- Volume 4, Issue 10, 2022
Volume 4, Issue 10, 2022
- Research Articles
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Comparison of clinical severity, genotype and toxin gene expression of binary toxin-producing Clostridioides difficile clinical isolates in Japan
The emerging Clostridioides difficile strain BI/NAP1/027 has been reported to be associated with more severe clinical symptoms and higher mortality rates, thought in part due to production of a novel binary toxin alongside conventional A and B toxins. However, recent studies suggest that this may not always be the case. Therefore, the purpose of this report was to investigate the correlation between clinical severity and microbiological characteristics of CDT-producing C. difficile isolates in Japan. Eight Japanese isolates of CDT producing C. difficile were investigated using genotyping, cytotoxic activity assays and toxin gene expression. Correlation with clinical severity was performed retrospectively using the patient record. Three of eight patients were assessed as having severe C. difficile infection (CDI). PCR ribotyping resolved six ribotypes including ribotype 027. No specific genes were identified determining severe compared with non-severe cases. Positive correlation of expression levels of tcdA, tcdB and cdtB were observed although these expression levels were not correlated with cytotoxicity. CDI severity index neither correlated with toxin gene expression level nor cytotoxicity. These data indicate that the possession of the CDT gene and toxin gene expression levels may not relate to C. difficile cytotoxicity or clinical severity.
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Development of skin sebum medium and inhibition of lipase activity in Cutibacterium acnes by oleic acid
More LessCutibacterium acnes is associated with the exacerbated inflammation of acne vulgaris, which occurs through the immune induction and pathogenicity factor production. Sebum, which is not present in the growth medium currently used to study acne, is present in acne pustules in differing concentrations among the pathological stages, such as the initial formation and inflammatory phase. To evaluate the effect of C. acnes on inflammation exacerbation in acne pustules in vitro, we developed an skin sebum medium containing artificial sebum and studied the growth and pathogenicity factor production of C. acnes in the skin sebum medium.
The growth and lipase activity of C. acnes ATCC11828 were tested using skin sebum medium containing different sebum concentrations. Only lipase activity decreased in the skin sebum medium culture containing 0.5 % sebum when compared with that without sebum, while both growth and lipase activity decreased in cultures with 1.0 % sebum. Therefore, the growth and lipase activity of C. acnes changed in the presence of sebum. Furthermore, when the growth and lipase activity of C. acnes were tested in skin sebum medium containing sebum components, unsaturated fatty acids, such as oleic acid and triolein, led to a decrease in lipase activity without inducing a change in growth. In the presence of oleic acid, C. acnes lipase activity decreased noncompetitively in a concentration-dependent manner.
Our data showed that C. acnes growth and lipase activity changed upon sebum addition to the skin sebum medium, and acne inflammation caused by C. acnes needs to be studied under conditions similar to those in acne pustules.
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Post-operative antibiotics for cutaneous abscess after incision and drainage: Variations in clinical practice
More LessBackground. Acute cutaneous abscess is a common surgical condition that mostly requires incision and drainage. Despite this, there is no standardized national or international guidance on post-operative antibiotics prescription. Traditionally, antibiotics are not indicated unless complications and/or risk factors such as immunocompromisation, diabetes or cellulitis exist. We aimed to study the local practice for post-operative antibiotics prescription for cutaneous abscesses in a UK university teaching hospital.
Methods. Retrospective data collection for emergency general surgical admissions for a period of 6 months was carried out. All patients with cutaneous abscesses were included in this analysis. Scrotal, breast and limb abscesses were excluded. Patients’ demographics, co-morbidities and complications, including local (cellulitis, necrosis) and systemic (e.g sepsis), were studied. Approval for access to patient data was granted by the local clinical governance department prior to the commencement of this study. Computations were performed using IBM SPSS version 26. Chi square (X 2), Pearson correlation (r), one or two samples t-test (one or two tailed) were applied.
Results. A total of 148 patients were included. The mean age was 40 years (55 % males). The most common site of abscess was perianal (27.7 %), followed by pilonidal (20.3 %) and axilla (16.9 %). A total of 107 (73 %) were managed surgically with incision and drainage, and of these 92 (86 %) were managed within 24 h. Altogether, 83 (76 %) were prescribed post-operative antibiotics, while only 25 (23 %) had indications. The most used post-operative empirical antibiotics was co-amoxiclav (59 %). There was a significant relationship between ‘abscess site’ × ‘antibiotics’ [X 2 (36)=54.8, P=0.023]. A total of 103 patients’ average duration of post-operative antibiotics was 7.2 (sd 2.9) days. Ten patients subject to readmission spent an average of 8.4 (sd 3.8) days on antibiotics.
Conclusions. There were variations in clinical practice regarding post-operative antibiotic prescription for cutaneous abscesses. Research is required in the future in cooperation with microbiologists to develop a standardized evidence-based treatment protocol for the management of such a common surgical condition.
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Escherichia coli harbouring strAB with reduced susceptibility towards gentamicin and amikacin: a single centre study from India
In this study we report the presence of streptomycin resistance gene strAB within clinical isolates of Escherichia coli where streptomycin is not used to treat Gram-negative infections. In total, 135 E. coli isolates were obtained for the study. PCR based detection of strAB was performed in the study isolates followed by assessment of horizontal transferability. Cloning of strAB was done in laboratory strain E. coli DH5α. Pre-cloning and post-cloning susceptibility of the strain was done for assessment of acquired resistance. Among tested isolates, 89 were found to harbour strAB and it was encoded within a IncI1 type plasmid. Cloning experiments revealed the strAB gene showed unusual non-susceptibility towards amikacin and gentamicin. The study highlighted that strAB, which has a role in streptomycin resistance, may also have a role in reduced susceptibility towards gentamicin and amikacin within a clinical setting.
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- Short Communications
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OXA-66 structure and oligomerisation of OXAAb enzymes
The OXA β-lactamases are responsible for hydrolysing β-lactam antibiotics and contribute to the multidrug-resistant phenotype of several major human pathogens. The OXAAb enzymes are intrinsic to Acinetobacter baumannii and can confer resistance to carbapenem antibiotics. Here we determined the structure of the most prevalent OXAAb enzyme, OXA-66. The structure of OXA-66 was solved at a resolution of 2.1 Å and found to be very similar to the structure of OXA-51, the only other OXAAb enzyme that has had its structure solved. Our data contained one molecule per asymmetric unit, and analysis of positions responsible for dimer formation in other OXA enzymes suggest that OXA-66 likely exists as a monomer.
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Genome dynamics mediated by repetitive and mobile elements in Xanthomonas citri pv. durantae
More LessXanthomonas is a highly evolved group of phytopathogenic bacteria infecting nearly 400 host plants having vast genomic resources available with heterogenicity in representation from different species and pathovars. Unfortunately, the wealth of data is extremely biased and restricted to a few Xanthomonas pathogens that infect economically important plants, while those reported to infect the most diverse plants remain neglected. In the present study, we report the first complete genome sequence of Xanthomonas citri pv. durantae that was reported to infect Duranta repens L. or golden dewdrop, a hedge plant of ornamental importance native to the American region. Phylogenomic analysis with its closest relatives placed it amongst X. citri pv. citri A* pathotype strains and further comparative studies revealed various large unique genomic regions of chromosomal origin. The association of integrative and conjugative elements and prophages with unique genomic regions suggests the role of mobilome in genome dynamics. A large number of IS elements and transcription activator-like effectors encoding genes on each of the four plasmids indicate the further scope of diversification in Xanthomonas .
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Performance evaluation of Novaplex SARS-CoV-2 variants assay kit series for SARS-CoV-2 detection using single nucleotide polymorphisms
More LessSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have received increasing attention globally because of their increased transmissibility and potential to escape immunity. Although whole-genome sequencing is the gold standard method for SARS-CoV-2 mutation detection and lineage determination, it is costly and time-consuming. However, SARS-CoV-2 variants can be identified based on select variant-specific single nucleotide polymorphisms (SNPs) in the spike protein-encoding gene (S). This study validated and compared the limit of detection (LOD) of L452R, N501Y, HV69/70 del and E484K as variant-specific SNPs of the S gene and RdRP as a SARS-CoV-2-specific gene, using the Novaplex SARS-CoV-2 variants assay kit series. For three SARS-CoV-2 lineages (B.1.617.2, B.1.1.7 and R.1), one strain per lineage was used. Variant-specific SNPs of the S gene were analysed using the Novaplex SARS-CoV-2 variants I assay and Novaplex SARS-CoV-2 variants II assay kits. Validation confirmed the LODs of the variant kits. The LOD for each target variant-specific SNP and RdRP was five RNA copies per reaction. The Novaplex SARS-CoV-2 variants assay kit series performs well and the LOD for SARS-CoV-2 detection and variant-specific SNP detection are consistent. The kits are suitable for use as routine laboratory tests for SARS-CoV-2 and variant-specific SNP detection in a single step, saving time and labour.
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Co-infection of SARS-CoV-2 with other respiratory pathogens in patients with liver disease
More LessRespiratory illness caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) was first documented in Wuhan, China, in December 2019, followed by its rapid spread across the globe. Accumulating evidence has demonstrated viral/bacterial co-infection in the respiratory tract could modulate disease severity and its outcome in COVID-19 infection. In this retrospective study, 300 chronic liver disease patients with radiologically confirmed lower respiratory tract infection were enrolled from September 2020 to December 2021. In all of them, along with SARS-CoV-2, other respiratory viral/bacterial pathogens were studied. In total, 23.7 % (n=71) patients were positive for SARS-CoV-2. Among the positive patients, 23.9 % (n=17) had co-infection with other respiratory pathogens, bacterial co-infections being dominant. The SARS-CoV-2 negative cohort had 39.7 % positivity (n=91) for other respiratory pathogens, the most common being those of the rhinovirus/enterovirus family. Ground glass opacity (GGO) with consolidation was found to be the most common radiological finding among SARS-CoV-2 positive co-infected patients, as compared to only GGO among SARS-CoV-2 mono-infected patients. Accurate diagnosis of co-infections, especially during pandemics including COVID-19, can ameliorate the treatment and management of suspected cases.
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- Case Reports
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Cefiderocol to manage chronic, multi-drug-resistant Burkholderia cepacia complex infection in a patient with cystic fibrosis: a case report
More LessIn cystic fibrosis (CF) patients, Gram-negative Burkholderia cepacia complex (Bcc) infections are associated with recurrent pulmonary exacerbations. Bcc organisms are innately resistant to many antibiotics, and infection with B. cenocepacia is a contraindication to lung transplantation. We report a CF patient with severe lung disease, colonized with Bcc, with a history of around nine exacerbations per year for over 10 years, for whom antibiotic regimens (including targeted and broad-spectrum antibiotics) had not cleared infection or extended the interval between exacerbations. After receiving a 2 week cefiderocol-containing regimen, the patient remained stable for more than 5 months without the need for additional antibiotics or hospital admissions for respiratory exacerbations.
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Case report: a genomics-guided reclassification of a blood culture isolate misassigned by MALDI-TOF as Yersinia pestis
In this report, we describe a case where Gram-negative rods were isolated from a blood culture which subsequently presented a discordant Yersinia species result by MALDI-TOF. Rapid sequencing provided high-resolution identification of the isolate as Yersinia pseudotuberculosis , which was subsequently confirmed by biochemical tests.
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Human parvovirus B19 infection in a pregnant patient resulting in severe hydrops, foetal death and persistent infection
Human parvovirus B19 (B19V) is the aetiological agent of erythema infectiosum. Primary infection during pregnancy can be transmitted to the foetus and cause foetal abnormalities related to depletion of erythrocyte progenitor cells, including congenital anaemia, hydrops, and foetal death. In this paper we report the detection of B19V infection in a pregnant patient, which onset occurred without appreciable signs and symptoms until she developed inappropriate contractions for gestational age and fluid loss. B19V infection resulted in severe hydrops fetalis with a fatal course for the foetus, while persisted in the mother at least 12 months after foetal death. The objective of this report is to highlight the importance of optimizing B19V diagnosis through early suspicion and testing during pregnancy. Knowing the mother’s immune status before or at the beginning of gestation can contribute, together with early diagnosis, to improve the management of patients at risk.
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