Feature Papers in Medical Microbiology in 2024

Ebola virus (EBOV) causes Ebola virus disease (EVD), a severe and often fatal hemorrhagic fever. Although much research has focused on host miRNA expression during EBOV infection, it has been discovered that EBOV itself also produces miRNAs. However, further studies are needed to fully comprehend the role of these EBOV-encoded miRNAs in infection and disease development. This study aimed to identify known and novel EBOV-encoded miRNAs and their potential functions in the pathogenic mechanisms of EBOV. We reanalyzed previously available small RNASeq data to identify the miRNAs and predict their cellular targets and functions. We identified four EBOV-encoded miRNAs—EBOV-mir-M1 (4390–4414), EBOV-mir-M4, EBOV-mir-M2 (8288–8309), and EBOV-mir-M3 (9885–9906)—expressed specifically in Ebola-infected human adult retinal pigment epithelial (ARPE) cells. EBOV-mir-M1 (4390–4414) was expressed up to 19 times more than the other three miRNAs. The identified miRNAs were predicted to target genes associated with pathways such as calcium signaling, MAPK signaling, type I interferon signaling, and cytokine-mediated signaling, which play critical roles in Ebola infection and pathogenesis. This study contributes to our understanding of the role of EBOV-encoded miRNAs in infection and pathogenesis by demonstrating the expression of these miRNAs in human ARPE cells, providing insights into the mechanisms underlying EBOV pathogenesis. 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

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

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

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

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

Traditional methods of detecting foodborne pathogens take several days to produce the required results. Furthermore, various molecular techniques (e.g., PCR) that also produce reliable results in the detection of pathogenic bacteria have been introduced, but the cost–time ratio required does not allow them to be considered a substantial solution to this specific problem. Three-dimensional (3D) printing technology provides the ability to design and manufacture microfluidic analytical devices using conventional 3D printers, which, in combination with colorimetric loop-mediated isothermal amplification (LAMP), may further simplify the process. The overall reduction in time and cost may provide the opportunity to upscale this diagnostic modality. Moreover, unlike most microfluidic analytical devices, this technique is simpler and more user-friendly, as it does not require any expertise or additional equipment apart from a conventional oven. A 3D-printed microfluidic analytical device in combination with LAMP was developed and tested for the simultaneous detection of foodborne pathogens in food samples. A total of 150 commercial food specimens (50 milk, 50 chicken, 50 lettuce samples) were analyzed for possible contamination with Salmonella typhimurium, Listeria monocytogenes and Escherichia coli. The 3D-printed microfluidic device was 100% precise for both negative (80 samples) and positive samples (7 samples were positive for S. typhimurium, 28 for L. monocytogenes, and 35 for E. coli) for all pathogens. Overall, the amount of data analyzed led to a high level of confidence in the precision of this device. As such, this new 3D device in combination with LAMP provides a precise detection method for food pathogens with a low detection limit. Full article

Retroviral and hepatitis B infections can be potential threats to foetomaternal health through inducing distortions of the architecture and structure of the placenta. Improved insights into the effects of these infections on placental morphology would be integral to our understanding of maternal and neonatal health. Aim: To histomorphologically and stereologically investigate selected placental structures in virus-infected (HIV [human immunodeficiency virus] and hepatitis B virus [HBV]) and uninfected women at term. Method: This cross-sectional study involved the screening of 237 placentae collected at term (38 ± 2 weeks) from the maternity delivery units and surgical theatres of the LEKMA and Weija/Gbawe Municipal Hospitals in Accra. Venous blood samples from the umbilical vein and placenta basal plate blood were screened for HIV, HBV, and hepatitis C virus (HCV) using serological test kits (RDT). A total of 34 placentae were selected, comprising 20 cases and 14 controls that were gestational age-matched. Using stereology and a systematic random sampling technique with test point and intersection counting of photomicrographs, the mean volume densities of syncytial knots, syncytial denudations, foetal capillaries, and intervillous spaces of the placentae were estimated on a total of 2720 photomicrographs. Results: On stereological assessment, there was a statistically significant difference in the mean volume densities of syncytial knots (HIV-infected = 0.562 ± 0.115, HBV-infected = 0.516 ± 0.090, control group = 0.171 ± 0.018, p = 0.001), syncytial denudations (HIV-infected = 0.121 ± 0.022, HBV-infected = 0.111 ± 0.016, control group = 0.051 ± 0.00, p = 0.004), and foetal capillaries (HIV-infected = 0.725 ± 0.152, HBV-infected = 0.902 ± 0.078, control group = 0.451 ± 0.064, p = 0.006) among the different groups of placentae (control) at term. A statistically significant decrease in intervillous space (p = 0.022) was recorded in HBV-infected placentae compared to the control (from 15.450 ± 1.075 to 11.32 ± 0.952). Conclusion: Placental viral infections might lead to significant increases in syncytial knots, foetal capillaries, and syncytial denuded areas of the chorionic villi and a significant decrease in intervillous spaces. This finding could signify evidence of advanced gestation, placental malperfusion, hypermaturity of the placenta, and a possible vertical transmission of the viral antigen to the foetus, which may be crucial in understanding perinatal outcomes. Full article

Biofilms exert a profound impact on various facets of human life. Positive instances of biofilm usage involve their capacity to immobilize pollutants such as heavy metals, while adverse cases result in infections like urinary tract infections. Therefore, the study of biofilm engineering emerges as crucial. Employing a bibliographic research approach, this paper delves into biofilm engineering, identifying key species like Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus, among others. The investigation also unveils major research subjects and corresponding institutions dedicated to biofilm research. A comprehensive understanding of biofilm engineering holds profound implications for advancing knowledge in this domain. 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

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

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

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

Urinary tract infections (UTIs) cause a significant infectious burden in the community and demand a coordinated approach from all first-line health professionals. Uncomplicated UTIs refer to infections in non-pregnant females without any underlying localized or generalized pathology, diagnosed through history by the presence of specific local symptoms and in the absence of systemic ones like fever. Uncomplicated UTIs are usually caused by Escherichia coli species; thus, empirical antibiotic treatment can be immediately initiated. A percentage of patients can experience a resolution of symptoms without therapy; however, this “wait and observe” approach is supported only by the relevant British guidelines. There are limited quality studies in the literature on adjuvant treatment options; these can include BNO 145, a phytotherapeutic medicine, and XHP, a medical technology product. Despite being licensed by the European Medicines Agency on the basis of traditional use, there is inadequate support in the medical literature for the use of cranberry extracts and Arctostaphylos uva-ursi extracts. The use of antibiotics is associated with higher response rates and urine culture sterilization as well as lower recurrence/relapse rates; on the other hand, side effect rates are also higher. In choosing the proper empirical antibiotic therapy, one has to take into account individual patient characteristics and community resistance patterns as well as the antimicrobial resistance pressure exerted by the wide use of a specific antibiotic. There is a need for a common framework through which all frontline health practitioners should operate when faced with a case of uncomplicated UTI. In Greece, there are three different guidelines for UTI treatment, developed by the Ministry of Health, the National Organization for Medicines, and the Hellenic Society for Infectious Diseases. The authors of the present study aim at synthesizing these guidelines as well as relevant guidelines from international scientific or other national regulatory organizations while taking into account local resistance patterns. The authors propose the first-line use of either fosfomycin, nitrofurantoin, or pivmecillinam. The use of trimethoprim/sulfamethoxazole is discouraged due to increased resistance of Greek community E. coli isolates. Fluoroquinolone use should be avoided due to high E. coli community resistance (exceeding 20% for Greece), along with their unfavorable benefit/side effect balance in uncomplicated UTIs, as well as the overall community resistance pressure exerted by their use. A 5-day regimen remains superior to a 3-day one; the latter may be suitable for certain, not yet adequately characterized, patients. Full article

The endometrial cavity was considered sterile until the second half of the 20th century. Through modern technological advances and the sequencing of the bacterial 16S rRNA gene, it was proven that the area possesses its own unique microbiome, which can be categorised into two types, Lactobacillus-dominant (LD, with a Lactobacillus spp. abundance percentage greater than 90%) and non-Lactobacillus-dominant (non-LD, with a Lactobacillus spp. abundance percentage smaller than 90%), with other species like Bifidobacterium, Gardnerella, Prevotella, and Streptococcus also being prominent. The aim of this study was to investigate the possible correlation of the endometrial microbiome to female infertility, through the identification and appraisal of studies published in the databases PubMed, Web of Science, and Scopus. Moreover, 12 studies met the research criteria, including the analysis of endometrial fluid or tissue samples from infertile women through PCR, culturomics-based, or NGS methods. According to most of these studies, a eubiotic LD-type microbiome seems to be best for maximising endometrial receptivity and pregnancy chances, whereas a dysbiotic non-LD-type microbiome, with increased α-diversity and a higher number of pathogens, has a harmful effect. There were few studies that presented contradictory results without, however, a satisfactory explanation. Thus, more time and a greater number of studies are required to clarify contradictions and achieve more certain results. Full article