Microbiology

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Clinic Profile

The Microbiology Department of the Nicosia General Hospital operates as a Reference Laboratory for both the hospitals of the Public Health Service and private laboratories, while offering state-of-the-art diagnostic methods, research and education. It has the capacity to provide high-quality and full-spectrum microbiology services, from routine cultures and antimicrobial susceptibility tests to specialized molecular diagnostic tests.

The Department offers its services to the Nicosia General Hospital and to all Health Centers of the Nicosia District. In addition, the Department has three National Reference Laboratories, recognized by the Ministry of Health, and the National Influenza Center (NIC), recognized by the World Health Organization. The Department operates as a Reference Laboratory for specialized tests throughout the island of Cyprus and covers important Public Health issues, such as epidemics and emerging diseases (e.g. 2009 Influenza Pandemic, EBOLA Virus Outbreak, SARS-CoV-2 Pandemic, Epidemic Monkey Pox Virus).

SERVICES OFFERED BY THE MICROBIOLOGICAL DEPARTMENT:

Diagnostic tests for bacteria, fungi, parasites and viruses

Staining for direct microscopy
Culture for bacteria and fungi
Antigen detection by various methods such as immunochromatography,

immunofluorescence and Elisa

Direct detection of DNA / RNA by molecular methods
Strain identification by standard and molecular methods
Antimicrobial susceptibility testing by the following methods: Kirby-Bauer, MIC

(Minimum Inhibitory Concentration), BMD (Broth Micro Dilution) according to EUCAST guidelines, E-test and molecular methods

Genotyping and drug resistance testing by molecular methods
Serogroup and serotype determination of bacterial strains

The Department offers a significant number of molecular tests

Qualitative and quantitative detection of microorganisms and genes by conventional PCR, Reverse Transcription PCR, Real-Time PCR and Multiple Target PCR
Determination of genotypes, resistance to antiviral and antituberculosis drugs by the hybridization method
Multiple Target PCR, a fully automated molecular detection system that can simultaneously detect fourteen to forty-three (14-43) different pathogens / targets that cause various infectious diseases depending on the site of infection, within one hour.
Meningitis/Encephalitis Group (14 organisms)
Respiratory Group (23 organisms)
Gastrointestinal Group (22 organisms)
Blood Culture Identification Group (43 organisms & antimicrobial resistance genes)
Pneumonia Group (34 organisms & antimicrobial resistance genes)
Joint Infection Group (39 organisms & antimicrobial resistance genes)

Specialized Laboratories maintained in the Department of Microbiology

National Reference Laboratory for Mycobacteria
National Reference Laboratory for Salmonella and other Enteric Pathogens
National Reference Laboratory for Antimicrobial Resistance Surveillance
National Influenza Center (WHO recognized)
Referral Laboratory for Neisseria meningitides, 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 Laboratory receives samples from all over Cyprus (OHHC and private sector) for microscopy and culture for the Mycobacterium tuberculosis complex, as well as for non-tuberculous mycobacteria. The test is offered free of charge by the Ministry of Health and includes the following:

Microscopy with acid-fast 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 species level using PCR and reverse hybridization technique
Susceptibility testing for first- and second-line drugs for Mycobacterium tuberculosis and susceptibility testing for non-tuberculous Mycobacteria
According to the guidelines within the Department, there is the possibility of performing a molecular test for the amplification/multiplication of nucleic acid directly on specific samples with the ability to detect the Mycobacterium tuberculosis complex, Rifampicin resistance (Cepheid Xpert MTB / RIF Assay) and also drug resistance mutations (Isoniazid, Fluoroquinolones, Second-Line Drugs and Ethionamide)

National Reference Laboratory for Salmonella and other Enteric Pathogens

In addition to routine clinical samples, the Department of Microbiology, in the context of its role as a Reference Laboratory, also receives Salmonella strains from laboratories of the National Institute of Health and the private sector for serotyping. In addition, it accepts Campylobacter strains for species and sensitivity identification as well as samples for the detection of verotoxin from enterohaemorrhagic Escherichia coli. According to current European guidelines, there is the possibility of PCR detection of Clostridium difficile toxins in order to confirm a positive test with the Elisa method that precedes as a screening test.

National Reference Laboratory for the Monitoring of Antimicrobial Resistance

Collection of antimicrobial resistance data from all hospitals of the State Health Services Organization (SHSO) and some private hospitals participating in the National Health System, as the Coordination Center of the National Network of Microbiological Departments and sending to the ECDC database, TESSy (European Surveillance System). These data are also automatically transferred from the TESSy platform, through the participation and collaboration of the Microbiology Department with the WHO, to the Global Antimicrobial Resistance Surveillance System (GLASS).

National Influenza Center (WHO NIC Cyprus)

Molecular detection of all circulating Influenza viruses including Avian Influenza Virus. The National Influenza Center collects all positive samples from across Cyprus for typing and further detection of both the subtypes of Influenza A virus and the lineage (B/Yamagata and B/Victoria) of Influenza B virus. As part of its role, it accepts samples from the community across Cyprus through the Sentinel program for molecular investigation and detection of Influenza, SARS-CoV-2 and RSV viruses.

It collaborates with the WHO Collaborating Centre London (Francis Crick Institute) to send an indicative number of positive samples for further analysis (WGS, antiviral susceptibility, etc.) both for epidemiological purposes and for the geographical contribution of Cyprus to the formulation of the Influenza vaccine, which is renewed every year, according to the data on circulating viruses in each country.

Referral Laboratory for Neisseria meningitides, Streptococcus pneumoniae, Haemophilus influenzae and Neisseria gonorrhoeae
Serogrouping for Neisseria meningitides and serotyping for Streptococcus pneumoniae and Haemophilus influenzae and Neisseria meningitides
Susceptibility testing for Neisseria gonorrhoeae

Referral Laboratory for Bacteria, Fungi and Resistance Mechanisms (Molecular Methods)
Simultaneous molecular detection of Chlamydia trachomatis and Neisseria gonorrhoeae in a fully automated system in urine (men) and in cervical or vaginal swab or urine (women)
Molecular detection of Pneumocystis jiroveci in BAL and induced sputum
Molecular detection of carbapenemase produced by enterobacteria (CPE), such as the VIM, KPC, NDM, OXA-48 genes
Detection of molecular antimicrobial resistance in Staphylococcus aureus strains of type mecA and Panton Valentine toxin (PVL) production
Detection of molecular antimicrobial resistance in Enterococcus spp strains of type VanA, VanB
Simultaneous molecular detection by Multiplex PCR of pathogenic bacteria, fungi and parasites and resistance mechanisms in Upper Respiratory, Lower Respiratory, Cerebrospinal Fluid, Joint Fluid and Gastrointestinal System Samples

Virus referral laboratory (Molecular methods)
Viral load determination for HIV, HBV, HCV, CMV, BK Virus, JC and Epstein Barr Virus
Genotyping for HCV, HBV
Drug resistance determination for HBV
RSV detection and influenza A & B virus typing and subtype determination from nasopharyngeal swabs and BAL
Ebola virus detection
MERS-CoV Detection
SARS-CoV-2 Detection
Monkey Pox Virus Detection
HSV1, HSV2, VZV Virus Detection
HPV Detection and its most important genotypes
Zika, Dengue, Chikungunya and Yellow Fever Virus Detection

Public health and emerging diseases

Timely preparation to meet diagnostic needs and measures to prevent any transmission

2009 influenza pandemic
MERS-CoV-2 epidemic in 2012
Ebola outbreak in 2014
SARS-CoV-2 pandemic in 2019
Mpox (Monkeypox) outbreak in 2022

The Microbiology Department, which also has a Biosafety Laboratory 3, is always ready to deal with any emerging disease that poses a risk to Public Health

ACTIVITIES:

External Quality Assessment

Continuous participation of the Department in various External Quality Assessment programs in collaboration with international organizations (NEQAS, INSTAND e.V, Labquality, ECDC, WHO, etc.).

Accreditation

Accreditation for the six (6) laboratories of the Microbiology Department by The Cyprus Organization for the Promotion of Quality- Cyprus Accreditation Agency (CYS-CySAB).

The Department’s Quality System meets the requirements of the revised ISO 15189: 2022 standard for more than 48 accredited methods corresponding to 96% of the published results for 2022.

https://www.gov.cy/meci-cysab/documents/diapisteymenoi-foreis

National Focal Point for Microbiology

Represented by the Director of Microbiology Department, Dr. Despo Pieridou at ECDC

www.ecdc.europa.eu

Participation in European programs

The Microbiology Department participates in various Programs and Working Groups funded by the European Union through the ECDC network (European Centre for Disease Prevention and Control – http://ecdc.europa.eu/en/Pages/home.aspx) and the WHO (World Health Organization)

Antimicrobial Resistance Surveillance Network (EARS-Net)

National Coordinator Dr Panagiotas Maikanti

www.ecdc.europa.eu/en/activities/surveillance/EARS-Net

European Antimicrobial Resistance Genes Surveillance Network (EURGen-Net)

www.ecdc.europa.eu/en/about-us/who-we-work/disease-and-laboratory-networks/EURGen-net

European COVID-19 reference laboratory network (ECOVID-LabNet)

National Coordinator for the Laboratory Sector Dr Christos Karagiannis

www.ecdc.europa.eu/en/about-us/who-we-work/disease-and-laboratory-networks/european-covid-19-reference-laboratory-network

European Diphtheria Surveillance Network (EDSN)

www.ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/edsn

Tuberculosis Disease Network

www.ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/tuberculosis-disease-network

European Food- and Waterborne Diseases and Zoonoses Network (FWD-Net)

www.ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/fwd-net

European Gonococcal Antimicrobial Surveillance Programme (Euro-GASP)

www.ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/euro-gasp

European Invasive Bacterial Disease Surveillance Network (EU-IBD)

www.ecdc.europa.eu/en/about-us/networks/disease-and-laboratory-networks/eu-ibd

European Clostridium difficile infection surveillance network (ECDIS-net) project.

www.ecdc.europa.eu/sites/default/files/media/en/publications/Publications/Clostridium-difficile-infections-surveillance-protocol-version-2.1.pdf

European Legionnaires’ Disease Surveillance Network (ELDSNet)

www.ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/eldsnet

European survey on carbapenemase-producing Enterobacteriaceae (EuSCAPE) project

https://www.ecdc.europa.eu/sites/default/files/media/en/publications/Publications/antimicrobial-resistance-carbapenemase-producing-bacteria-europe.pdf

European Influenza Surveillance Network (EISN)

www.ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/eisn

European Antimicrobial Resistance Genes – Reference Laboratory Capacity (EURGen-RefLabCap) project.

Application of whole genome sequencing (WGS) and genomic surveillance for carbapenem and/or colistin resistant Enterobacterales, Pseudomonas aeruginosa, Acinetobacter baumannii.

National Coordinator Dr Christos Karagiannis

https://www.eurgen-reflabcap.eu