Microbiology

Profile

The Microbiology Department provides services to the Nicosia General Hospital and to all the Health Centres of the Nicosia District. At the same time, it functions as a Reference Laboratory for specialised examinations for SHSO hospitals and private laboratories and/or hospitals, while at the same time it offers modern diagnostic methods, research and training. It has the capacity to offer high quality services across the entire spectrum of microbiology, including standard and specialised cultures, antimicrobial susceptibility tests and molecular diagnostic tests.

The Department comprises three National Reference Laboratories recognised by the Ministry of Health, the National Influenza Centre (NIC) recognised by the WHO and referral laboratories. The department’s role is key to public health priorities such as epidemics and emerging diseases (e.g. Influenza Pandemic 2009, EBOLA Outbreak, MERS-CoV Epidemic, SARS-CoV-2 Pandemic) while offering consultation for the evaluation of results, antibiotic regimens, prevention and control of hospital infections, hygiene and epidemiological topics.

SERVICES OFFERED BY THE MICROBIOLOGICAL DEPARTMENT:

• Diagnostic tests for bacteria, fungi, parasites and viruses
• Staining for direct microscopy
• Bacteria and fungi cultures
• Antigen detection by various methods such as immunochromatography, immunofluorescence and ELISA
• Direct DNA / RNA detection by molecular methods
• Strain identification by standard and molecular methods
• Antimicrobial susceptibility testing using the following methods: Kirby-Bauer, MIC and molecular methods according to EUCAST guidelines
• Genotyping by molecular methods
• Determination of serogroup and serotype of bacterial strains

The Department offers a broad range of molecular tests:

• Qualitative and quantitative detection of microorganisms and genes by conventional PCR, Reverse Transcription PCR, Real Time PCR and Multiplex PCR
• Genotyping and determination of resistance to antiviral or anti-tuberculosis drugs using molecular hybridisation methods
• Multiplex PCR, a fully automated molecular detection system which, within an hour, can simultaneously detect sixteen to thirty-four different pathogens / targets that are responsible for various infectious diseases, depending on the site of infection.
• Meningitis / encephalitis panel (16 microorganisms)
• Respiratory panel (20 microorganisms)
• Gastrointestinal panel (22 microorganisms)
• Blood culture Identification panel (27 microorganisms & targets)
• Pneumonia panel (34 microorganisms & targets)

Specialised labs:

• National Reference Laboratory for Mycobacteria
• National Reference Laboratory for Salmonella and Other Intestinal Pathogens
• National Reference Laboratory for Monitoring Antimicrobial Resistance
• National Influenza Centre (WHO recognized)
• Referral laboratory for Neisseria meningitidis, Streptococcus pneumoniae, Haemophilus influenzae and Neisseria gonorrhoeae
• Referral Laboratory for Bacteria and Fungi (Molecular Methods)
• Referral Laboratory for Viruses (Molecular Methods)

National Reference Laboratory for Mycobacteria

The lab receives samples from all over Cyprus (SHSO and private sector) for microscopy and cultures for the Mycobacterium tuberculosis complex, but also for non-tuberculous Mycobacteria. The test is offered free of charge by the Ministry of Health and includes the following:

• Microscopy with acid-resistant stain (Kinyoun)
• Culture
• Continuous automated monitoring in a liquid culture system (Bactec® MGIT 960) and
• Solid media: Löwenstein – Jensen and Stonebrink
• Identification of mycobacteria at the species level using PCR and reverse hybridisation assay
• Susceptibility testing for first- and second-line drugs for Mycobacterium tuberculosis and susceptibility testing for non-tuberculous Mycobacteria
• According to the Department’s guidelines, the molecular test can be performed by direct enrichment/amplification of nucleic acid in specific samples (Cepheid Xpert MTB / RIF Assay)
• National Reference Laboratory for Salmonella and Other Intestinal Pathogens

In addition to routine clinical samples, the Department of Microbiology as a reference lab receives Salmonella strains from SHSO and private sector laboratories for serotype determination. It also accepts Campylobacter strains for taxonomic identification at the species level and susceptibility testing as well as samples for the detection of verotoxin from enterohaemorrhagic Escherichia coli strains. According to the current European guidelines, toxins from Clostridium difficile can be detected by PCR for validation purposes on positive ELISA test.

National Reference Laboratory for the Monitoring of Antimicrobial Resistance

The lab collects antimicrobial resistance data from all hospitals of the State Health Services Organisation (SHSO) and uploads them to the ECDC, TESSy (European Surveillance System) database. Since the department participates and collaborates with WHO the data are automatically forwarded from the TESSy platform to the Global Antimicrobial Resistance and Use Surveillance System (GLASS).

• Reference Laboratory for Neisseria meningitidis, Streptococcus pneumoniae, Haemophilus influenzae and Neisseria gonorrhoeae
• Determination of serogroup for Neisseria meningitidis and serotype for Streptococcus pneumoniae and Haemophilus influenzae
• Reference Laboratory for Bacteria, Fungi and Resistance Mechanisms (Molecular Methods)
• Simultaneous molecular detection of Chlamydia trachomatis and Neisseria gonorrhoeae using a fully automated system for urine samples, cervical or vaginal smears
• Molecular detection of Pneumocystis jiroveci in bronchoalveolar lavage (BAL) and induced sputum
• Molecular identification of Carbapenemase-producing Enterobacteriaceae (CPE), by detection of carbapenemase encoding genes such VIM, KPC, NDM and OXA-48
• Molecular detection of antimicrobial resistance in mecA-positive Staphylococcus aureus strains and production of Panton Valentine toxin (PVL)
• Molecular detection of antimicrobial resistance in of VanA- or VanB-type Enterococcus spp strains
• Referral Laboratory for Viruses (Molecular Methods)
• Determination of viral load for HIV, HBV, HCV, CMV, BK and JC viruses
• Genotyping for HCV, HBV
• Determination of drug resistance for HBV
• Detection of RSV and Influenza A & B, including its subtype from nasopharyngeal swaps and BAL
• Ebola virus detection
• MERS-CoV detection
• SARS-CoV-2 detection
• Public health and emerging diseases
• Timely preparation and maintaining high readiness levels to meet the needs for diagnostic and prevention measures against emerging infectious diseases
• Influenza pandemic 2009
• EBOLA outbreak in 2014
• SARS-CoV-2 2019-2020
• MERS-CoV Detection

The Microbiology Department, which facilitates also a Biosafety Level 3 Lab, is always ready to deal with any emerging infectious disease that poses a risk to public health

ACTIVITIES:

ECDC National Reference Point for Microbiology in Cyprus

External Quality Control: Continuous participation of the Department in various External Quality Control programmes in collaboration with international Organisations (NEQAS, INSTAND e. V., Labquality, ECDC, WHO, etc.).

Accreditation:

Accreditation for the six (6) laboratories of the Department of Microbiology by the Cyprus Organisation for the Promotion of Quality & Cyprus Accreditation Body (CYS-CYSAB). The Quality System of the Department meets the requirements of the revised ISO 15189: 2012 standard for more than 48 accredited methods corresponding to the 96% of the published results in 2019.

http: //www.mcit.gov.cy/mcit/cys/cys.nsf/index_2?OpenForm

Participation in European and Global Programmes:

The Microbiology Department participates in various European Union-funded Programmes and Working Groups through the ECDC network

European Center for Disease Control and Prevention

http: //ecdc.europa.eu/en/Pages/home.aspx) and the WHO (World Health Organization)