- Volume 6, Issue 8, 2024

Protists are important key players in the microbial loop and influence their environment by grazing, which leads to the return of nutrients into the soil and reduces pathogen pressure on plants. Specifically, protists on and around plant roots are important for plants’ development and growth. For this study, the fourth most important crop in the world, Hordeum vulgare, was selected. Seeds of H. vulgare were inoculated with Acanthamoeba castellanii alone or with additional soil bacteria at the beginning and during the experiment. The germination of the seeds and the growth of the plants in pouches were monitored over 3 weeks. No differences were found in leaf growth, root growth, root and leaf nitrogen content or ammonia content of the liquid from the pouches. In contrast, the relative increase in root and leaf dry weight showed a small difference compared to the controls. The results of this experiment demonstrated that seed inoculation with A. castellanii alone or with additional unidentified soil bacteria did not have a major effect on the growth and development of barley. Nevertheless, small changes in plant development were detected, indicating that A. castellanii should be considered for further investigation of co-inoculations with plant growth-promoting bacteria and additional nutrients.

Gilliamella is a genus of bacteria commonly found as symbionts of corbiculate bees. Research into energy metabolism by this genus has predominantly been done through in vivo and in vitro experiments focused on the type species Gilliamella apicola. This study examined 95 publicly available genomes representing at least 18 Gilliamella species isolated predominantly from the hindgut of corbiculate bees. Energy metabolism pathways were found to be highly conserved across not only the Gilliamella but also other members of the family Orbaceae. Evidence suggests Gilliamella are capable of fermentation of both fumarate and pyruvate. Fermentation of the former produces succinate. Fermentation of the latter can produce acetate, ethanol, formate, and both isoforms of lactate for all Gilliamella and acetoin for some G. apicola strains. According to genomic evidence examined, all Gilliamella are only capable of respiration under microoxic conditions, while higher oxygen conditions likely inhibits respiration. Evidence suggests that the glycolysis and pentose phosphate pathways are essential mechanisms for the metabolism of energy sources, with the TCA cycle playing little to no role in energy metabolism for all Gilliamella species. Uptake of energy sources, i.e. sugars and derivatives, likely relies predominantly on the phosphoenol-pyruvate-dependent phosphotransferase system. Differences in the utilized energy sources may confer fitness advantages associated with specific host species.

Bacteria of the species Oceanotoga teriensis belong to the family Petrotogaceae, are Gram-negative bacilli, are moderately thermophilic and are included in the group of thiosulfate-reducing bacteria, being capable of significantly accelerating corrosion in metallic structures. However, no in-depth study on the genome, antibiotic resistance and mobile elements has been carried out so far. In this work, the isolation, phenotypic and genotypic characterization of the multi-resistant O. teriensis UFV_LIMV02 strain was carried out, from water samples from an offshore oil extraction platform in Rio de Janeiro (Brazil). We determined that the isolate has a genome of 2 812 778 bp in size, with 26 % GC content, organized into 34 contigs. Genomic annotation using Rapid Annotation using Subsystem Technology revealed the presence of genes related to resistance to antibiotics and heavy metals. By evaluating the antimicrobial resistance of the isolate using the disc diffusion technique, resistance was verified for the classes of antibiotics, beta-lactams, fluoroquinolones, aminoglycosides, sulfonamides, lincosamides and rifamycins, a total of 14 antibiotics. The search for genomic islands, prophages and defence systems against phage infection revealed the presence of five genomic islands in its genome, containing genes related to resistance to heavy metals and antibiotics, most of which are efflux pumps and several transposases. No prophage was found in its genome; however, nine different defence systems against phage infection were detected. When analysing the clustered regularly interspaced short palindromic repeat (CRISPR) systems, four CRISPR arrays, classified as types I-B and III-B, with 272 spacers, can provide the strain with immunity to different mobile genetic elements and bacteriophage infection. The results found in this study show that the isolate UFV_LIVM02 is an environmental bacterium, resistant to different classes of antibiotics, and that the proteins encoded by the predicted genomic islands may be associated with the development of greater resistance to antibiotics and heavy metals. They provide evidence that environmental bacteria found in offshore oil exploration residues may pose a risk for the spread of antibiotic resistance genes. More comprehensive studies on the microbial community present in oil waste are needed to assess the risks of horizontal gene transfer.

Soil samples from a remote Japanese island (Kozushima) were processed and investigated for organisms exhibiting antimicrobial activity against pathogenic strains. A Pseudomonas strain demonstrating antimicrobial activity against Staphylococcus aureus (S. aureus) was identified, prompting further investigation. Whole-genome sequencing was employed to identify the species and conduct phylogenetic analysis, followed by in silico molecular analysis. Chemotaxonomic and biochemical analyses were conducted to further characterize the strain. Genomic analysis identified the strain of interest as Pseudomonas batumici (P. batumici), originally isolated from soil of the Black Sea coast of the Caucasus in 1980. P. batumici Koz11 is the second P. batumici strain to be isolated and identified outside its initial area of discovery. Similar to the type strain, P. batumici Koz11 showed antimicrobial activity against various S. aureus strains, including methicillin-resistant S. aureus (MRSA) and vancomycin-resistant S. aureus (VRSA). However, the previously reported ‘batumin gene cluster’, which synthesizes antimicrobial compounds, was absent from P. batumici Koz11. This study provides new insights into P. batumici. Since the type strain of P. batumici is exclusively deposited in the Ukrainian Collection of Microorganisms, the Koz11 strain may serve as a surrogate to facilitate continued study of P. batumici.

Objectives. This study aimed to determine patterns of respiratory, blood-borne and uropathogenic microbial pathogens among SARS-CoV-2-infected patients in a COVID-19-(coronavirus disease 2019) dedicated tertiary care hospital in Dhaka, Bangladesh.

Design.This was a cross-sectional study.

Setting. In a COVID-19-dedicated tertiary care hospital in Dhaka, Bangladesh, conducted from March to June 2021.

Participants. Hospitalized individuals with COVID-19 infection regardless of age or sex.

Primary and secondary outcome measures. The percentage of co-infected COVID-19 patients and the characterization of the micro-organisms responsible for co-infection served as the primary outcome measures. Finding any associations between co-infection and age, co-infection and sex and co-infection and comorbidity was the secondary outcome variable.

Interventions. Not applicable.

Results. Out of 79 patients, 61 % were male, and the mean age was 49.53 years. Co-infection was seen in 7.7 % of patients, out of which 5.1 % of isolates were from urine samples, followed by 2.6 % from blood. Bacteria isolated from urine were Enterococcus (2.6 %), coagulase-negative Staphylococcus (CONS) (1.3 %) and Enterobacter spp. (1.3 %). Pseudomonas spp. was the only organism isolated from blood sample. Mixed growth was found in nasopharyngeal and throat swabs, with the predominant species being Staphylococcus aureus and Streptococcus spp. At the time of data collection, 55.7 % of patients had been given antimicrobials, and 30.4 % of patients had been given a single antimicrobial. HBsAg was positive in 1.3 % of patients and none were anti-hepatitis C or dengue NS1Ag positive.

Conclusion. Microbial infection has been seen to be associated with SARS-CoV-2 infections and is of great value in prescribing antimicrobials and reducing fatal outcomes of hospitalized patients.

Papillomaviruses (PVs) are double-stranded, circular, epitheliotropic DNA viruses causing benign warts (papillomas) or inducing dysplasia that can progress to cancer. Although they have been identified in all vertebrate taxa, most classified types are human PVs (HPVs); relatively little is known about PVs in other species. Here we characterize a novel Gammapapillomavirus type, PtepPV1, from a nasal swab of a wild red colobus (Piliocolobus tephrosceles) in Kibale National Park, Uganda. The virus has a genome of 6576 bases, encoding the seven canonical early (E) ORFs (E6, E7, E1, E2, E4, E1^E4 and E8^E2) and two late (L) ORFs (L1 and L2) of the gammapapillomaviruses, and is 81.0% similar to HPV-mSK_118, detected in a cutaneous wart from an immunocompromised human patient, in the L1 gene at the amino acid level. Alphapapillomaviruses (genus Alphapapillomavirus) cause anogenital carcinomas such as cervical cancer and have been described previously in several nonhuman primates. However, the first gammapapillomavirus (genus Gammapapillomavirus), which cause transient cutaneous infections, was not described until 2019 in a healthy rhesus macaque (Macaca mulatta) genital swab. The new virus from red colobus, PtepPV1, has many genomic features encoded by high-risk oncogenic PVs, such as the E7 gene LXSXE and CXXC motifs, suggesting potential for pRb and zinc-finger binding, respectively. To our knowledge, PtepPV1 is also the first reported nonhuman primate PV found in the nasal cavity. PtepPV1 expands the known host range, geographical distribution, tissue tropism and biological characteristics of nonhuman primate PVs.

Clostridium septicum gas gangrene is a severe and deadly infection caused by an anaerobic, spore-forming, Gram-positive bacillus. As previously described, two entities are observed: traumatic and spontaneous (or non-traumatic) forms. In this report, we aim to describe the case of a fulminant and ultimately fatal C. septicum myonecrosis occurring in a patient who was first admitted for refractory cardiac arrest and placed on veino-arterial extracorporeal membrane oxygenation (ECMO). Building upon prior studies that have documented cases of spontaneous gas gangrene caused by C. septicum, we provide an updated compilation, focusing on microbiological characteristics of C. septicum, along with the diagnostic and therapeutic challenges associated with spontaneous gas gangrene. Additionally, the specific clinical situation of our case illustrates the seriousness of this infectious complication that combined both spontaneous and traumatic gas gangrene risk factors. We thus, discuss the antibiotic coverage prior to the initiation of ECMO procedure.

Introduction. Invasive fungal infections require early diagnosis for treatment. Microscopic observation of biopsy and blood culture is the gold standard for the identification of the causative fungus, but it is difficult to identify the causative pathogen by a sterile abscess biopsy.

Case Presentation. We present a case report of breakthrough invasive trichosporonosis in a 65-year-old Japanese male with acute myeloid leukaemia receiving antifungal prophylaxis. Blood cultures showed no fungal growth, and a liver biopsy and a removed spleen with abscess showed fragmented fungi, but no fungal identification was possible. This report demonstrates that retrospective analyses were able to identify the causative fungus.

Conclusion. We narrowed down the candidate fungi by deep sequencing of the ITS1 region of fungal genome and confirmed that the fungus observed in the specimen was Trichosporon asahii by in situ hybridization using a DNA probe targeting 26S rRNA.

Introduction. Mycotic aneurysms, characterized by vessel wall dilation resulting from infections including bacteria, fungi, and viruses, are a rare but severe consequence of systemic infections. The term ‘mycotic’ was coined by William Osler to describe the first instance of a fungal-induced infected aneurysm. These aneurysms, accounting for 0.6% of aneurysms in Western countries, carry a higher risk of rupture compared to uninfected aneurysms. While the femoral artery, aorta, and intracranial arteries are commonly affected, pathogens causing mycotic aneurysms vary across regions. Diagnostic challenges arise from nonspecific symptoms such as fever, and discomfort. To prevent the substantial morbidity and mortality associated with mycotic aneurysms, timely identification and treatment are paramount. We present a case series highlighting mycotic aneurysms caused by some rare pathogens – Salmonella Paratyphi A, Streptococcus pneumoniae, and Pseudomonas aeruginosa.

Methods. This case series involves three patients diagnosed with mycotic aneurysms due to unusual pathogens. We describe each patient’s clinical presentation, medical history, physical examination findings, laboratory results, imaging studies, and the diagnostic process leading to the identification of the causative pathogens.

Results. The first patient is a 70-year-old gentleman who presented with a ruptured infra-renal abdominal aortic pseudoaneurysm caused by Salmonella Paratyphi A. The second patient is a 66-year-old gentleman with a Streptococcus pneumoniae-associated descending thoracic aortic pseudoaneurysm. The third patient is a 70-year-old gentleman with a ruptured descending thoracic aortic aneurysm with an occult aorto-oesophageal fistula due to Pseudomonas aeruginosa infection. The description highlights unique clinical features, laboratory findings, imaging results, and the management approaches undertaken in each patient.

Conclusion. Mycotic aneurysms, pose diagnostic challenges due to their nonspecific symptoms. Early identification and intervention are essential to mitigate the severe complications associated with these aneurysms. The presented cases underscore the need for a comprehensive approach to diagnosis and management, ensuring optimal outcomes for patients affected by mycotic aneurysms.