- Volume 4, Issue 11, 2022
Volume 4, Issue 11, 2022
- Research Articles
-
-
-
Plasmids of the urinary microbiota
Studies of the last decade have identified a phylogenetically diverse community of bacteria within the urinary tract of individuals with and without urinary symptoms. Mobile genetic elements (MGEs), including plasmids and phages, within this niche have only recently begun to be explored. These MGEs can expand metabolic capacity and increase virulence, as well as confer antibiotic resistance. As such, they have the potential to contribute to urinary symptoms. While plasmids for some of the bacterial taxa found within the urinary microbiota (urobiome) have been well characterized, many urinary species are under-studied with few genomes sequenced to date. Using a two-pronged bioinformatic approach, we have conducted a comprehensive investigation of the plasmid content of urinary isolates representative of 102 species. The bioinformatic tools plasmidSPAdes and Recycler were used in tandem to identify plasmid sequences from raw short-read sequence data followed by manual curation. In total, we identified 603 high-confidence plasmid sequences in 20 different genera of the urobiome. In total, 70 % of these high-confidence plasmids exhibit sequence similarity to plasmid sequences from the gut. This observation is primarily driven by plasmids from E. coli , which is found in both anatomical niches. To confirm our bioinformatic predictions, long-read sequencing was performed for 23 of the E. coli isolates in addition to two E. coli strains that were sequenced as part of a prior study. Overall, 66.95 % of these predictions were confirmed highlighting the strengths and weaknesses of current bioinformatic tools. Future studies of the urobiome, especially concerning under-studied species in the urobiome, should employ long-read sequencing to expand the catalogue of plasmids for this niche.
-
-
- Short Communications
-
-
-
Genomic analysis of the progenitor strains of Staphylococcus aureus RN6390
More LessRN6390 is a commonly used laboratory strain of Staphylococcus aureus derived from NCTC8325. In this study, we sequenced the RN6390 genome and compared it to available genome sequences for NCTC8325. We confirmed that three prophages, Φ11, Φ12 and Φ13, which are present in NCTC8325 are absent from the genome of RN6390, consistent with the successive curing events leading to the generation of this strain. However, we noted that a separate prophage is present in RN6390 that is not found in NCTC8325. Two separate genome sequences have been deposited for the parental strain, NCTC8325. Analysis revealed several differences between these sequences, in particular, between the copy number of esaG genes, which encode immunity proteins to the type VII secreted anti-bacterial toxin, EsaD. Single nucleotide polymorphisms were also detected in ribosomal RNA genes and genes encoding microbial surface components recognizing adhesive matrix molecules (MSCRAMM) between the two NCTC8325 sequences. Comparing each NCTC8325 sequence to other strains in the RN6390 lineage confirmed that sequence assembly errors in the earlier NCTC8325 sequence are the most likely explanation for most of the differences observed.
-
-
-
-
Conjugative IncHI2/HI2A plasmids harbouring mcr-9 in colistin-susceptible Escherichia coli isolated from diseased pigs in Japan
More LessColistin is a last resort antimicrobial used for the treatment of gram-negative bacterial infections. Plasmid-mediated colistin resistance (mcr) genes are a cause of global concern, and, thus far, mcr-1–10 have been identified. In a previous study, we screened mcr-1–5 in Escherichia coli derived from diseased pigs in Japan and reported a high prevalence of mcr-1, -3 and -5. However, the previous report on the prevalence of mcr genes was inaccurate. In the present study, we aimed to clarify the prevalence of all reported variants of mcr in E. coli derived from the diseased pigs, which were previously screened for mcr-1–5. Additionally, we also characterized the mcr-9-positive E. coli , which was detected in this study. We screened mcr in 120 E. coli strains from diseased pigs and mcr-positive E. coli and an mcr-carrying plasmid were also characterized. One mcr-9-positive colistin-susceptible E. coli strain was detected (0.8 %). Plasmid-mediated mcr-9 was transferred to E. coli ML4909 as the recipient strain, and it was located on IncHI2/HI2A plasmid p387_L with other antimicrobial resistance genes (ARGs). The region harbouring ARGs including mcr-9, was similar to that on the Klebsiella pneumoniae chromosome harbouring mcr-9 isolated in Japan. mcr-3, -5 and -9 were detected (4.2 %) in colistin-susceptible strains. mcr-9 was found to be disseminated via the plasmid IncHI2/HI2A p387_L and transferred and inserted into chromosomes via a transposon. Our results suggest that mcr genes should be monitored regularly, regardless of their susceptibility to colistin.
-
- Case Reports
-
-
-
Acetobacter tropicalis bacteraemia in an immunocompromised patient: case report
More LessIntroduction. The published literature characterizing the bacterial genus Acetobacter primarily explores the role of these organisms in the fermentation industry. Reports of human infections caused by Acetobacter species are rare and are primarily associated with immunocompromised patients.
Case Presentation. A young patient with refractory acute myeloid leukaemia received a peripheral blood stem cell transplant at our institution. Both pre- and post-transplant courses were complicated by polymicrobial bloodstream infections. During this time a bacterium, later identified as Acetobacter tropicalis , was isolated from blood cultures. A. tropicalis was recovered in consecutive blood cultures for approximately 1 week; during this time the patient’s condition deteriorated, ending in fatal cardiorespiratory failure.
Conclusion. This case provides the first report of a human infection with A. tropicalis , although the significance of this finding in a complex patient is hard to establish. This illustrates how the routine implementation of molecular identification techniques by clinical microbiology laboratories will result in the reporting of more rare or novel micro-organisms involved in human infections.
-
-
-
-
Prosthetic valve endocarditis due to highly beta-lactam-resistant Streptococcus oralis: a case report
There are limited reports of patients with prosthetic valve infective endocarditis (IE) or recurrent IE due to highly beta-lactam-resistant viridans group streptococci. We present a case in which a patient with native valve IE due to beta-lactam-susceptible Streptococcus oralis developed prosthetic valve IE due to highly beta-lactam-resistant S. oralis . A 79-year-old man with a history of native aortic valve IE caused by beta-lactam-susceptible S. oralis 21 months prior to admission and aortic valve replacement was admitted to our hospital with a 2-week history of general malaise and low-grade fever. Transesophageal echocardiography showed a 20 mm vegetation on the prosthetic aortic valve, and emergency cardiovascular surgery was performed on admission day 2. Three sets of blood cultures on admission were positive for highly beta-lactam-resistant S. oralis . Vancomycin and cefazolin were administered as initial treatment. After the surgery, the patient was given vancomycin and gentamicin for 2 weeks, followed by vancomycin for 4 weeks. He was relapse-free at the 6-month follow-up. For patients with native valve IE due to S. oralis who have undergone valve replacement more than 1 year earlier, given the possibility of methicillin-resistant Staphylococcus aureus as well as S. oralis resistance to beta-lactams, it may be advisable to start vancomycin as an initial treatment and continue it until the infecting micro-organism has been proven to be susceptible to beta-lactams.
-
-
-
Case report: a fatal case of Aspergillus felis infection in an immunocompetent host
We report a fatal case of Aspergillus felis invasive rhinosinusitis with secondary cerebral abscesses in an immunocompetent host despite aggressive surgical debridement and combination antifungals. Whilst this organism is known to cause fatalities in cats, only a few cases in humans have been documented, all of which had significant immunosuppression. This is the first human death due to A. felis described in an immunocompetent host.
-