Journal of medical microbiology最新文献

Background. Bacteria significantly influence human health and disease, with bacterial biosynthetic gene clusters (BGCs) being crucial in the microbiome-host and microbe-microbe interactions.Gap statement. Despite extensive research into BGCs within the human gut microbiome, their roles in the oral microbiome are less understood.Aim. This pilot study utilizes high-throughput shotgun metagenomic sequencing to examine the oral microbiota in different niches, particularly focusing on the association of BGCs with periodontitis.Methodology. We analysed saliva, subgingival plaque and supragingival plaque samples from periodontitis patients (n=23) and controls (n=16). DNA was extracted from these samples using standardized protocols. The high-throughput shotgun metagenomic sequencing was then performed to obtain comprehensive genetic information from the microbial communities present in the samples.Results. Our study identified 10 742 BGCs, with certain clusters being niche-specific. Notably, aryl polyenes and bacteriocins were the most prevalent BGCs identified. We discovered several 'novel' BGCs that are widely represented across various bacterial phyla and identified BGCs that had different distributions between periodontitis and control subjects. Our systematic approach unveiled the previously unexplored biosynthetic pathways that may be key players in periodontitis.Conclusions. Our research expands the current metagenomic knowledge of the oral microbiota in both healthy and periodontally diseased states. These findings highlight the presence of novel biosynthetic pathways in the oral cavity and suggest a complex network of host-microbe and microbe-microbe interactions, potentially influencing periodontal disease. The BGCs identified in this study pave the way for future investigations into the role of small-molecule-mediated interactions within the human oral microbiota and their impact on periodontitis.

Introduction. Streptococcus uberis is a common cause of mastitis in cattle, leading to significant economic losses. The widespread use of antimicrobials has contributed to the emergence of resistance, which poses a severe challenge in controlling S. uberis infection.Aim. The objective of this study was to gain insights into the antimicrobial resistance (AMR) and epidemiological typing of S. uberis isolated from milk collected from bovine mastitis on dairy farms in Thuringia.Methodology. In this study, 84 S. uberis isolates were obtained from cattle with clinical mastitis in Thuringia, their phenotypic and genotypic AMR were analyzed and their phylogenetic relationship was explored using whole-genome sequencing.Results. Genetically heterogeneous strains were found on the farms, but clusters of highly similar strains also circulated within the same farms. All isolates were sensitive to ampicillin, penicillin, ceftiofur, and vancomycin. However, 42.9%, 42.9%, 22.6%, 19.0%, and 13.0% were resistant to tetracycline, doxycycline, clindamycin, pirlimycin, and erythromycin, respectively. Thirty-nine strains were phenotypically resistant to two or more tested antibiotics. We identified a plasmid associated with macrolide and lincosamide resistance in 12% of the strains.Conclusion. The emergence of S. uberis strains resistant to multiple antibiotics highlights the importance of S. uberis surveillance and the prudent use of antimicrobials.

Mycoplasma pneumoniae is a leading cause of community-acquired pneumonia among school-aged children and young adults. Infections occur throughout the year but tend to surge during winter months across Europe. A characteristic epidemic cycle, where a substantial surge in the number of infections occurs, is seen approximately every 1-4 years and hypothesized to be driven by changes in immunity and a shift in circulating variants. Once thought to be an organism of low virulence, it has now been found to possess several virulence factors, including toxin production, biofilm formation and evasion of antibody-mediated immunity. The lack of a cell wall and reduced metabolic pathways limit the options for antibiotic treatment. Acquired macrolide resistance is a growing concern, with >80% of cases in China being macrolide-resistant. Although efforts have been made to develop a vaccine, there are still substantial hurdles to overcome in relation to vaccine-enhanced disease, which results from an inappropriate immune response among vaccinated individuals.

Introduction. Sepsis rates are increasing, with Gram-negative organisms representing a large proportion of bloodstream infections. Rapid antibiotic administration, alongside diagnostic investigations, is required for the effective management of these patients.Gap statement. Current diagnostics take ~48 h for a final report; therefore, rapid diagnostics are required.Aim. This study investigated a novel antibiotic sensitivity method, the scattered light integrating collector (SLIC), combined with a rapid identification method using matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) technology to determine if an accurate identification and susceptibility result can be provided within 4 h of a positive blood culture report.Methodology. A total of 47 blood cultures containing Gram-negative bacteria from 46 patients were processed using the MALDI-TOF Biotyper Sepsityper for identification directly from the blood and the SLIC instrument for susceptibility testing. All organisms were also tested using the current standard workflow used in the host laboratory. Categorical agreement (CA), major errors (MaEs) and very major errors (VMEs) were determined.Results. SLIC produced susceptibility results with a 71.9% CA, 30.6% MaE and 17.5% VME. The median difference in time to the final result was 44.14 (43 : 05-45 : 15) h earlier compared to the current method.Conclusion. We conclude that SLIC was unable to consistently provide sufficiently accurate antibiotic susceptibility results compared to the current standard method.

Introduction. Rotavirus A is the most common pathogen causing diarrhoea in children less than 5 years, leading to severe complications such as dehydration, electrolyte imbalances, acidosis, myocarditis, convulsions, pneumonia, and other life-threatening conditions.Gap statement. There is an urgent need for a rapid and efficient nucleic acid detection strategy to enable early diagnosis and treatment, preventing rotavirus transmission and associated complications.Aim. This article aimed to develop a nuclear acid sequence-based amplification (NASBA)-Cas12a system for detecting rotavirus A using fluorescence intensity or lateral flow strips.Methodology. The NASBA technology was combined with the clustered regularly interspaced short palindromic repeats-Cas12a system to establish a NASBA-Cas12a system for detecting rotavirus A.Results. The NASBA-Cas12a system could detect rotavirus A at 37 ℃ within 70 min and had no cross-reactivity with other viruses, achieving a limit of detection of 1.2 copies μl^-1. This system demonstrated a sensitivity of 100%, specificity of 90%, positive predictive value of 97.22% and negative predictive value of 100%. The kappa value was 0.933, indicating that the NASBA-Cas12a system was highly consistent with reverse transcription-PCR.Conclusion. The NASBA-Cas12a system exhibited high sensitivity and specificity for detecting rotavirus A, showing great potential for clinical application.

Introduction. Fungal infections are relevant health risks for individuals with acquired immunodeficiency in the resource-limited tropics, but available surveillance data are scarce. For Candida auris and Cryptococcus spp., the evolution from environmental reservoirs to human pathogens causing life-threatening diseases is currently discussed as a public health concern in the context of climate change and limited treatment options.Gap statement. Uncovering the gastrointestinal tract as an epidemiological niche of fungi emerging from the environment into individuals for whom fungal infections are not diagnosed.Aim. To contribute to data on the local epidemiology of C. auris and Cryptococcus spp. in Western African Ghana by analysing gastrointestinal samples of Ghanaian individuals.Methodology. Four real-time PCR assays targeting C. auris and five real-time PCR assays targeting Cryptococcus spp. were applied with stool samples of 875 non-age-stratified Ghanaian HIV patients and 30 Ghanaian control individuals without known HIV infection. Also, 664 samples from Ghanaian children under 2 years of age were investigated. The true abundance of the target micro-organism was considered as unlikely in the case of one or fewer positive signals, likely in the case of two to three positive signals and highly likely in the case of four or more positive signals per sample in the real-time PCR assays.Results. The combined application of sensitive, target-specific real-time PCR assays indicates that neither C. auris, Cryptococcus neoformans complex nor Cryptococcus gattii complex were part of the gut microbiota of Ghanaian individuals with or without HIV infection.Conclusion. Despite the significant disease burden from these pathogens in immunosuppressed Ghanaian individuals, detection from gastrointestinal samples was unlikely, which should be taken into account when discussing screening strategies for these fungi of public health concern. In contrast, the detection of these fungi from such samples should not routinely be considered as commensal colonization flora.

Introduction. Imipenemase (IMI) enzymes are an uncommon class A carbapenemases that have been isolated from aquatic environments and, occasionally, from clinical isolates of Enterobacterales.Aim. We describe a cluster of three patients infected by IMI-1 carbapenemase-producing Enterobacter ludwigii (IMI-1-Elud) in a tertiary university hospital in Gran Canaria, Spain.Methodology. Antimicrobial susceptibility was determined using the Vitek2 AST-N355 card and antibiotic gradient strips. The modified carbapenem inactivation method (CIM) test was performed in cases where the ertapenem MIC value was higher than 0.125 mg l^-1. The carbapenemase was identified by PCR and DNA microarray and later characterized by whole-genome next-generation sequencing (NGS) with Illumina.Results. Three patients presented thoracic or abdominal infections caused by IMI-1-Elud ST1677 from 14 June 2022 to 14 July 2022. All patients underwent at least one gastroscopy during their admission, and two of them were located in adjoining rooms. Isolates were resistant to carbapenems, colistin and fosfomycin but susceptible to ciprofloxacin. IMI/NMC-A carbapenemase was detected by PCR and hybridization test and confirmed by NGS as IMI-1. All patients underwent at least one gastroscopy, and two of them were in nearby rooms. Patients showed microbiological and clinical improvement following focus drainage and targeted antibiotic treatment with a fluoroquinolone.Conclusions. This study reports the first documented global outbreak of patients infected with IMI-1-Elud. The source appeared to be related to endoscopes. Contact transmission may also have played a role. A screening method such as the modified CIM test is crucial for detecting less common carbapenemases that might not be identified by rapid molecular or immunochromatographic tests, as these often do not include bla _IMI genes, which could lead to the undetected dissemination of carbapenemase-producing Enterobacterales. Effective infection source control and targeted treatment are essential for achieving a favourable clinical outcome.

Introduction. Prototheca is an opportunistic pathogen that can infect both humans and animals, of which Prototheca wickerhamii (P. wickerhamii) being the most significant pathogenic green algae.Gap statement. The incidence of human diseases caused by Prototheca has been on the rise, yet there is a significant gap in genetic research pertaining to the pathophysiological aspects of these infections.Aim. The aim of this study is to present the whole genome data from the clinical isolate InPu-22_FZ strain and to understand its genomic characteristics through comparative genomic analysis and phylogenetic tree analysis. Functional annotation of protein-coding genes and analysis of their pathogenicity are also conducted.Methodology. We described the high-quality de novo genome assembly of the clinical isolate InPu-22_FZ strain, achieved by combining Nanopore ONT and Illumina NovaSeq sequencing technologies. Phylogenetic tree was constructed to study the evolutionary relationship between the InPu-22_FZ strain and other species. The average nucleotide identity (ANI) analysis was used to assess the similarity between different species. Additionally, the size, distribution and composition of synteny blocks were also analysed to infer the evolutionary relationships of the genomes.Results. The size of the assembled nuclear genome was 18.47 Mb with 48 contigs. Key features of the genome include high overall GC content (63.31%), high number (5478) and proportion (62.24%) of protein-coding genes and more than 96.71% of genes annotated for gene function. Phylogenetic analyses showed that the InPu-22_FZ strain and other P. wickerhamii clustered into one clade with a bootstrap value of 99% and collinearity analysis revealed high levels of collinearity with ATCC 16529. The ANI analysis revealed only a relatively high similarity (89-93%) to available P. wickerhamii genomes, suggesting the overall genomic novelty of InPu-22_FZ strain. Interestingly, the analysis of the pathogen-host interaction database unveiled and demonstrated reduced virulence of this strain, albeit it was isolated from a chronic upper-limb cutaneous infection.Conclusion. The study provides an in-depth insight into the genomic structure and biological function of the InPu-22_FZ strain, revealing the genetic basis of its pathogenicity and virulence.

Seven drug-resistant Elizabethkingia anophelis isolates were obtained from inpatients in three medical settings in Myanmar between February 2017 and January 2021. All isolates were resistant to β-lactams and colistin. Among these, four isolates were resistant to amikacin with minimum inhibitory concentration (MIC) of ≥64 µg ml^-1. Six of the seven isolates harboured genes encoding intrinsic β-lactamases, including bla _B, bla _CME and bla _GOB, whereas one isolate harboured bla _B, bla _CME and an incomplete bla _GOB gene. Phylogenetic analysis based on whole-genome sequences revealed that several E. anophelis isolates in Myanmar formed their own clusters, whereas others were similar to isolates found in the USA. This is the first report of the emergence of Elizabethkingia species in Myanmar.