Acta Microbiologica Hellenica

In early 2020, Greece was affected by the SARS-CoV-2 epidemic, and since then, the continuous emergence of fast-spreading variants has caused surges of new SARS-CoV-2 infections. In this study, we performed genomic, phylogenetic, and epidemiological analyses to investigate the SARS-CoV-2 epidemic in northwestern Greece. From March 2020 to February 2022, nasopharyngeal samples obtained from patients suspected to have COVID-19 were tested for SARS-CoV-2 detection. Complete SARS-CoV-2 genomic sequences were generated from selected positive samples. Northwestern Greece experienced four distinct waves of the epidemic following the first wave, which was mainly observed in Attica and other parts of Greece. The positivity index was rising throughout the pandemic waves in several geographical units, with the highest levels recorded in prominent tourist destinations characterized by high agricultural density. The phylogenetic analyses revealed 34 different lineages, with B.1, B.1.1, B.1.1.305, B.1.1.318, B.1.177, B.1.1.7, B.1.617.2, AY.43, and BA.1 being the most prevalent lineages in the region. Although multiple lineages were co-circulating, each pandemic wave was dominated by a different lineage. The SARS-CoV-2 epidemic in northwestern Greece was characterized by the successive introduction of new lineages, resulting in surges of new SARS-CoV-2 infections. Full article

The cycle threshold (Ct) value of PCR, used to detect SARS-CoV-2 viral load, has been associated with disease severity in adults, but few studies have examined these relationships in pediatric patients. The aim of this study was to evaluate the relationship between the Ct value at hospital admission and the duration of fever, length of hospital stay, and the need for medical interventions in pediatric patients with COVID-19. We conducted a retrospective study of 124 pediatric patients with a positive nasopharyngeal swab for SARS-CoV-2 between April 2020 and March 2022. A negative correlation was observed between the Ct value and the duration of fever (p = 0.012), with a similar trend for length of hospital stay (p = 0.25). A low Ct value was also associated with the development of MIS-C (p = 0.026) and the need for respiratory support and steroid therapy (p = 0.036). The Ct value may be useful in stratifying pediatric patients with COVID-19, helping to predict the duration of fever and hospital stay, as well as the need for medical interventions. Full article

Biofilms are bacterial communities on surfaces within an extracellular matrix. Targeting biofilm-specific bacteria is crucial, and natural compounds with reported antibiofilm activity have garnered significant interest. The study evaluated the antibacterial and antibiofilm activity of Erythrina senegalensis leaf extract against multidrug-resistant (MDR) Gram-negative bacteria, including Salmonella Typhimurium, S. Typhi, S. Enteritidis, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The leaf extract was prepared using aqueous and ethanol solvents, and qualitative phytochemical screening revealed the presence of various bioactive compounds such as tannins, saponins, cardiac glycosides, flavonoids, terpenoids, alkaloids, anthraquinone, reducing sugar, and ketones. A Kirby–Bauer disc diffusion assay was performed to test the susceptibility of antibiotics, and the antibacterial efficacy of the aqueous and ethanol extracts of E. senegalensis was determined using the cup-plate method, while the antibiofilm activities were determined using the crystal violet titer-plate method. The aqueous and ethanol extracts of E. senegalensis revealed the presence of tannins, saponins, cardiac glycosides, flavonoids, terpenoids, alkaloids, anthraquinone, reducing sugar, and ketones. The study found that the Gram-negative bacteria isolates that were MDR were S. Typhimurium, S. Enteritidis, and P. aeruginosa, while K. pneumoniae was resistant to beta-lactam and fluoroquinolones, and S. Typhi was susceptible to all antibiotics tested. Statistically, susceptibility to antibiotics had an inverse, weak, and significant relationship with biofilm production (r = −0.453, −0.106, −0.124, −0.106, −0.018, n = 10, p < 0.05). The aqueous extract showed good biofilm inhibition against K. pneumoniae and P. aeruginosa, and poor biofilm inhibition against S. Enteritidis, while S. Typhimurium and S. Typhi exhibited no biofilm inhibition. The ethanol extract did not demonstrate any antibiofilm activity against the tested Gram-negative pathogens. The study suggests that the Gram-negative bacteria’s capacity to form biofilms is negatively associated with their antibiotic resistance phenotypes, and the aqueous extract of E. senegalensis exhibited moderate antibiofilm activity against K. pneumoniae, P. aeruginosa, and S. Enteritidis. Full article

Tuberculosis has had a long-standing prevalence in Greece over the last century, going hand in hand with the country’s overall socioeconomic situation. The current study explores aspects of tuberculosis in Greece since the interwar period and up to the present. Apparently, ignorance of the nature of the disease coupled with false medical perceptions sealed the fate of patients while unwittingly influencing public opinion and making societies hostile toward patients. Such paradigms are of great and timeless value for the cohesion and functioning of societies, not excluding modern ones. Although the present-day situation in Greece is utterly different from that in the previous century, considering the limited number of cases and minimal impact of the disease, new challenges have emerged, such as the under-reporting of cases, the emergence of multidrug-resistant tuberculosis, latent tuberculosis or the management of large refugee flows in the Eastern Mediterranean involving citizens from countries with a high prevalence of the disease. On the other hand, the study of tuberculosis is nowadays more urgent than ever, given the global concerns regarding the future of the disease in the midst of the COVID-19 pandemic, which has put enormous pressure on national health systems. Full article

The United States Centers for Disease Control and Prevention (CDC) has categorized Clostridioides difficile infection (CDI) as a significant concern in extended-care facilities, hospitals, and outpatient clinics. However, little is known about CDI in low- and middle-income countries. This study determined CDI prevalence and impact in outpatient adults presenting with diarrhea in Nigeria. Toxigenic culture and PCR were used to detect and validate C. difficile. Prior antibiotic use, medical history, and demographic data were also obtained. Descriptive and inferential statistics were used for data analysis. The patient demographics were 35.48% (22/62) for the 18–24 years age group and 32.26% (20/62) for both the 25–30 years age group and the 31+ years group, with an average age of 29.7 years. Forty-eight percent of the patients (30/62) tested positive for CDI, and the prevalence increased with age. Most patients (86.67%, 52/60) reported moderate/severe cases of diarrhea and 67.7% had no knowledge of antibiotics. The results showed that 62.30% of the cases were hospitalized with the duration of diarrhea being significantly associated (r = 0.98, p ˂ 0.001) with the length of hospitalization. These results suggest that C. difficile is common among diarrhea patients in this population and that Nigerian hospitals’ infection prevention and control measures must include this pathogen. Full article

Neutrophil gelatinase-associated lipocalin (NGAL) is a protein secreted by activated neutrophils and certain tissues. The aim of this study was to investigate the prognostic role of urinary neutrophil gelatinase-associated lipocalin (uNGAL) in hospitalized COVID-19 patients with regard to mortality. The prospective observational cohort study involved 86 hospitalized adult COVID-19 patients. Patients’ urine samples were collected upon admission and 48–72 h after admission. General anamnesis and clinical status information were obtained from medical records. Within 24 h of sample collection, urine aliquots were centrifuged, the supernatant was separated, and samples were frozen at −80 °C until uNGAL concentration measurement, which was performed within two years of sample collection. The patients were categorized into groups based on disease outcome (survived/deceased). Data analysis was performed to identify predictive factors and diagnostic indicators for the unfavorable outcome group using logistic regression and ROC curve methods. Logistic regression associated age, cardiomyopathy, invasive mechanical ventilation, and uNGAL concentration (follow-up sampling) with mortality. ROC analysis identified uNGAL concentration (follow-up sampling) as an indicator of mortality, with a cut-off value of >23.8 ng/mL. This study concludes that there is an association between disease outcome and uNGAL concentration in COVID-19 patients. However, understanding the dynamics of uNGAL concentration during COVID-19 remains limited, which is crucial for its effective clinical application. Full article

Newcastle disease, which affects poultry and is endemic in many nations across the world, is caused by Avian Paramyxovirus-1 (APMV-1). This experimental study was conducted from January to June 2021 at the National Veterinary Institute (NVI) to evaluate the virus viability and antibody titer of Newcastle disease vaccines (Hichner’s B1, Lasota, and ThermostableI2) stored at different temperature storage conditions. Chickens (12 treatment groups and 1 control group) were vaccinated and challenged with the virulent ND virus (0.5 × 10^6.5 embryonic lethal dose fifty (ELD₅₀)). The immune responses (antibody titers) of chickens were evaluated using hemagglutination (HA) and hemagglutination inhibition (HI) assays. The Newcastle disease vaccines (Hachiner’s B1 (ND-HB1), ND-Lasota, and ND-Thermostable I2) stored at +4 °C HI-induced antibody titers of 151 (±103.3), 136 (±53.4), and 145 (±91) on day 14, respectively, whereas on day 21, they increased to 160 (±82) for ND-HB1 and 144 (±74.5) for ND-Lasota. ND-Thermostable I2 showed a decrement to 133 (±44.8). All three vaccines stored at different temperature storage conditions (+4, +23, and +30 °C) used in this experiment induced antibody titers greater than 128 on day 28 post-vaccination, except the Newcastle disease vaccine Thermostable I2 stored at +30 °C. The vaccines collected from private veterinary drugstores (customer vaccines Hachiner’s B1 and ND-Thermostable I2) used in this experiment induced very low antibody titers, less than 128 antibody titers, from days 14 to 21. Statistically significant induced mean antibody titers were observed for chickens that received vaccines stored at different temperature storage conditions for 72 h (p < 0.05), except for the ND-HB1 mean HI-induced antibody titer at days 7 and 28. Further, vaccine protection was confirmed by inoculation of both the vaccinated (treatment groups) and control groups by the virulent ND virus, where the control group started dying three days post-challenge but all chicks that received the vaccines survived. Overall, this study showed the impact of temperature storage conditions on the antibody titer and their effect on the titer of the viable virus in the vaccine, and thereby its protective capacity, warranting appropriate cold chain management of the vaccines along the value chain. Full article

Hepatic abscesses (HAs) are suppurative cavities caused by the infiltration of liver parenchyma by microbes. The etiology of HAs can include biliary disease, intra-abdominal infections, bile duct ischemia following pancreaticoduodenectomy, liver transplantation, and rarely septicemia, among others. While HA of a bacterial origin is rare, intra-abdominal biliary infections can be seen after appendicitis or proctitis. Empiric treatment generally involves antibiotic coverage and percutaneous drainage. Due to a high health care association, Clostridioides difficile infection (CDI) is becoming more frequent and has increasing antibiotic resistance. While generally limited to the gastrointestinal tract, extra intestinal CDIs are generally related to bacteremia, and related HAs are even rarer, with their prognostic courses not well described. A literature search was performed evaluating case reports and manuscripts relating to CDI-related HA. Articles with relevant information were analyzed for quality. Those fitting predetermined selection criteria and the level of evidence were included in this study. While most affected patients reported recent hospitalization and significant comorbidities, some of them reported no apparent risk factors at all. While all included individuals had HA, only 33.3% had CD-related bacteremia. Treatment of HA was managed with drainage as well as antibiotics and was generally successful, with one death. As CDI becomes more prevalent, studies such as this will be needed to address the management of associated HA. Full article

Gene therapy is an emerging field of medicine that can target and treat previously untreatable blinding or lethal diseases. Within the field of ophthalmology, gene therapy has emerged to treat retinal degenerative disorders, but its exact role is in its infancy. While this exciting frontier is rapidly expanding, these typically viral-based gene therapy vectors trigger a host immune response. Thus, a better understanding of the host immune response to gene therapies is critical, in that harnessing immunity to these vectors may improve treatment efficacy and reduce the risk of vision loss from inflammation. As such, we will discuss innate and adaptive immunity to gene therapy vectors, and avenues through which this response may be harnessed to improve visual outcomes. Full article

The search for effective inhibitors of HIV-1 replication remains a critical research area of research in virology and immunology. Natural products have emerged as promising candidates for antiviral therapies. In the present study, we assessed the potential inhibitory activity of Philippine crocodile serum at both pre- and post-infection stages of the HIV-1 replication cycle. Freshly collected crocodile serum samples were used in a cell culture-based assay with peripheral blood mononuclear cells. HIV-1 reverse transcriptase activity in the treated cell culture system was assessed using colorimetric enzyme immunoassay. The crocodile serum at 0.5% and 0.25% vol/vol concentrations showed an inhibitory activity against HIV-1 replication both in pre-infection interactions (68.61 ± 1.67% and 69.95 ± 2.24%, respectively) and post-infection interactions (65.68 ± 2.93% and 69.92 ± 0.45%, respective). These findings suggest that Philippine crocodile serum may have potential as a natural inhibitor of HIV-1 replication and warrant further investigation into its therapeutic use. Full article

Bacteriophages, or phages, are microscopic viruses that specifically infect and replicate within bacterial hosts. Their unique ability to target and control bacterial populations makes them valuable tools with applications ranging from human medicine and agriculture and environmental management to biotechnology. In this comprehensive review, we explore the diverse and promising medical and non-medical applications of bacteriophages, highlighting their pivotal role across various niches. From safeguarding food production through pathogen control to their innovative utilization in wastewater treatment, bacteriophages prove to be versatile agents. To achieve applications of phages on a larger scale, it is necessary to make the legal framework more suitable and flexible, create special approval programs (e.g., for novel antimicrobial drugs), and promote targeted research and development activities on phages. Additionally, a more intensive exchange between academia, industry, regulatory authorities, and stakeholders in the health system should be pursued. Full article

Malaria remains a leading cause of morbidity and mortality worldwide, with significant efforts directed towards developing effective vaccines to curb its impact. The One Health concept, recognizing the interconnectedness of human, animal, and environmental health, offers a comprehensive approach to understanding and combating this disease. This review examines the development of malaria vaccine through the lens of the One Health framework, highlighting the integration of human, vector, and environmental factors in the fight against malaria. We discuss the current landscape of malaria vaccine development, including the deployment of the RTS,S/AS01 vaccine and the progress of other candidates such as the R21/Matrix-M and PfSPZ vaccine. The challenges posed by the complex lifecycle of the malaria parasite, its genetic diversity, and the environmental factors influencing transmission are explored. This review also discusses emerging technologies and innovations that could enhance vaccine efficacy and delivery. Additionally, we consider ethical, social, and economic factors critical to the successful implementation of vaccination programs. In concluding, this review underscores the importance of adopting a One Health approach to malaria vaccine development, advocating for integrated efforts to address the multifaceted challenges of malaria control and eradication. Full article

A potential biocontrol agent for American foulbrood (AFB), the Paenibacillus bacteriophage phJNUCC32, was isolated from Baengnokdam in Halla Mountain. This study aimed to investigate its genomic characteristics through whole-genome sequencing. The genome of phJNUCC32 was found to be 62,871 base pairs in length, with a G + C content of 51.98%. Phylogenetic analysis classified phJNUCC32 within the unclassified Caudoviricetes bacteriophage category. The genome prediction confirmed the absence of virulence factors and antibiotic-resistance genes, ensuring its genetic safety. A total of 63 coding DNA sequences were identified, revealing a modular arrangement. Notably, the annotation of gene function indicates that phJNUCC32 harbors the holin/lysin system, suggesting significant potential for controlling bacterial infections in AFB and agriculture. Full article

The number of confirmed positive tests of various sexually transmitted infections has grown recently in the United Kingdom. The objective of this study is to propose a deterministic compartmental model to investigate gonorrhoea spread in Northern Ireland between 2012 and 2022. The differential equation based model includes both symptomatic and asymptomatic spread, spontaneous recovery and treatment compartments. After fitting our model to the monthly number of new positive tests, we found that the basic reproduction number is approximately $1.0030$. In addition, we derive the endemic equilibrium of the model, which exists if and only if ${\mathcal{R}}_0>1$. The sensitivity analyses of the basic reproduction number and the endemic values of the compartments of treated individuals indicate that infection spreading time can have a significant impact on gonorrhoea spread. Full article

Vaccination has emerged as the most effective tool in the battle against COVID-19. To optimize vaccination protocols, a deeper understanding of the immune response to vaccination, including influential factors and its duration, is essential. This study aimed to assess the humoral response in vaccinated individuals with or without prior SARS-CoV-2 infection. A prospective observational study was conducted across 14 private healthcare structures in Greece. Anti-spike IgG titers were measured at different timepoints following the initial vaccination and booster doses of the BNT162b2, mRNA-1273, ChAdOx1 nCoV-19, and Ad26.COV2.S vaccines. A total of 505 participants were included in the first phase, evaluating the humoral response after the initial vaccination, and 311 participants were involved in the second phase, assessing the effects of booster vaccination. All vaccines elicited high anti-S IgG titers initially, followed by a subsequent decline that was addressed by the booster vaccination. The humoral response was sustained up to one year after the booster vaccination. mRNA vaccines induced higher anti-S IgG titers compared to vector vaccines, with mRNA-1273 eliciting higher titers than BNT162b2. Vaccination resulted in higher antibody titers than natural infection alone; however, convalescent patients who received vaccination had significantly higher anti-S IgG titers compared to those who received the booster vaccine without previous SARS-CoV-2 infection. Lower antibody titers were observed in men and older patients (>51.5 years old), as well as smokers, although the decline rate was lower in these subgroups. These results underscore the importance of booster doses and reveal the potential influence of age, gender, smoking habits, and vaccine type on varying humoral responses. Long-term monitoring of antibody persistence, evaluation of cellular immune responses, and assessment of vaccine efficacy against emerging variants should be considered to enhance our understanding of immunity dynamics and inform vaccine development and deployment strategies. Full article

Our intention was to trace the origins of names that every microbiologist comes to pronounce or write down in her/his daily practice and, particularly, to elucidate the etymological debt of this medical field to the two great languages of classical antiquity, Greek and Latin. According to the system of binomial nomenclature established by Linnaeus in the 1750s to give a unique name to each species, consisting of two terms, the name of the genus and the name of the species, combinations were based on Greek and Latin. The two major cocci consist of a literally classical example. Streptococci, named so by Bilroth from the Greek word “στρεπτόν—strepton” (necklace), and staphylococci, baptised by Ogston from “staphyli—σταφύλι” (grape), were both so named due to their appearance under microscopy. Two well-known species of these genera bear Latin names denoting colour, greenish for S. viridans and golden for S. aureus. Other bacteria display the discovering scientist like, E. coli for Escherich, Brucella from Bruce, or Pasteurella from Louis Pasteur. Similar pathways also exist for viruses, even back to Hippocrates, like Herpesviruses from “έρπης—herpes” (creeping) or Arenaviruses from “arena—sand”, and fungi, as mycology itself originates from “μύκης—myces”, Greek for fungus, and Aspergillus from the verb “aspergo” (to sprinkle). Full article

Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a significant public health threat, given the associated increased healthcare burden and mortality rate. The objective of the current study was to investigate the association between the incidence of CRKP bacteremia, antibiotic consumption, and infection control measures in a tertiary-care hospital spanning the years 2013–2018. The analyzed indices included the incidence of CRKP bacteremia, antibiotic consumption, the use of hand hygiene solutions, and isolation rates of multidrug-resistant (MDR) carriers. In the total hospital, the incidence of CRKP bacteremia exhibited an absolute decrease during the study period, although this decrease did not reach statistical significance. Antibiotics used to treat CRKP infections, including carbapenems, colistin, tigecycline, and fosfomycin, as well as all classes of antibiotics, correlated positively with an increased incidence of CRKP bacteremia. On the contrary, increased use of scrub disinfectant solutions correlated negatively with a decreased incidence of CRKP bacteremia (IRR: 0.74, 95%CI: 0.59–0.93, p-value: 0.008) in the Adults ICU. Additionally, increased isolation rates of MDR carrier patients correlated negatively with a decreased incidence of CRKP bacteremia (IRR: 0.35, 95%CI: 0.13–0.97, p-value: 0.044). In conclusion, the implementation of multimodal infection control measures in our hospital contributed to the containment of CRKP, particularly in specific hospital sectors. However, the study suggests the need for additional strategies to overcome the endemic plateau. Full article

The COVID-19 pandemic has led to an unprecedented surge in respiratory illness cases worldwide. Although uncommon, pulmonary cavitation has been reported as a potential complication of COVID-19. This case series report describes four cases of COVID-19 patients with lung cavities, highlighting the various causes and clinical manifestations of this complication, and a review of the literature on the presence of lung cavities in COVID-19 patients. In two cases, the cavities were most likely due to secondary bacterial superinfections, with one case being complicated by multi-drug-resistant bacteria. Another case developed cavities secondary to a fungal infection, while the third case was directly caused by SARS-CoV-2 invasion in the lungs. The presence of cavities with or without air-fluid level or pneumothorax in COVID-19 patients should be considered as a potential complication of this infection, especially in those with respiratory symptoms. Physicians should remain vigilant for the development of pulmonary cavitation in COVID-19 patients, particularly those receiving high doses of steroids. Additionally, spontaneous pneumothorax should be considered an alarming sign in COVID-19 patients. Full article