Journal of medical microbiology最新文献

Introduction. Colorectal cancer (CRC) is a malignant tumour in which dysbiosis of the gut microbiome is a contributing factor in the development of cancer. However, the species composition and species-specific changes in the gut microbiome related to CRC still require comprehensive investigation.Hypothesis. There is a significant difference in gut microbiome between CRC patients and healthy individuals.Aim. The microbiome-based association test methods are used for the association between the microbiome and host phenotypes, and linear discriminant analysis effect size (LEfSe) analysis is employed to search for microbial biomarkers associated with CRC.Methodology. We conducted a meta-analysis of microbiome data from multiple cohorts, totalling 1,462 samples and 320 genus-level features. Considering the data obtained under different experimental conditions, we removed the batch effect using conditional quantile regression. Then, we employed the common analysis processes and methods of microbiome data, including microbial diversity analysis, microbiome-based association test analysis and microbial differential abundance analysis.Results. The experimental results showed that there were significant differences in α-diversity between the CRC group and the healthy group, as well as in the overall microbial community (PERMANOVA P-value less than 0.05). LEfSe analysis also demonstrated the genus-level features enriched in the gut of CRC patients and the genus-level features enriched in the gut of healthy individuals. Notably, the batch effect-corrected data exhibit more significant performance than the raw data.Conclusion. Gut microbiome composition is a significant factor associated with the development of CRC. Enterobacter and Fusobacterium enriched in the gut of CRC patients may be CRC-related microbial biomarkers, while Bacteroides and Faecalibacterium enriched in the gut of healthy individuals are core genera of the healthy gut. In addition, batch effects in microbiome data caused by differences in sample handling may lead to false discoveries, especially large-scale microbiome data. These findings could deepen the understanding of the role played by gut microbes in CRC and are expected to provide recommendations for the diagnosis of cancer and the development of new microbial therapies.

Introduction. Pseudomonas aeruginosa contains a wide range of extracellular and cell-associated virulence factors that support its pathogenesis. The most variable portion of lipopolysaccharide, O-polysaccharide, confers serogrouping and is crucial for virulence.Gap Statement. Despite their importance, P. aeruginosa serotypes and associated virulence factors are not well described at the level of strains obtained from Ethiopian clinical samples.Aim. To characterize the serotypes and virulence factors of P. aeruginosa isolates from patients admitted to two hospitals in Addis Ababa, Ethiopia.Methodology. Whole-genome sequencing was performed to characterize genes responsible for serotypes and virulence factors.Results. Eight distinct serotypes were identified, with O6 (50%) and O11 (14.1%) being the most common and O9 (1.6%) being the least common. Serotype O6 was the most frequent serotype in all infections, and the percentage of O11 (38.5%) was high in burn wound isolates. The percentage of multidrug resistance was 56.6%. High levels of resistance to ciprofloxacin (51.8%) and ceftazidime (50.6%) and low levels of resistance to ceftazidime-avibactam (4.8%) were observed. Multidrug-resistant phenotypes were more common for the O11 (88.9%) and O5 (66.7%) serotypes. There were four (6.3%) exoU+ strains and one (1.6%) exoU+exoS+ multidrug-resistant strain, all of which were O11 serotypes. The frequencies of toxA, exoY, pilA and exoT were 93.8%, 96.9%, 17.2% and 96.9 %, respectively.Conclusion. This study showed the presence of highly virulent multidrug-resistant P. aeruginosa strains in Ethiopia, and continuous molecular surveillance is essential for monitoring the spread of these strains and creating efficient management strategies.

Coronavirus disease 2019 (COVID-19) patients may present with a wide clinical spectrum, including extrapulmonary involvement, such as neurological damage. Although the pathogenesis of neurological COVID-19 still remains unclear, some studies have discussed the potential association between tissue injury and severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) infection in the central nervous system (CNS) and/or immune imbalance. These two mechanisms are non-mutually exclusive; however, exacerbated inflammatory-response-induced neurological damage appears to be more aligned with COVID-19 pathogenesis, whereas SARS-CoV-2 infection/replication in the CNS remains widely discussed. Herein, we dissect this last issue, highlighting some evidence on SARS-CoV-2 neuroinvasion, as well as discussing gaps that should be addressed for a better understanding of its potential neurotropism, specifically in the CNS. Finally, we propose some deeper reflections on the SARS-CoV-2 neurotropic potential.

Introduction. The oral microbiota is the second most complex microbial community in the human body. It has been suggested that poor oral health may be associated with an increased risk of obesity.Hypothesis/Gap Statement. However, both previous observational and mechanistic studies on oral microbiota do not take into account the obesity-related acanthosis nigricans (AN), which is the most common dermatological manifestation in individuals with obesity.Aim. This study aimed to investigate the altered composition, function and diagnostic value of the oral microbiota in obesity with or without acanthosis nigricans (AN).Methodology. We characterized the oral bacteria signature in a Chinese cohort (ChiCTR2300073353) of 99 patients with obesity and obesity-related AN (Ob_AN) and 50 healthy controls using 16S rRNA gene V3-V4 region sequencing.Results. The microbial richness (abundance-based coverage estimators and observed species indices) was significantly greater in the Ob_AN and obesity groups than in the control group; however, microbial diversity (Shannon index) did not differ significantly. Distinct separation in the microbial community amongst the three groups was observed. Prevotella species, including Prevotella melaninogenica, Prevotella nanceiensis and Prevotella pallens, were associated with composition alterations and predicted functions (significant downregulation of ATP-binding cassette transporters) associated with microbial dysbiosis in the obesity and Ob_AN groups. Moreover, Prevotella and Lautropia genera assessments could indicate obesity and obesity-related AN risk.Conclusions. The notable reduction of plenty of oral microbiota and high levels of Prevotella spp. may play a critical role in obesity with AN. Oral microbiota may serve as biomarkers for diagnosing, preventing and even treating obesity-related AN.

Introduction. The relationship between analgesic use and gut microbiota alterations has garnered increasing attention. However, the causal link between these two factors remains to be elucidated. Given the prevalence of analgesic use and the significant role of gut microbiota in human health, clarifying this relationship is of great importance.Hypothesis/Gap Statement. Existing observational studies are limited in their ability to establish causality between analgesic use and gut microbiota alterations. Therefore, there is a need for robust causal inference methods to explore this relationship and uncover the underlying mechanisms.Aim. This study aims to investigate the causal associations between genetic susceptibility to four common analgesics (NSAIDs, salicylic acid, opioids, and anilides) and gut microbiota composition, as well as circulating metabolites, using a two-sample Mendelian randomization approach.Methodology. A two-sample Mendelian randomization was used to investigate the potential association between genetic susceptibility to four analgesic uses and gut microbiota composition, as well as circulating metabolites. Summary-level statistics of genome-wide association studies were obtained from primarily European ancestry cohorts, including 466,457 participants from the UK Biobank and 18,340 individuals from the MiBioGen consortium.Results. Only one suggestive causal association was found between NSAID use and elevated abundance of gut microbiota, namely group Eubacterium xylanophilum. In addition, salicylic use was correlated with an increased abundance of the family Prevotellaceae (P=0.006), while it was negatively associated with the abundance of 8 microbiota traits, including genus Clostridiumsensustricto1, Adlercreutzia, Akkermansia, family Clostridiaceae1, Verrucomicrobiaceae, phylum Verrucomicrobia, class Verrucomicrobiae and order Verrucomicrobiales with P value ranging from 0.009 to 0.043. No clear evidence was found between opioid and anilide use and gut microbiota alteration. Meanwhile, salicylic use was potentially causally associated with four metabolites, including acetoacetate, creatinine, omega-3 fatty acids and triglycerides in very large high-density lipoprotein, with P values ranging from 0.005 to 0.046.Conclusion. The results of this study offer powerful evidence that the long-term use of salicylic acid may substantially impact gut microbiota composition and circulating metabolites. Further investigations are needed to uncover the underlying mechanisms.

Bacterial resistance remains a major challenge in the therapeutic field. Beta-lactam antibiotics are widely used to treat Enterobacteriaceae, especially third-generation cephalosporins (3GCs), which are used in infections caused by bacteria resistant to first- and second-line antibiotics. However, these bacteria have been able to develop resistance against the used antibiotics through the production of extended-spectrum beta-lactamase (ESBL) enzymes. These enzymes inactivate 3GCs and are sensitive to beta-lactamase inhibitors such as clavulanic acid. This resistance is acquired by plasmids (IncF, IncI, IncK…) which carry mobile genetic elements (insertion sequence, transposon…) with genes coding for these enzymes, namely, the bla _CTX-M, bla _SHV and bla _TEM, which code for the most frequent types of ESBL (CTX-M, SHV and TEM). Unfortunately, when ESBLs are not identified in time, appropriate treatment is delayed, reducing the chances of cure. Current data highlight the spread and dangerousness of ESBL-producing bacteria worldwide and confirm the priority given to these bacteria by the World Health Organization, which insists on vigilance in identifying them, both in patients and through surveillance studies. The aim of the current review is to provide a better understanding of ESBLs, to highlight their historical evolution and to show the importance of their genetic environment in the dissemination and spread of these enzymes worldwide, as well as the techniques used to detect them in laboratory studies. Current data demonstrate the degree of danger posed by ESBL-producing bacteria and confirm the priority given to these bacteria by the World Health Organization for the development of new antimicrobial agents.

Introduction. Actinomyces species colonizing the human oropharynx and gastrointestinal and urogenital tract are associated with a wide range of infections. The isolation of Actinomyces spp. from sterile clinical samples is regarded as significant.Gap Statement. Increased use of advanced diagnostics has caused an increased detection of Actinomyces in the bloodstream, the clinical significance of which is unclear.Aim. To investigate the clinical factors associated with true Actinomyces bacteraemia that could aid in differentiating it from transient Actinomyces bacteraemia.Methodology. We conducted a retrospective study of all inpatients with Actinomyces bacteraemia from two tertiary care centres from 1 January 2006 to 26 September 2021. Data were collected on demographic and clinical characteristics, comorbidities, primary source of infection and outcomes. True bacteraemia was defined as Actinomyces bacteraemia with systemic manifestations of infection.Results. A total of 82 cases of positive blood cultures were identified, of which 33 (40.2%) were true bacteraemia, based on clinical criteria. Patients with true bacteraemia were more likely to be older (P=0.007), have chronic skin ulcers (P<0.001), have a history of central line placement within 3 months of their presentation (P=0.04), have had a fever within 72 h of admission (P=0.05) and have presented with an abscess (P<0.001) compared with patients with transient bacteraemia. True bacteraemia was more likely to be associated with positive tissue cultures (P=0.02) and an infectious disease consultation than transient bacteraemia. Skin and soft tissue (27.3%) was the most common source followed by intra-abdominal (21.1%). Among true bacteraemia, the most common species was Actinomyces meyeri with a ratio of 1:8 (transient versus true bacteraemia). All-cause mortality was 30.3% in patients with true bacteraemia compared with 4.1% in patients with transient bacteraemia (P<0.001).Conclusion. Predictors of true Actinomyces bacteraemia included older age, fever within 72 h of admission, presence of abscess and chronic skin disease. Actinomyces species exhibit varying degrees of invasiveness, with A. meyeri potentially showing higher invasive potential. Better awareness and involvement of infectious disease specialists is recommended in determining the clinical significance of transient Actinomyces bacteraemia and can help implement antibiotic stewardship and patient safety and improve outcomes. Further research will help to identify the true importance of these isolates.