Sequencing technologies for the elusive DNA molecule: let’s have a closer look

Evangelia Voulgari, Nicholaos Spanakis, Athanassios Tsakris
Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece

Over the past decade, impressive progress has been made in the field of genome sequencing due
to the introduction of novel platforms capable of massive parallel sequencing. Herein we aim to
present in a concise manner the extraordinary journey which has taken place and the following
evolutionary technological pathway, beginning from the early days of Sanger sequencing and
leading up to the newer second and third generation platforms. Several commonly used next generation
sequencing (NGS) technologies will be presented and compared with Sanger sequencing
and some of the challenges facing these newer platforms will also be debated.

Key words
sequencing, platforms, next generation sequencing

Bartonella infections: clinical manifestations, diagnostic techniques and treatment

Maria Mavrouli, Georgia Vrioni, Joseph Papaparaskevas, Violetta Kapsimali
Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece

Bartonella spp. are fastidious, hemotropic, Gram-negative bacteria responsible for emerging and reemerging
diseases around the world. The majority of human infections are caused by Bartonella
henselae, Bartonella quintana and Bartonella bacilliformis. Clinical manifestations of Bartonella infection
range from mild and self-limited to life-threatening disease, which must be treated with the appropriate
antimicrobial regimen. The severity of Bartonella infection correlates with the immune
status of patients. As diagnostic techniques improve, the spectrum of clinical disease is expanding
and includes regional lymphadenopathy, bacteremia, fever of unknown origin, endocarditis, bacillary
angiomatosis and peliosis hepatis. This review summarizes current knowledge regarding the microbiology,
clinical manifestations, diagnostic techniques and treatment of Bartonella infections.

Key words
Bartonella, lymphadenopathy, bacillary angiomatosis,
peliosis hepatis, immunofluorescence, treatment

Laboratory influenza surveillance in Νorthern Greece, 2014-2015

Angeliki Melidou, Maria Exindari, Georgia Gioula, Nicolaos Malisiovas
National Influenza Centre for N. Greece, 2nd Department of Microbiology, Medical School,
Aristotle University of Thessaloniki, Thessaloniki, Greece

Following the influenza pandemic in 2009, the influenza virus continues to threaten public health
with its yearly epidemics. This is a review of the laboratory influenza surveillance in northern
Greece, during 2014-2015. Starting from the 40th week of 2013 until the 20th week of 2014, 519
clinical samples were examined. The three influenza A(H1N1)pdm09, A(H3N2) and B types were
detected at 39.1% of the cases. Further molecular analysis of the haemagglutinin and neuraminidase
genes from representative samples followed in order to assess the effectiveness of the
vaccine and of the most frequently used antiviral drugs. Α(Η1Ν1)pdm09 strains were antigenically
related to the vaccine virus strains, B strains were antigenically related to another strain, which
was selected for the 2015-2016 vaccine, while A(H3N2) viruses exhibited important antigenic drift,
that reduced the vaccine effectiveness. No resistant strains to oseltamivir were detected. As the
World Health Organization suggests, constant influenza surveillance is essential at a national and
international level.

Key words
influenza, N. Greece, genetic characterization,
vaccine, oseltamivir

Evolution of candidemia incidence and susceptibility testing of Isolated Candida strains during a decade in a tertiary general hospital in Greece

Maria Orfanidou, George Gkanteris, Helen Vagiakou
Department of Microbiology, General Hospital of Athens “G. Gennimatas”, Athens, Greece

Recent studies reveal an increase in the incidence of candidemia and changes in the species of
the isolated Candida strains, as well as in their drug susceptibility. The aim of this study was to
evaluate the isolated Candida strains from blood cultures and their susceptibility in a tertiary hospital
in Greece, during two periods of three years each (Period 1(P1): 1/1/2004-31/12/2006 and
Period 2 (P2): 1/1/2012-31/12/2014). During the study periods blood cultures were sent to the laboratory
for diagnosing bloodstream infections. The origin of the strains was for Period 1: Internal
Medicine 32/71 (45.1%), Surgical Department 24/71 (33.8%), Intensive Care Unit (ICU) 15/71
(21.1%) and for Period 2: 88/152 (57.9%), 35/152 (22.4%), 29/152 (19.1%), respectively. According
to our results, Candida strains isolated in Period 1 were 71 (2.7%) and in Period 2, 152 strains (4.5%).
In Period 1 C. albicanswas the predominant strain (29/71, 41%), followed by C. parapsilosis (15/71,
21%), C. glabrata (13/71, 18%), C. tropicalis (7/71, 10%) and C. famata (2/71, 3%). In contrary, in Period
2 C. parapsilosis was the predominant strain (63/152, 41.4%), followed by C. albicans (53/148,
34.9%), C. glabrata (14/152, 9.2%), C. famata (9/152, 5.9%) and C. tropicalis (5/152, 3.3%). Resistance
rate in Period 1 was: fluconazole 8.8%, voriconazole 1.2%, flucytosine 1.2%. Resistance rate in Period
2 was: fluconazole 10.8%, voriconazole 1.3%, flucytosine 1.3%. All Candida strains were fully
susceptible to caspofungin and amphotericin B in both periods. In the two study periods a significant
increase (p: 0.0258), approximately double, in the incidence of candidemia was observed.
Noticeable, was the predominance of C. parapsilosis in Period 2 (p: 0.0014), unlike with the predominance
of C. albicans in Period 1. No significant differences were observed in the resistance rate
in the two periods concerning fluconazole, flucytosine and voriconazole. Echinocandins and amphotericin
B seems to be the most effective treatment in our hospital. Taking into consideration,
the different response of Candida species in antifungal agents in vivo, identification of Candida
strains in species level and assess of their susceptibility patterns seems to be a necessity.

Key words
candidemia, evolution, epidemiology, identification,
susceptibility, tertiary care hospital

The evolution of infectious diseases and Microbiology in Greece during 19th century through the lectures of Athens Medical Society (1835 – 1900)

Constantinos Tsiamis1, Georgia Vrioni1, Evangelos Vogiatzakis2, Athanassios Tsakris1
1 Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
2 Department of Microbiology, General Chest Hospital “Sotiria”, Athens, Greece

The aim of this study is to present the nosological spectrum of Greece during the 19th century.
The source of information for the study have been the lectures of the Athens Medical Society
during the period 1835-1900, which include microbiology-related issues that cut across various
medical domains such as Microbiology, Epidemiology, Hygiene, Pathology, Pediatrics, Gynecology,
Ophthalmology, Otolaryngology and Venereology-Dermatology. The analysis of these communications
reveals that Greece was affected by the same infections as Europe, with plague,
malaria, smallpox, cholera, typhus, tuberculosis and rabies, among others, essentially making up
a fixed endemic spectrum of the country. From the mid-19th century onwards, the existing spectrum
was enriched with meningitis, scarlet fever, pertussis, echinococcosis, diphtheria, trachoma
and leprosy. As far as the majority of these diseases are concerned, the situation remained invariant
until the first decades of the 20th century, mainly due to the lack of appropriate antimicrobial
therapy but also because of the poor organisation of the sanitary system.

Key words
Athens Medical Society, Greece, History of Microbiology,
Public Health