Journal of medical microbiology最新文献

Introduction. Following two large foodborne outbreaks of the gastrointestinal pathogen, enteroaggregative Escherichia coli (EAEC), in Germany in 2011 and the UK in 2014, the UK Health Security Agency (UKHSA) implemented enhanced surveillance strategies for EAEC.Gap Statement. The surveillance of diarrhoeagenic E. coli in England focuses on Shiga toxin-producing E. coli (STEC), and the true clinical and community burden of EAEC is unknown. This gap extends globally, as many countries lack the infrastructure, diagnostic tools and healthcare facilities to resource surveillance programmes for EAEC.Aim. The aim of the study was to review the microbiological typing data and demographic data linked to isolates and cases diagnosed from 2016 to 2023 and to assess the risk to public health.Methodology. Faecal samples that tested positive by PCR for diarrhoeagenic E. coli at local microbiology diagnostic laboratories were referred to the UKHSA for confirmation and culture. Isolates identified as EAEC were sequenced on the Illumina HiSeq and NextSeq platforms. Sequence type, serotype and antimicrobial resistance (AMR) profile were derived from the genome sequence. Age, sex and travel histories were linked to the typing data.Results. There was a total of 1,402 notifications of EAEC, exhibiting a fivefold increase in diagnoses from 93 in 2016 to 524 in 2023. The most common sequence types (STs) were ST34 (n=202/1,402, 14.4%), ST10 (n=185/1,402, 13.2%), ST200 (n=183/1,402, 13.1%) and ST678 (n=101/1,402, 7.2%), and the most common serotypes were O92:H33 (n=130/1,402, 9.3%), O175:H31 (n=78/1,402, 5.6%) and O99:H10 (n=78/1,402, 5.6%). Most cases were female (n=748/1,372, 54.5%) and/or were aged <10 (n=387/1,372, 28.2%), within which 299 out of 387 (77.3%) were <5 years old. Of the 756 out of 1,386 (54%) cases that had a travel history, 597 out of 756 (79%) reported foreign travel within 7 days of onset of symptoms. AMR was detected in 1,030 out of 1,402 (73.5%) isolates with resistance to fluoroquinolone (n=810/1,402, 57.8%) and beta-lactam (n=807/1,402, 57.6%) antibiotics being the most common.Conclusion. Given the burden of disease caused by EAEC in the community, the high proportion of infections in children and travellers, the risk of the emergence of hybrid STEC/EAEC pathotypes and the high proportion of AMR, we recommend that EAEC should be part of the diagnostic algorithm in the UK.

Mycobacterium avium complex disease is difficult to treat, with high failure and recurrence rates despite multidrug, macrolide-based treatments. The bacterial mechanisms involved in this drug tolerance and persistence are incompletely understood. Recent evidence has suggested persistence through metabolic adaptations indicative of the viable but nonculturable state, including a decreased respiratory rate and a switch to lipid accumulation and metabolism. To assess the contribution of switching to viable but nonculturable state to macrolide tolerance, we performed time-kill kinetics assays for clarithromycin against M. avium. In these experiments, we performed Auramine-O (for acid-fastness, representing active mycobacteria) and Nile red (for lipid accumulation) staining and stimulation using resuscitation-promoting factors of Mycobacterium tuberculosis. Loss of auramine staining, increased Nile red staining and increased population sizes after stimulation with resuscitation-promoting factors support the hypothesis that clarithromycin induces a viable but nonculturable state in M. avium. Induction of a viable but nonculturable state is one of the mechanisms of macrolide tolerance in M. avium. It might be one of the drivers of the high failure and recurrence rates of macrolide-based treatments. Antimicrobials active against viable but nonculturable M. avium may improve treatment outcomes.

Introduction. Schmallenberg virus (SBV) is an arthropod-borne virus and belongs to the Simbu serogroup within the family Peribunyaviridae, genus Orthobunyavirus. Infection of naïve ruminants at critical stages of gestation can result in severe congenital malformations or abortion.Gap statement. Tools to measure virus infection parameters in cell culture such as replication efficiency, as well as neutralization assays, are mainly available in the form of assays based on the evaluation of cytopathic effects. The methods are labour-intensive and low-throughput, as they require long incubation periods of several days. Tools such as tagged SBV that allow for fast and automated readout are missing.Aim. We aimed to develop a tagged SBV that can be used for assays with fast and automated read-out.Methodology. We report the construction of a recombinant SBV stably expressing the nanoluciferase (nluc) enzyme (rSBV_nluc). Using reverse genetics, the nluc gene was integrated into the genome of an SBV variant naturally harbouring a large deletion within the Gc-head domain. The nluc gene was inserted into this locus.Results. The nluc-tagged virus showed in vitro no signs of attenuation and identical replication properties when compared to the parental virus in baby hamster kidney (BHK-21) cells. Our results demonstrate a new approach for rapid access to SBV replication. By performing nluc assays, we were able to track viral replication and also virus uptake in detail. We further evaluated neutralization properties of an SBV variant, which is lacking a major part of its antigenic domain (Gc-head) and developed a nanoluciferase activity-based serum neutralization assay.Conclusion. Overall, the nluc-tagged SBV is a suitable tool that further facilitates the study of viral infection dynamics and allows for high-throughput assays.

Introduction. Enterotoxigenic Escherichia coli (ETEC) are one of the leading causes of gastrointestinal infections globally, primarily affecting children in low- and middle-income countries and travellers to endemic regions.Gap Statement. The surveillance of diarrhoeagenic E. coli in England focuses on Shiga toxin-producing E. coli, and the true clinical and public health burden of ETEC is unknown. This gap extends globally, as many countries, particularly those in endemic regions, lack the infrastructure, diagnostic tools and healthcare facilities to resource surveillance programmes for ETEC.Aim. The aim of this study was to utilize available data to describe the epidemiology, genomic diversity and antimicrobial resistance (AMR) of ETEC in England.Methodology. A total of 587 isolates of ETEC cultured from faecal specimens referred to the Gastrointestinal Bacteria Reference Unit at the UK Health Security Agency for further testing, from 2015 to 2023, were sequenced to determine sequence type (ST), serotype, virulence and AMR profiles, and integrated with epidemiological data obtained from referral forms.Results. Overall, the number of ETEC notifications increased annually, with a 35.5-fold increase from 2015 to 2023. There were more female cases (51.7%) than males (48.3%), with the highest proportion of cases belonging to the 50-59 age group (18.6%). Nearly half of the cases (49.5%) were travel-associated, with Egypt, Pakistan, India, Turkey and Mexico being the top travel destinations. At least 139 STs and 132 serotypes were identified, with the most common ST-serotype profiles being ST4 O6:H16 (n=74) and ST182 O169:H41 (n=66). Genome-derived AMR data revealed widespread resistance to fluoroquinolones and β-lactams, including third-generation cephalosporins, and over 40% of isolates (n=239/587) were resistant to three or more classes of antimicrobials.Conclusion. We observed an increase in notifications of multidrug-resistant ETEC over the last decade, mainly associated with travellers' diarrhoea. Nationwide expansion of PCR-based diagnostics for ETEC, alongside strengthening collaboration with public health agencies and genomic data sharing at a local, national and international level, is critical for strengthening surveillance and accurately assessing the true burden of ETEC locally and on a global scale.

Introduction. Antimicrobial susceptibility testing (AST) of Neisseria gonorrhoeae isolates is recommended in the UK to ensure antimicrobial stewardship and detection of multi-drug and extensively resistant cases. In diagnostic and reference laboratories, this testing is primarily carried out via a gradient strip. However, agar dilution methodology may also be used for high-throughput testing.Gap statement. N. gonorrhoeae is not a validated species on all ETEST (bioMérieux, France) gradient strip formulations available, and, therefore, additional comparative validation data are required to support use in clinical laboratory settings.Aim. To determine the reproducibility of ETEST for AST of N. gonorrhoeae, and to demonstrate the comparability of susceptibility results obtained using agar dilution and gradient strip methods.Methodology. Modal ETEST MICs for six well-characterized World Health Organization N. gonorrhoeae control strains, against eight antimicrobials, were calculated. ETEST modal MICs were compared to published and local, historical agar dilution MICs. MICs were interpreted using European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. Concordance of ETEST modal MICs, within essential and categorical agreement, for each strain was calculated.Results. Overall, 95.80% of modal ETEST MICs were within essential agreement with published MICs. Where variance from exact concordance was noted, a systematic shift was observed to lower MICs in this study. On three occasions, variance from the published MIC resulted in a categorical classification change. On two occasions, the modal ETEST MIC in this study was two doubling dilutions lower than the published MIC. Neither resulted in a categorical classification change. When modal ETEST and agar dilution MICs were compared, overall essential agreement was 83.30%. However, this increased to 94.4% when concordance was analysed for clinically important antimicrobials: azithromycin, cefixime and ceftriaxone. Again, a systematic shift to lower MICs for ETEST was observed in this study. Categorical agreement was 83.3% for all antimicrobials and 100% for clinically important antimicrobials.Conclusion. Excellent concordance was demonstrated for MICs generated using ETEST with published MICs. Good concordance was observed for MICs generated using two different susceptibility testing methodologies. Where variance was noted, MICs generally read lower on ETEST in this study. ETEST remains fit for purpose for the AST of N. gonorrhoeae, a clinically important pathogen.

Introduction. The TriVerity™ test (Inflammatix Inc.) uses the patient's mRNA expression patterns from whole blood to provide a site-agnostic likelihood of bacterial infection and/or viral infection. The test also reports an illness severity score, an all-cause predictor of the need for critical care (mechanical ventilation, vasopressor therapy or renal replacement therapy) within 7 days of testing.Hypothesis/Gap Statement. Differentiating the source and assessing disease severity in patients presenting to the emergency department (ED) with signs and symptoms of sepsis remains an unmet medical need.Aim. The results of the TriVerity test were compared to the EPIC sepsis score, systemic inflammatory response syndrome criteria, discharge diagnoses, location of patient discharge and an assessment of potential cost savings in unnecessary resource utilization.Methodology. Blood was retained from 30 patients presenting to the ED with signs and symptoms suggestive of sepsis. Remnant EDTA-preserved blood from routine medical testing was transferred into PAXgene tubes, stored frozen and retrospectively tested with TriVerity.Results. TriVerity was correctly correlated with clinical diagnosis and outcomes in 29 of 30 patients with one false negative (low severity score for sepsis diagnosis, admitted for bladder cancer and on pre-existing antibiotic therapy). For two patients with a positive TriVerity bacterial and severity score, antibiotic treatment may have been initiated 6-9 h earlier if tested prospectively. Twelve patients were discharged home with a mean ED length of stay of 7.25 h, of which 7 (58 %) had a positive EPIC sepsis score (>5) and all had a low TriVerity severity score. If this test were performed prospectively at ED presentation, a net savings of $351 per patient is estimated in direct laboratory, radiology and ED costs alone, without consideration of potentially shorter hospital stays or changed disposition.Conclusion. The TriVerity test may enable early consideration of ruling in or out of bacterial and/or viral infection, provide severity assessment of adult patients presenting to the ED suspected of, and help reduce unnecessary utilization of laboratory and ED resources.

Clostridioides difficile infection is a global issue, representing a huge financial burden on healthcare systems worldwide which is further exacerbated by high recurrence rates. Infection is closely linked with the gut microbiome status, with successful C. difficile colonization usually occurring when there is dysbiosis. Our understanding of the molecular mechanisms underlying microbiota-mediated colonization resistance has advanced significantly in recent years, although the nuanced crosstalk occurring between C. difficile, the gut microbiota and host mucosa has yet to be fully elucidated. Deciphering these three-way interactions is critical for the development of effective therapeutic and prophylactic strategies. This review will discuss known interactions between this pathogen, the microbiota and the host in addition to the tools available to dissect complex microbial interchanges.

Introduction. Intestinal dysbiosis is associated with systemic health, and approaches targeting the microbiome can influence the host. Oral and intestinal microbiota are interrelated; therefore, we aimed to determine whether non-surgical periodontal treatment (NSPT) affects systemic health through its impact on the intestinal microbiota.Hypothesis/Gap Statement. Although the association between oral and gut microbiota has been suggested, there is limited evidence regarding how periodontal therapy may influence intestinal microbial composition. We hypothesized that NSPT in patients with periodontitis would lead to favourable changes in the gut microbiome, which may parallel improvements in clinical periodontal parameters.Aim. This study aimed to investigate the effect of NSPT on both oral and intestinal microbiota and to evaluate whether changes in gut microbial composition correlate with periodontal clinical outcomes.Methodology. Five systemically healthy individuals with grade C periodontitis and five systemically and periodontally healthy individuals were included. Saliva and stool samples were collected at baseline and 1 month after NSPT. DNA extractions were performed and subjected to 16S ribosomal RNA gene sequencing on the Illumina Novaseq at the V3-V4 hypervariable regions.Results. Grade C periodontitis patients displayed distinct oral and gut microbiomes compared to healthy individuals. NSPT resulted in a reduction in the diversity of both saliva and stool samples in healthy individuals (P>0.05). Salivary Fusobacteriota levels (P<0.05) and the gut Firmicutes/Bacteroides ratio decreased after NSPT. Moreover, changes in gut microbiota significantly correlated with improvements in periodontal probing depth and clinical attachment level in periodontitis patients.Conclusion. The improvement in clinical periodontal parameters after NSPT correlates with a positive shift in the gut microbiome towards health. Although the number of participants was limited, these findings support a strong relationship between periodontal and gut status. Further studies with larger cohorts and long-term follow-up are required to confirm these results.

Introduction. Klebsiella pneumoniae (Kp) is a major cause of nosocomial infections, with its evolving pathotypes including multidrug-resistant, hypervirulent (hvKp) and convergent strains posing significant diagnostic and treatment challenges due to combined antimicrobial resistance and virulence.Gap Statement. While there is a pressing requirement for thorough detection of Kp pathotypes, current assays in resource-limited environments are unable to effectively focus on essential carbapenemase and hypervirulence genes with the necessary reliability and precision.Aim. To develop and validate a multiplex PCR (m-PCR) assay capable of simultaneously detecting Kp isolates including those carrying partial or full virulence markers, alongside antimicrobial resistance.Methodology. In this study, an m-PCR assay was designed and optimized for the simultaneous detection of key biomarkers associated with hypervirulent (rmpA, rmpA2, iucA, peg344 and iroB), carbapenem-resistant (bla _NDM, bla _OXA-48-like and bla _KPC) and convergent Kp pathotypes in clinical isolates. The assay was evaluated on clinical isolates and validated against whole-genome sequencing (WGS) data for accuracy, specificity and sensitivity.Results. The developed m-PCR assay exhibited 100% specificity when compared to WGS data, successfully detecting all target genes without cross-amplification in ATCC control strains. The assay demonstrated high sensitivity, efficiently amplifying bacterial genomes from minimal DNA input as low as 1 ng µl^-1. Additionally, validation through sequencing confirmed the accuracy of detected amplicons.Conclusion. This m-PCR assay offers a rapid, sensitive and specific diagnostic tool for differentiating Kp pathotypes in clinical settings, aiding in timely intervention and improved infection control measures.