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Mucormycosis is found in co-infection with bacteria in >50% of the cases. Most of these cases were reported among people with haematological diseases. The two most frequent bacteria found were Pseudomonas aeruginosa and Klebsiella pneumoniae. Almost 40% of the identified bacteria were reported as multidrug resistant.

Introduction. Antimicrobial resistance (AMR) is a growing global concern. Clonal lineages of CTX-M β-lactamase-producing Escherichia coli (CTXE) and quinolone-resistant E. coli (QREC) were disseminated among the deer population in a famous tourist destination (Nara Park; NP) in Japan. Hypothesis/gap statement. The molecular characteristics of CTXE or QREC isolates, which could pose a threat to public health, have not been elucidated. Aim. This study aimed to characterize the genetic traits of CTXE and QREC isolates derived from NP deer and compare them with lineages prevalent worldwide. Methodology. Sixteen CTXE and three QREC isolates recovered from NP deer faeces between 2018 and 2020 were analysed using whole-genome sequencing (WGS). For endemic lineages, phylogenetic trees were constructed against the isolates registered in the EnteroBase database using the core genome SNP scheme. Results. The most prevalent lineage in NP deer was ST3580. Several pandemic lineages, such as sequence type (ST) 38, ST58 and ST117, were included. The QREC lineages prevalent among deer were designated as extra-intestinal pathogenic E. coli or uropathogenic E. coli (UPEC). Thirteen of the 24 antimicrobial resistance genes (ARGs) were considered high-risk ARG families. Chromosomal integration of bla _CTX-M-15 was observed in all plasmid-negative isolates. Phylogenetic analysis suggested relationships between NP isolates and isolates sourced from the environment or poultry. Conclusion. ST3580 has a high potential for clonal dissemination. Furthermore, multiple clinically relevant lineages of CTXE and QREC are endemic in NP deer; however, they could be less virulent than isolates belonging to the same lineages, which could cause severe infectious diseases. Further studies are required to investigate the relationship between chromosomal integration of plasmid-encoded genes and the stable propagation of AMR bacteria in wildlife and the environment.

Introduction. Virological failure is one of the main causes of failing to treat, and better management of HIV infection requires understanding and controlling the factors that contribute to this phenomenon. The main objective was to characterize the patients of the active file of the Brazzaville Outpatient Treatment Center in virological failure to identify predictive factors leading to virological failure. Methods. Conducted between June and December 2020, this was a cross-sectional study. Patients enrolled were HIV-1-infected patients from the Brazzaville Outpatient Treatment Center receiving a potent combination therapy for at least 6 months but experiencing virological failure. Viral load was measured using the automated Abbott Real-time HIV-1 m2000rt System. Sociodemographic and clinical data were collected from a computerized patient record software called Santia. For the identification of the independent predictors of virological failure, statistical analysis was performed. Results. A total of 109 patients with virological failure were recruited. The median age of the patients was 45 years (interquartile range: 37-52 years) and women were more represented (74%). More than half of the patients had World Health Organization stage IV HIV and the median duration of antiretroviral treatment was 96 months. The most followed treatment regimen was AZT+3TC+EFV (or nevirapine) with 48%, while the median viral load was 12985 copies ml^-1. Conclusion. In our study, we did not identify any sociodemographic or clinical variables predictive of virological failure. However, we felt that it would be desirable to carry out a study with temporal follow-up and the possibility of sequencing in order to identify the different circulating genotypes and resistance mutations.

This Technical Resource describes genome sequencing data for 61 isolates of the bacterial pathogen Xanthomonas campestris pv. campestris collected from Brassica and Raphanus crops between 2010 and 2021 in Serbia. We present the raw sequencing reads and annotated contig-level genome assemblies and determine the races of ten isolates. The data can be used to test hypotheses and phylogeographic analyses and inform the design of informative molecular markers for population genetics studies. When combined with phenotypic data, they could be used to dissect relationships between genotypes and phenotypes such as host range and virulence. Finally, these genome sequences expand our inventory of plasmids known to reside in this pathogen.

Background. Hepatitis B virus (HBV) is the most implicated cause of severe liver disease and hepatocellular carcinoma worldwide. Studies have shown that the basal core protein (BCP) and precore protein (PC) of HBV play a significant role in HBV-related carcinogenesis. There is a paucity of data on the type and effect of BCP and PC mutations in Nigeria. This study aims to genotype HBV and investigate any mutations within the BCP and PC among HBV patients in Ibadan, Nigeria. Methods. Forty HBV-DNA-positive patients were recruited into this study, and the viral load assay and genotyping by nested multiplex PCR were done. The partial X gene region was amplified and Sanger sequenced. The BPC and PC genomic regions were then analysed using bioinformatics. Results. Twenty-three participants recorded HBV DNA viral load of >20 000 IU, while 17 had <20 000 IU and 28 samples were genotyped. Five genotypes (A, B, C, D and E) and four mixed genotypes (AC, AD ACD and ABCD) were detected. Genotype AC was the most frequently encountered, while genotypes E and B were the least encountered. Mutation was highest in ages 34-45 years. Double mutation A1762T and G1764A within the BCP region was the most encountered mutation. Conclusions. We report a diverse HBV genetic landscape, with mixed infections between genotypes with BCP double-mutation A1762T/G1764A, signalling the likelihood of poor HBV-related liver disease prognosis. Our findings contribute to our understanding of the molecular characteristics of HBV and its potential implications for disease progression and management among HBV-infected Nigerians.

Introduction. Systemic human infections caused by Erysipelothrix rhusiopathiae have been increasingly reported especially within immunocompromised hosts and those with significant occupational exposure to livestock and aquatic animals. We report a case of E. rhusiopathiae bacteraemia in a patient with systemic lupus erythematosus (SLE) and present a literature review on clinical outcomes and microbiologic diagnosis for this organism. Casepresentation. A 43-year-old female patient was reporting a 1-month history of intermittent fevers. She recently increased her immunosuppression medication for her underlying SLE on the advice of her rheumatologist. The patient sustained a finger laceration from butchering cattle meat 2 weeks after the onset of her initial symptoms, with worsening index finger swelling and increased febrile episodes. Two weeks post-injury, multiple blood cultures were drawn, and each isolated Gram-positive bacilli. Given her recurrent intermittent fevers, there was a concern for ongoing infection, and therefore, intravenous vancomycin was started with prompt referral to an outpatient parenteral antibiotic therapy clinic. The Gram-positive bacillus was confirmed as E. rhusiopathiae via matrix-assisted laser desorption/ionization-time of flight analysis. Given intrinsic resistance to vancomycin, vancomycin was switched to intravenous ceftriaxone as targeted antimicrobial therapy for 2 weeks. Reassuringly, there was no echocardiographic evidence of infective endocarditis, warranting the prolonged treatment course. Post-treatment, she remained symptom-free with the resolution of joint symptoms and fevers. Conclusion. Our report illustrates a case of E. rhusiopathiae bacteraemia from an immunodeficient host, with prompt microbiologic diagnosis and intervention with appropriate antimicrobial coverage. Literature reflects the rarity of this infection, predilections to specific susceptible hosts and the importance of raising awareness of zoonotic infections.

Salmonella enterica serotype Enteritidis is a generalist serotype that adapts to different hosts and transmission niches. It has significant epidemiological relevance and is among the most prevalent serotypes distributed in several countries. Salmonella Enteritidis causes self-limited gastroenteritis in humans, which can progress to systemic infection in immunocompromised individuals. The Salmonella pathogenicity mechanism is multifactorial and complex, including the presence of virulence factors that are encoded by virulence genes. Poultry products are considered significant reservoirs of many Salmonella serotypes, and Salmonella Enteritidis infections are often related to the consumption of chicken meat and eggs. This study reports the whole-genome sequence of Salmonella Enteritidis PT4 strain 578. A total of 165 genes (3.66%) of the 4506 coding sequences (CDS) predicted in its genome are virulence factors associated with cell invasion, intestinal colonization, and intracellular survival. The genome harbours twelve Salmonella pathogenicity islands (SPIs), with the SPI-1 and SPI-2 genes encoding type III secretion systems (T3SS) showing high conservation. Six prophage-related sequences were found, with regions of intact prophages corresponding to Salmon_118970_sal3 and Gifsy-2. The genome also contains two CRISPR systems. Comparative genome analysis with Salmonella Enteritidis ATCC 13076, Salmonella Typhimurium ATCC 13311, and Salmonella Typhimurium ATCC 14028 demonstrates that most unshared genes are related to metabolism, membrane, and hypothetical proteins. Finally, the phenotypic characterization evidenced differences among Salmonella Enteritidis PT4 578 and the other three serotypes regarding the expression of the red, dry, and rough (rdar) morphotype and biofilm formation. Overall, the genomic characterization and phenotypic properties expand knowledge of the mechanisms of pathogenicity in Salmonella Enteritidis PT4 578.

Non-typhoidal Salmonella lung infections are rare and are usually confined to immunocompromised hosts. Previous case reports have found that usually patients have either gastroenteritis or bacteraemia in addition to pulmonary involvement. We present the first known reported case of a Salmonella Weltevreden lung abscess and empyema in an immunocompetent patient without gastroenteritis. Despite the use of antimicrobials active against the pathogen, the patient needed surgical intervention to achieve adequate source control. While S. Weltevreden has previously been associated with returned travellers, especially from Southeast Asia, its incidence in Queensland is now increasing. Therefore, it is important for clinicians to be aware of its potential severity as well as the range of presentations.

Peritoneal dialysis is a blood purification technique used in cases of end-stage chronic kidney failure, based on the filtering capabilities of the peritoneum. Infections, often caused by poor asepsis during catheter manipulation, are generally attributed to Staphylococcus epidermidis and Staphylococcus aureus. Corynebacterium, usually considered non-pathogenic, is rarely involved in these infections. We present a case of peritonitis due to Corynebacterium amycolatum in a patient undergoing peritoneal dialysis. The diagnosis was made based on cytobacteriological examination of the dialysate fluid, which on two occasions showed high levels of white blood cells with a predominance of neutrophilic polymorphonuclear and a monomorphic appearance of colonies on agar medium, whose identification by biochemical tests and antibiotic sensitivity study confirmed the presence of C. amycolatum. The patient was successfully treated with vancomycin, resulting in symptom resolution and sterilization of the dialysate fluid. Although rare, the involvement of Corynebacterium species underscores the importance of confirming its pathogenicity. Further studies are needed to better understand the epidemiology of these infections and guide future treatments. This case also highlights the need for a rigorous approach to confirming the pathogenicity of Corynebacterium despite its traditional classification as a contaminant.