- Volume 6, Issue 6, 2024

Conjugation of plasmids from Escherichia coli is essential for the genetic manipulation of Streptomyces spp. To facilitate intergeneric conjugation from E. coli to Streptomyces the conjugative machinery required for genetic transfer is usually provided by the non-transferable helper plasmid, pUZ8002. Here we present the complete nucleotide sequence of pUZ8002, describe the previously undocumented creation process, and provide details of the sequence relative to the parental pUZ8 plasmid and another previously published pUZ8002 sequence.

ChatGPT and Bard (now called Gemini), two conversational AI models developed by OpenAI and Google AI, respectively, have garnered considerable attention for their ability to engage in natural language conversations and perform various language-related tasks. While the versatility of these chatbots in generating text and simulating human-like conversations is undeniable, we wanted to evaluate their effectiveness in retrieving biological knowledge for curation and research purposes. To do so we asked each chatbot a series of questions and scored their answers based on their quality. Out of a maximal score of 24, ChatGPT scored 5 and Bard scored 13. The encountered issues included missing information, incorrect answers, and instances where responses combine accurate and inaccurate details. Notably, both tools tend to fabricate references to scientific papers, undermining their usability. In light of these findings, we recommend that biologists continue to rely on traditional sources while periodically assessing the reliability of ChatGPT and Bard. As ChatGPT aptly suggested, for specific and up-to-date scientific information, established scientific journals, databases, and subject-matter experts remain the preferred avenues for trustworthy data.

Mycoplasmosis, attributed to Mycoplasma gallisepticum, poses a significant challenge to poultry farming, leading to substantial economic losses and persistent infections within flocks. This bacterium harbours various surface proteins that are crucial for adhesion, transporter activity and evasion of the host immune response, facilitating its pathogenicity. One such key surface lipoprotein, referred to as pMGA or vlhA haemagglutinin, plays a pivotal role in adhesion processes. In this study, the clonal regions pMGA1.2 and pMGA1.3, as reported by Markham (M83178.1), were investigated to elucidate differences or similarities in the whole DNA sequences of M. gallisepticum field strains. The aim was to analyse sequence diversity within this region. Six internal primers were designed to amplify the target sequence, and isolates were obtained from both eggs and chickens sourced from laying hen flocks. Identification revealed 17 strains of M. gallisepticum and four strains of Mycoplasma synoviae, which were confirmed through the mgc2 and 16S rRNA genes, respectively. Positive and negative controls were established using the MGS6 and MSWUV1853 strains. Amplification results indicated a higher frequency of amplification proximal to the C-terminal region, with segments 4 (33.3 %) and 6 (27.8 %) being the most prevalent. Notably, none of the field strains exhibited the same amplification pattern as MGS6, and none of the strains characterized as M. synoviae amplified any primer set. Upon translation, the amino acid sequences from segments 4 and 6 were found to be compatible with conserved sequences within the Myco_haema protein domains of the genus Mycoplasma, specifically corresponding to Q7NAP3_MYCGA VlhA.3.04. The observed homology suggests a potential genetic transfer, while the variability identified in the pMGA or vlhA gene region of the field strains may have significant implications for protection against M. gallisepticum infection in chickens.

Introduction. Malassezia globosa is a yeast species that belongs to the mycobiota of humans and animals, associated with dermatological disorders, such as dandruff. This is a chronic scalp skin disorder characterized by flaking and itching. Treatments include commercial shampoo with different formulations that contain antifungal activities like zinc pyrithione (ZPT) or piroctone olamine (PO). The effectiveness of these formulations has been evaluated for decades for dandruff symptom relief of volunteers. To date, non-mammalian, in vivo methods exist to test formulations of these actives.

Aim. To evaluate in vivo in Galleria mellonella larva, two commercial antifungal shampoos (shampoo with 1 % ZPT and 1.6 % zinc Carbonate and shampoo with 0.5 % PO) against this species.

Methodology. G. mellonella larvae were inoculated with M. globosa on abraded cuticular surface. Then, integument cell viability, histological changes, and fungal burden were evaluated.

Results. Larvae inoculated with M. globosa showed higher lesion melanization and tissue damage. In addition, M. globosa population showed to increase over time. Concerning the shampoo’s effectiveness, both formulations significantly reduced M. globosa burden and tissue damage.

Conclusion. G. mellonella larvae were allowed to evaluate M. globosa superficial infection and antifungal effectiveness. Shampoos with ZPT and PO showed a positive effect on inoculated larvae.

Introduction. The coronavirus illness caused by SARS-CoV-2 can cause multiple organ involvement, with varying degrees of severity. Besides inhalation as a route for transmission, feco-oral has also been proposed. Its transmission to sewage systems is a growing public health issue.

Objective. To detect SARS-CoV-2 RNA in non-respiratory samples (saliva, urine, and stool) collected from COVID-19 cases, in Bihar.

Methods. This cross-sectional observational study was conducted from January 2021 to March 2022 on human non-respiratory samples. A total of 345 samples including saliva (116), stool (97), and urine (132) were collected from 143 COVID-19 cases. Samples were analysed for SARS-CoV-2 by multiplex RT-PCR targeted against E, ORF 1ab, and RdRp genes.

Results. In this study, out of 143 cases, a total of 107 (74.8 %) were positive for SARS-CoV-2 RNA in at least one of the non-respiratory samples.

Conclusion. There is a high prevalence of SARS-CoV-2 virus in non-respiratory samples.

Infectious endophthalmitis is a severe ophthalmic emergency. This infection can be caused by bacteria and fungi. For efficient treatment, the administration of antimicrobial drugs to which the microbes are susceptible is essential. The aim of this study was to identify micro-organisms in biopsies of Mexican endophthalmitis patients using metagenomic next-generation sequencing and determine which antibiotic resistance genes were present in the biopsy samples. In this prospective case study, 19 endophthalmitis patients were recruited. Samples of vitreous or aqueous humour were extracted for DNA extraction for metagenomic next-generation sequencing. Analysis of the sequencing results revealed the presence of a wide variety of bacteria in the biopsies. Resistome analysis showed that homologues of antibiotic resistance genes were present in several biopsy samples. Genes possibly conferring resistance to ceftazidime and vancomycin were detected in addition to various genes encoding efflux pumps. Our findings contrast with the widespread opinion that only one or a few bacterial strains are present in the infected tissues of endophthalmitis patients. These diverse communities might host many of the resistance genes that were detected, which can further complicate the infections.

Background. The increasing resistance of clinical Enterobacteriaceae isolates to commonly prescribed antibiotics has been reported around the world. Data are generally lacking on the prevalence and antibiotic susceptibility profile of clinical Enterobacteriaceae isolates from Kaduna, northwest Nigeria. This study thus aimed to determine the diversity and antibiotic resistance profile of clinical Enterobacteriaceae isolates recovered from clinical specimens from patients admitted to two selected healthcare institutions in Kaduna.

Methods. This was a prospective cross-sectional study conducted between September and December 2021. Non-duplicate clinical bacterial isolates recovered from various specimens were collected and identified using rapid biochemical identification kits. The susceptibility of identified Enterobacteriaceae to various antibiotics and phenotypic detection of carbapenemase enzymes were thereafter determined. The data were analysed and visualized using R software version 4.3.1.

Results. Of the 500 bacterial isolates recovered from specimens collected for the purpose of clinical bacteriology diagnostics, 108 (21.6 %) were identified as Enterobacteriaceae, with Pantoea agglomerans (52, 48.1 %) and Klebsiella oxytoca (19, 17.6 %) being the most prevalent. The isolates exhibited high resistance to azithromycin (69 %) and ceftazidime (42 %), while exhibiting low resistance to amikacin (7 %) and imipenem (10 %). Among the carbapenem-resistant Enterobacteriaceae (CRE) isolates, a significant proportion (12/17, 70.6 %) tested positive for carbapenemase activity.

Conclusion. This study reports a high prevalence of multidrug-resistant Enterobacteriaceae in Kaduna, northwest Nigeria. The emergence of pathogenic P. agglomerans and an alarmingly high prevalence of carbapenemase-producing CRE were also observed. The presence of carbapenemase producers in an area with low carbapenem usage and resistance rates raises significant concerns. Continuous surveillance and robust antibiotic stewardship policies are imperative to preserve the efficacy of carbapenems in this region.

Introduction. Streptococcus pyogenes [group A streptococci (GAS)] is the causative agent of pharyngitis and various other syndromes involving cellulitis, streptococcal toxic shock syndrome (STSS), and necrotising fasciitis. Although the prevalence of GAS infections globally remains high, necessitating the widespread use of β-lactam antibiotics, GAS have remained largely susceptible to these agents. However, there have been several reports of GAS with reduced susceptibility harbouring mutations in genes for penicillin-binding proteins (PBPs). The objectives of this study were to examine the in vitro β-lactam susceptibility patterns of group A streptococci, determine the prevalence of drug resistance, and ascertain whether such resistance could be attributed to mutations in specific PBP genes.

Methods. In this study, we sought to use Sanger sequencing to identify mutations in PBP genes of Streptococcus pyogenes isolated from patients that required inpatient and outpatient care that could confer reduced PBP affinity for penicillin and/or cephalosporin antibiotics. All isolates were screened for susceptibility to penicillin, amoxicillin, and cefazolin using E-test strips.

Results. While there were no documented cases of reduced susceptibility to penicillin or amoxicillin, 13 isolates had reduced susceptibility to cefazolin. Examination of pbp1a by Sanger sequencing revealed several isolates with single amino acid substitutions, which could potentially reduce the affinity of PBP 1A for cefazolin and possibly other first-generation cephalosporins.

Conclusion. Penicillin and penicillin-derived antibiotics remain effective treatment options for GAS infections, but active surveillance is needed to monitor for changes to susceptibility patterns against these and other antibiotics and understand the genetic mechanisms contributing to them.

Frequent vaccine failure leading to recurrent outbreaks of Foot-and-Mouth Disease (FMD) in livestock populations necessitates the development of a customizable vaccine platform comprising potential antigenic determinants of circulating lineages of FMD viruses. Artificially designed, chimaeric protein-based recombinant vaccines are novel approaches to combat the phylogenetically diverse FMD Virus (FMDV) strains. Among seven recognized serotypes, only serotypes O and A are dominantly circulating in Bangladesh and neighbouring countries of Asia, where transboundary transmission, recurrent outbreaks and emergence of novel lineages of FMDV are highly prevalent. The objective of this study was to develop multi-epitope recombinant proteins, procuring immunogenicity against circulating diverse genotypes of FMDV serotypes O and A. Two chimaeric proteins, named B1 (41.0 kDa) and B3 (39.3 kDa), have been designed to incorporate potential B-cell and T-cell epitopes selected from multiple FMDV strains, including previously reported and newly emerged sub-lineages. After expression, characterization and immunization of guinea pigs with a considerable antigen load of B1 and B3 followed by serological assays revealed the significant protective immunogenicity, developed from the higher (100 µg) doses of both antigens, against most of the currently prevalent serotype O and A strains of FMDV. The efficient expression, antigenic stability, and multivalent immunogenic potency of the chimaeric proteins strongly indicate their credibility as novel vaccine candidates for existing serotypes O and A of FMDV in Bangladesh and surrounding territories.

Gymnopus fusipes is an understudied root rot pathogen associated with multiple tree species and is linked to episodes of oak decline across the United Kingdom and Europe. Although the reported distribution of G. fusipes is broad, many observations rely solely on visual identification of fruiting bodies, which can be unreliable, and lack confirmation by molecular and/or isolation data to verify this broad ecological range. Given the paucity of information regarding the true ecological distribution of G. fusipes, it is difficult to predict and model the potential distribution of the species under both current and future climate scenarios. In this study, to determine the growth capabilities of G. fusipes across a range of ecologically relevant temperatures, five geographically diverse isolates of G. fusipes were grown at five different temperatures ranging from 4–37°C, to determine the optimal temperature for G. fusipes growth, and to establish whether geographically diverse isolates exhibit local adaptation to temperature tolerance. Incubation temperature had a significant effect on G. fusipes growth rate, with 25°C representing the optimum (P<0.001). Isolates had differing growth rates at each of the temperatures, with an isolate from the UK having the highest overall growth rate across all five temperatures tested (P<0.001), and at the optimum, increased by a mean value of over 4915 mm2. Local adaptation to temperature tolerance was not found in the isolates tested. These data demonstrate the optimal incubation temperature for future laboratory studies on G. fusipes and provide the first data on the growth rate of this pathogen across ecologically relevant climate ranges that may inform land managers, modellers, and policy makers in predicting the current and potentially future geographical limits of this widespread root rot pathogen.

Background and purpose. Coronavirus (COVID-19) is a contagious disease causing severe acute respiratory syndrome which had a catastrophic effect on the world population and resulted in more than 2.9 million deaths worldwide. Epidemiological investigations have recently announced blood type has an association with the incidence of COVID-19 infection. Consequently, research in this regard can be effective in determining a person’s susceptibility to a viral infection. Therefore, we investigated the relationship between blood types and the risk of COVID-19 in patients admitted to Khorshid laboratory, Tehran, Iran.

Materials and methods. From January to March 2020, 50 nasal and throat swapb samples of patients’ secretions were obtained from patients who were admitted to Khorshid laboratory. They were confirmed to have COVID-19 virus RNA and real-time polymerase chain reaction (PCR)-ABI, and their blood type was determined simultaneously. After collecting data to determine the relationship between COVID-19 infection and blood type, a confidence interval of 90 % was considered using SPSS 16.

Results. The mean age of the patients was measured at 38.4±6.3 years. According to PCR results, 100 % of the subjects with COVID-19 showed blood type A. In addition, the ratio of blood type A to the percentage of reference type O was higher (P=0.009).

Conclusion. There was a significant relationship between ABO blood type and susceptibility to COVID-19. As the current study suggests, those with blood type A are at a higher COVID-19 infection risk than those with blood type O.

The ethanolic (80 %), methanolic (80 %) and aqueous decoction (100 % distilled water) of whole plant of Oxalis corniculata Linn (Indian Sorrel) was evaluated for its anti‐microbial and antioxidant properties by in vitro methods. Methanolic (80 %) and ethanolic (80 %) decoctions showed significant antibacterial property against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Salmonella typhi bacterial strains. In comparison to Chloramphenicol (C30) against bacteria, 80 % ethanolic decoctions showed significant effect, among the decoctions. Nowadays though the standard soap is in huge demand but it’s also facing major backlash due to the presence of synthetic compounds in it, which over long use may cause harmful effects on the skin health. Therefore, the organic soaps which are made up of natural ingredients, herbs or any sort Ayurvedic compound have fewer side effects on the human skin and are much safer than standard daily soap. The formulated therapeutic soap exhibits a significant amount of reducing potential (high FRAP and TAC values) and antioxidant activity (DPPH, ABTS assay).

Objectives. Staphylococcus aureus is one of the most common pathogens attributed to hospital infections. Although S. aureus infections have been well studied in developed countries, far less is known about the biology of the pathogen in sub-Saharan Africa.

Methods. Here, we report on the isolation, antibiotic resistance profiling, whole genome sequencing, and genome comparison of six multi-drug resistant isolates of S. aureus obtained from a referral hospital in Kakamega, Western Kenya.

Results. Five of the six isolates contained a 20.7 kb circular plasmid carrying blaZ (associated with resistance to β-lactam antibiotics). These five strains all belonged to the same sequence type, ST152. Despite the similarity of the plasmid in these isolates, whole genome sequencing revealed that the strains differed, depending on whether they were associated with hospital-acquired or community-acquired infections.

Conclusion. The intriguing finding is that the hospital-acquired and the community-acquired isolates of S. aureus belonging to the same genotype, ST152, formed two separate sub-clusters in the phylogenetic tree and differed by the repertoire of accessory virulence genes. These data suggest ongoing adaptive evolution and significant genomic plasticity.

West Nile virus (WNV) is the most prevalent mosquito-borne virus and the leading cause of viral encephalitis in the continental United States. It belongs to the family Flaviviridae which includes other important human pathogens such as dengue virus (DENV), Japanese encephalitis virus (JEV) and Zika viruses (ZIKV). Despite several decades of research, no specific antiviral drugs are available to treat flavivirus infections. The present study characterizes the interaction between the WNV NS3 and NS5 proteins for the purpose of identifying hotspots in the protein-protein interaction which could be targeted for the development of antiviral therapeutics. We previously developed an interaction model in silico based on data available in the literature. Here, potential interacting residues on NS3 and NS5 were mutated in a WNV replicon, and seven mutations in the NS3 protein were found to drastically reduce viral replication. In addition to being well conserved among mosquito-borne flaviviruses, these residues are located on the protein’s surface in two clusters which might be interesting new targets for future drug development.

Group A streptococcus (GAS) can cause serious invasive disease in humans with a high mortality rate. An increase in GAS infections was reported in Ireland in 2022, and this increase has been sustained in 2023 and is paralleled by similar trends in Europe. Rising antimicrobial resistance is a global problem and presents significant challenges to clinicians treating GAS infection. There was a reported increase in clindamycin resistance in GAS isolates in Ireland in 2022. We examined antimicrobial susceptibility patterns of GAS isolates in our institution in 2022. Although all GAS isolates included in our study were susceptible to penicillin, we noted a high clindamycin resistance rate of 28 % in our invasive GAS isolates. We also noted high tetracycline and erythromycin resistance, 43 and 30 %, respectively. Our results could have implications for empiric antimicrobial prescribing guidelines for skin and soft tissue infections, which often include clindamycin as it inhibits the production of many virulence factors associated with GAS. In addition, macrolides are often the first line recommended antibiotic for patients with anaphylaxis to penicillin. This study emphasises the importance of continuous surveillance and antimicrobial susceptibility testing of invasive and non-invasive isolates in order to monitor trends in increasing antimicrobial resistance.

The hollow-fibre infection model (HFIM) is a valuable in vitro platform for emulating antimicrobial drug pharmacokinetic profiles. Despite its potential, standardized protocols for HFIM operation, especially concerning fastidious organisms, are lacking. This study addresses this gap by examining challenges in culturing Pasteurella multocida and Actinobacillus pleuropneumoniae, two fastidious organisms, in the HFIM. Our findings reveal effective strategies to prevent system clogging, involving multiple freeze–thaw cycles of horse blood, centrifugation and cell straining to enhance the clarity of the Mueller-Hinton fastidious medium defined by the European Committee on Antimicrobial Susceptibility Testing and Clinical and Laboratory Standards Institute. Additionally, we propose that the provision of a CO2 atmosphere, along with the utilization of gas-permeable tubing and gas vent filters, significantly facilitates the growth of fastidious organisms. Remarkably, both P. multocida and A. pleuropneumoniae were sustained for a period of up to 10 days under these optimized conditions. This study provides crucial insights into the modifications necessary to successfully culture fastidious organisms in the HFIM, paving the way for more accurate and representative in vitro models for antimicrobial drug testing. These advancements hold promise for advancing research in the field of antimicrobial pharmacokinetics and efficacy against challenging pathogens.