMC Microbiology 2023 23:115