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Microbiomes, environment and health

Microbiomes, environment and health

Our research interests primarily lie within the One Health approach to study the interactions between humans, livestock, environmental microbiomes, and transmission of antimicrobial resistance (AMR) to develop interventions for the public good. Microbiomes, Environment and Health research group is using whole genome sequencing to aid to understand the transmission and horizontal gene transfer in different related species and if they are transferable into human pathogens. We also use metagenomics approaches to analyse the total microbial communities (microbiomes), specifically the relative abundance and diversity of AMR genes and their transmission dynamics between humans, animals, and their associated environments. We have wide experience in newly developed, low-input Oxford Nanopore sequencing technologies to provide in-depth genomic analysis to identify novel or rare genetic features of relevant human and animal pathogens.

Group members

  • Hermine Mkrtchyan staff profile

    Professor Hermine Mkrtchyan

    Professor of Microbiology and Head of Research
    School of Medicine and Biosciences

    I use an interdisciplinary approach from laboratory to socioeconomic factors and policy implementation to address challenges of antimicrobial resistance (AMR) that require concrete global efforts.  

    I use an interdisciplinary approach from laboratory to socioeconomic factors and policy implementation to address challenges of antimicrobial resistance (AMR) that require concrete global efforts.  

Postdoctoral Research Associate

  • Dr Rory Cave

Postgraduate Research students

  • Mr Oscar Previtali
  • Miss Rim Wazni
  • Ms Rita Kmeid
  • Mr Julio Cesar

Current research themes

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  • Deciphering indoor air microbiomes
  • Enhancing opportunities for low-biomass microbiomes
  • Impact of natural green spaces and urban environments on human gut microbiome and health
  • Microbiomes, environment and health
  • Whole genome sequencing of emerging pathogens
  • Whole genome sequencing of pathogens in the food chain
  • DNA sequencing for public health
  • Surveillance of antimicrobial resistant bacteria within urban built environments
  • Application of DNA sequencing for food safety
  • Determining the impact of inclusion of seaweed in broiler finisher on poultry gut microbial diversity and antimicrobial resistance (AMR)
  • Long and short read sequencing of AMR important pathogens

Current projects

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Microbiomes, environment, and health

The human microbiome plays many key roles in the smooth daily operations of the human body. Our bodies harbour several microbial communities that are constantly exposed to and challenged by the environment, and exist simultaneously – eg in the mouth and throat, the gut, skin, nose, stomach and genitals – all of which constantly change across the lifecourse. However, how they develop, how they are impacted by the environment, and how precisely this impacts human physical and mental health is not well understood.  We use a cross-disciplinary approach to understand the impact of the environment on microbiome and health.

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Enhancing opportunities for low-biomass microbiomes

The microbiome has a great impact on disease and health across the life course, making understanding of the flow and relationship of microorganisms between the environment and humans increasingly important.

The current scientific debate of low-biomass microbial communities is far from settled and deserves methods for a rigorous investigation. Solving the technical challenges associated with the low-biomass microbiome samples are fundamental and crucial to improve our understanding of the role of these low-biomass microbial communities in health and disease. We bring together knowledge and technological advances to develop improved protocols and pipelines to transform the microbiome science and provide a unique opportunity to solve real-world problems, but also impact our ability to accurately diagnose diseases.

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Application of DNA sequencing for food safety

The microbiological safety testing of food is largely reliant on methods and standards developed decades ago. Recent microbiome research demonstrated a paradigm shift from traditional microbiology to genomics-based approaches. The Covid-19 pandemic has highlighted the value of DNA sequencing in the monitoring of pathogens. We seek to explore the potential for innovative sampling techniques and DNA sequencing-based methodology to improve food microbiology testing.

An artificial baby microbiome and genetic material of all the microbes.

DNA sequencing for public health

Indoor public places are crowded, and social distancing is difficult. In such contained spaces especially if have inappropriate levels and methods of air handling and exchange and hygiene practices, they might become incubators of pathogens.

Shared spaces (where there is high interaction of shared surfaces and with one another) pose special challenges for ventilation and hygiene and lead to an inevitable increase of indoor biological aerosols (bioaerosols).

We utilise new (meta)genomic methodologies and bioinformatics tools to comprehensively investigate the role of indoor air microbiomes as a vector for the transmission of antimicrobial resistant (AMR) important pathogens between humans and the environment.

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Developing approaches to avoid antibiotic overuse in COPD

To reduce the burden and improve clinical symptoms, almost all patients with Chronic obstructive pulmonary disease (COPD) and exacerbations are often prescribed long-term antibiotic regimes; choosing this approach, however, means that many patients may well receive unnecessary antibiotics, promoting selective pressure and antibiotic resistance, which is a public health concern globally. The problem worsens because many of the bacteria responsible for the infection are resistant to multiple antibiotics. We develop approaches using novel sequencing technologies that can help to avoid antibiotics overuse for COPD patients.

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Impact of natural green spaces and urban environments on human gut microbiome and health

Little is known about the direct correlations between the human gut microbiome, antibiotic exposure, diet, green space exposure, and the relationship between the socio-economic status of individuals. We use an interdisciplinary approach to conduct this community-based project combining social sciences, microbiome metagenomics, and bioinformatics.

PhD projects, topics and interests

We invite PhD applications for all above research themes.

Industrial/external partners

Seaweed Generation  
  • Centre for Innovation of Livestock Excellence  
  • Dr Raju Misra, UKHSE 
  • Dr Jennifer Cole, Royal Holloway University of London 
  • Dr Ali Shanom, University College London Hospital 
  • Prof Mark Holmes, University of Cambridge  
  • Dr Andrew Farlow, University of Oxford 
  • Prof Saheer Gharbia, UKHSE 
  • Prof Ajit Shah, Middlesex University London 
  • Prof Haroun Shah, Middlesex University London 
  • Multiple international partners 

Publications

  • Book chapters

    • Haroun N Shah, [...], Hermine V Mkrtchyan. 2020. MALDI TOF MS and currently related proteomic technologies in reconciling bacterial systematics. In: Trends in the Systematics of Bacteria and Fungi. Bridge, Paul, Smith, David and Stachebrandt, EErko. Eds. CAB Internationa, Wallingford, UK. ISBN 9781789244984.  

    • Serafim V, Xu Z, Mkrtchyan HV et al. Chapter 15: ‘Determination of Antimicrobial Resistance using Tandem Mass Spectrometry’. In " MALDI-TOF and Tandem MS for Clinical Microbiology". Wiley, 2017.  

    • Xu Z, Olkun A, Vranckx K, Mkrtchyan HV, et al. Chapter 21B: ‘Subtyping of Staphylococcus spp. Based upon MALDI-TOF MS Data Analysis’. In " MALDI-TOF and Tandem MS for Clinical Microbiology". Wiley, 2017. 

  • Publications (*corresponding author)

    • Rory Cave, Mary Ter-Stepanyan, Hermine V Mkrtchyan*. 2023. Short and long read sequencing revealed the detection and evolution of an IncF plasmid harbouring blaCTX-M-15 and blaCTX-M-27 genes in Escherichia coli ST131. Microbiology Spectrum.  

    • Jie Sheng, Rory Cave, Mary M Ter-Stepanyan, Nune Kotsinyan, Jiazhen Chen, Taijiao Jiang, Hermine V Mkrtchyan*. 2023. Whole genome sequencing and comparative genomics analysis of a newly emerged multidrug resistant Klebsiella pneumoniae ST967. Microbiology Spectrum. 

    • Rory Cave, Nune Kotsinyan, Mary Ter-Stepanyan, Hermine V Mkrtchyan*. 2022. UroPathogenic and Extended spectrum beta-lactamase Escherichia coli ST127 belonging to a new emerging lineage containing unique genetic adaption for urinary tract infections from remints of prophage insertion regions. Microbiology Spectrum. 

    • El-Deeb W, Cave R, Fayez M, Alhumam N, Quadri S, Mkrtchyan HV. 2022. Methicillin resistant staphylococci isolated from goats and their farm environments in Saudi Arabia genotypically linked to known human clinical isolates: a pilot study. Microbiology Spectrum. Visit the ASM Journals website for more information. 

    • Cole JA, Dodds K, Ayikoru M, Mkrtchyan HV. 2021. Unpacking vaccine ‘hesitancy’: the spectrum of vaccine acceptance. BMJ. Visit theBMJopinion website for more information.

    • Cole J, Dodds K, Ayikoru M, Mkrtchyan HV. Critical Health Geopolitics: (Un)healthy Spaces During the COVID-19 Pandemic. The UNESCO Social Sciences and COVID 19 pandemic. 2021. 

    • Rory Cave, Raju Misra, Jiazhen Chen, Shiyong Wang, Hermine V Mkrtchyan*. 2021. Comparative genomics demonstrated a link between staphylococci isolates from different sources; A Possible public health risk. Frontiers in Microbiol. Visit the Frontiers website for more information. 

    • Cave R, Cole J, Mkrtchyan HV*. 2021. Surveillance and prevalence of antimicrobial resistant bacteria from public settings within urban built environments: Challenges and opportunities for hygiene and infection control.  Review. Environment International. Visit the ScienceDirect website for more information.

    • Arman R. Badalyan., M.G. Hovhannisyan, G.N.Ghavalyan, Mary M. Ter-Stepanyan, Rory Cave, Jennifer A. Cole, Andrew W.K.Farlow, Hermine V. Mkrtchyan*. 2021. The knowledge and attitude of physicians regarding vaccinations in Yerevan, Armenia: Challenges for COVID-19. Vaccines 9(10), 1188; visit the MDPI website for more information.

    • El-Deeb W, […], Mkrtchyan HV. 2021 The effect of staphylococcal mastitis including resistant strains on serum procalcitonin, neopterin, acute phase response and stress biomarkers in Holstein dairy cows. PeerJ.9:e11511. 

    • Xu Z, Li X, Tian D, Sun Z, Guo L, Dong C, Tang N, Mkrtchyan HV*. 2020. Molecular characterization of methicillin-resistant and -susceptible Staphylococcus aureus recovered from hospital personnel. J Med Microbiol. doi: 10.1099/jmm.0.001272. Epub ahead of print. PMID: 33180019. 

    • Xu Z, Cave R, Chen L, Yangkyi T, Liu Y, Li K, Meng G, Niu K, Zhang W, Tang N, Shen J, Mkrtchyan HV*. 2020. Antibiotic resistance and molecular characteristics of methicillin-resistant Staphylococcus epidermidis recovered from hospital personnel in China. J Glob Antimicrob Resist. 22:195-201.  

    • El-Deeb W, Fayez M, Elsohaby I, Mkrtchyan HV, Alhaider A. 2020. Changes in blood biomarkers in Arabian horses with Clostridium difficile-induced enterocolitis. Comp Immunol Microbiol Infect Dis. 73:101525. doi: 10.1016/j.cimid.2020.101525. Epub 2020 Aug 7. PMID: 32877870. 

    • El-Deeb W. Elsohaby I, Fayez M, Mkrtchyan HV, El-Etriby D, ElGioushy M. 2020. Use of procalcitonin, neopterin, haptoglobin, serum amyloid A and proimflammatory cytokines in diagnosis and prognosis of bovine respiratory disease in feedlot calves under field conditions. Acta Trop. doi: 10.1016/j.actatropica.2020.105336. 

    • Zhen Xu, Jiazhen Chen, Kostas Vougas, Haroun Shah, Raju Misra, Hermine V Mkrtchyan*. 2019. Comparative proteomic profiling of methicillin susceptible and resistant Staphylococcus aureus. Proteomics 2020, 20, 1900221. doi: 10.1002/pmic.201900221. 

    • Jamrozy D, Misra R, Xu Zhen, Ter-Stepanyan MM, Karapetyan HD, Hambardzumyan ADz, Mkrtchyan HV*. 2019. Novel methicillin-resistant Staphylococcus aureus CC8 clone carrying SCCmec V with high similarity to element from coagulase negative staphylococci identified in a hospital setting in Armenia. Front. Microbiol. Visit the Frontiers website for more information. 

    • Cave R, Misra R, Chen J, Wang S, Mkrtchyan HV*. 2019. Whole genome sequencing revealed new molecular characteristics in multidrug resistant staphylococci. Nature Sci. Reports. DOI : 10.1038/s41598-019-45886-6. 

    • Xu Zhen, Raju Misra, Gavin K Paterson, Ronald R Cutler, Mark A Holmes, Saheer Gharbia, Mkrtchyan HV*. 2018. Whole genome sequence and comparative genomics analysis of multi-drug resistant environmental Staphylococcus epidermidis ST59. G3: Genes, Genomes, Genetics. Visit the Oxford Academic website for more information.

    • Zhen Xu, Haroun N Shah, Raju Misra, Jiazhen Chen, Wenhong Zhang, Yuting Liu, Ronald R Cutler, Hermine V Mkrtchyan*.  2018. The prevalence, antibiotic resistance and mecA characterization of coagulase negative staphylococci recovered from non-healthcare settings in London, UK.  Antimicrobial Resist & Inf Control. DOI : 10.1186/s13756-018-0367-4.  

    • Mkrtchyan HV*, Zhen X, Yacoub M, Ter-Stepanyan MM, Karapetyan HD, Cutler RR, Kearns AM, Pichon B, Hambardzumyan ADz. 2017. Detection of diverse genotypes of methicillin resistant Staphylococcus aureus from hospital personnel and the environment in Armenia. Visit the NIH website for more information. 6:19.doi: 10.1186/s13756-017-0169-0. Also visit the Antimicrobial Resistance & Infection Control page for more information.

    • Mkrtchyan HV, Xu Zhen, Cutler RR 2015. ‘Diversity of SCCmec elements in environmental staphylococci. BMC Microbiology 15:120; doi:10.1186/s12866-015-0451-3.

    • Zhen X, Mkrtchyan HV*, Cutler RR 2015. Antibiotic resistance and mecA characterization of coagulase-negative staphylococci isolated from three hotels in London, UK. Front. Microbiol. 09 September.

    • Mkrtchyan HV, Russell CA, Wang N, Cutler RR 2013. "Can public restrooms be an environment for bacterial resistomes?" PLoS ONE 8(1): e54223. doi:10.1371/journal.pone.0054223. 

    • Mkrtchyan HV, Cutler R. 2012. Identification of mecA genes in environmental staphylococcal isolates. International journal of infectious diseases vol. 16, 426.  

    • Mkrtchyan H*, Gibbons S, Heidelberger S, Zloh M, Khalatbari Limaki H  2010. Purification, characterization and identification of acidocin LCHV, an antimicrobial peptide produced by Lactobacillus acidophilus n.v. 317/402 strain Narine.  Int. J. Antimicrob. Agents, 35 (3): 255-260. 

    • Mkrtchyan HV. 2013. An importance of good hygiene. Microbiologist.  

    • Mkrtchyan H. 2011. New dedicated infection control service for schools. Independent Education Today. Issue 21, p. 13. 

    • Mkrtchyan H. 2011. Hands on protection for schools. Independent Education Today.  Issue 22.  

  • Conference papers

    • R. Cave […], Mkrtchyan HV. The detection and evolution of an IncF plasmid type harbouring both blaCTX-M-15 and blaCTX-M-27 genes from Escherichia coli ST131. ECCMID 2022. Copenhagen, Denmark. 

    • O. Privitali […], Mkrtchyan HV. Comparison of matrix assisted laser desorption ionization-time of flight mass spectrometry vs. metagenomics sequencing for the assessment of surfaces in healthcare settings in outbreak situations. ECCMID 2022. Copenhagen, Denmark. 

    • R. Cave […], Mkrtchyan HV. CC5 MRSA isolates from goats and the farm environment in Saudi Arabia phylogenetically linked to isolates recovered from humans in clinical samples from the USA and Europe ECCMID 2022. Lisbon, Portugal.  

    • Cole J, Dodds K, Ayikoru M, Mkrtchyan HV. Critical Health Geopolitics: (Un)healthy Spaces During the COVID-19 Pandemic. UNESCO: Social Sciences and COVID 19 pandemic. October 2021. Paris, France. 

    • Cole JA, Dodds K, Ayikoru M, Mkrtchyan HV. 2021. Unpacking vaccine ‘hesitancy’: the spectrum of vaccine acceptance. British Medical Journal. Visit thebmjopinion website for more information.

    • Zhen Xu, Tsetan Yangkyi，Liqin Chen, Yuting Liu, Jiazhen Chen, Ge Meng, Kaijun Niu, Wanqi Zhang, Jun Shen, Hermine V Mkrtchyan. Molecular characterization of Staphylococcus epidermidis recovered from healthcare personnel in a hospital in Tianjin, China. ECCMID 2019. Amsterdam, Netherlands.  

    • Cave R, Misra R, Mkrtchyan H. Whole genome sequencing (WGS) to unveil the molecular epidemiology of S. haemolyticus. ECCMID 2019. Amsterdam, Netherlands. 

    • Cave R, Serafm V, Sellami L, Shah A, Mkrtchyan H, Shah H. Comparative MALDI-TOF analysis of Staphylococcus spp. from the Environment including Antibiotic Resistant Strains. MSACL 2018. Salzburg, Austria. 

    • Cave R, Misra R, Mkrtchyan H. Diversity of SCCmec elements recovered from high-frequency hand-touched areas from general public setting from East and West London. ECCMID 2018. Madrid, Spain.  

    • Zhen Xu, Fin Ming, Haroun Shah, Ajit Shah, Mkrtchyan HV*. Comparative proteomic analysis of a wild type S. aureus, mecA negative strain grown in the presence and absence of oxacillin. IC2AR 2017. Invited Lecture. Lisbon, Portugal. 

    • Zhen Xu, Kathleen Vranckx, Haroun Shah, Ronald R Cutler, Bruno Pot, Hermine V Mkrtchyan.  Mass spectra-based systematics analysis of antibiotic resistant environmental staphylococci. ECCMID 2016. Amsterdam, Holland. 

    • Xu Zhen, Raju Misra, Mkrtchyan HV, Ronald R Cutler, Saheer Gharbia, Gavin K Paterson. Whole genome sequencing has revealed the transmission of antibiotic resistance and virulence genes in Staphylococcus epidermidis. ECCMID 2016. Amsterdam, Netherlands. 

    • Mkrtchyan HV, Cutler RR, Zhen X, Kearns AM, Pichon B, Yacoub M, Hambardzumyan ADz,  Ter-Stepanyan MM, Karapetyan HD. Characterisation of Methicillin resistant Staphylococcus aureus from hospital personnel and the environment in Armenia.  ECCMID 2015. Copenhagen, Denmark.  

    • Xu Zhen, Hermine V Mkrtchyan, Ronald R Cutler. Widespread distribution of multidrug resistance in community associated staphylococci. FEMS 2015. Maastricht, The Netherlands.  

    • Xu Zhen, Hermine V Mkrtchyan, Ronald R Cutler. Molecular characterization of methicillin-resistant coagulase negative Staphylococci isolated from environment. ESCMID 2014. Barcelona, Spain.  

    • Wang N, Mkrtchyan HV, Cutler RR. Rapid method to measure gaseous exchange from bacteria undergoing treatment of different antimicrobial/disinfectant agents in real time. FEMS 2013. Leipzig, Germany.   

    • Wang N, Nürnberg DJ, Mkrtchyan HV, Cutler RR. Survival and biofilm formation of multidrug resistant and multidrug susceptible environmental staphylococci. FEMS 2013. Leipzig, Germany.   

    • Mkrtchyan HV, Cutler RR. The diversity of SCCmec elements found in environmental staphylococci. ESCMID 2013. Invited talk. Berlin, Germany.  

    • Mkrtchyan HV, Cutler RR. The discovery of EMRSA-15 in environmental staphylococci isolates. IMED-2013. Vienna, Austria. 

    • Mkrtchyan HV, Cutler RR. Determination of mecA and PVL carriage in a methicillin susceptible Staphylococcus aureus isolated from a public washroom. ICAR 2012. Lisbon, Portugal.  

    • Mkrtchyan H, Cutler R. Identification of mecA gene in environmental Staphylococci isolates. ISID 2012. Bangkok, Thailand. 

    • Mkrtchyan H, Cutler R. Multiply drug resistant coagulase negative staphylococci isolated from public toilets. FEMS 2011. Geneva, Switzerland. 

Contact

Professor Hermine Mkrtchyan 

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