Journal of medical microbiology最新文献

Introduction. Gastrointestinal infections remain a leading cause of morbidity and mortality within the UK.Hypothesis. The Luminex^® NxTAG^® Gastrointestinal Pathogen Panel (NxTAG GPP) multiplex reverse transcriptase PCR assay performs equivalently to standard-of-care diagnostic approaches.Aim. To compare the analytical performance of the NxTAG GPP assay versus routine diagnostic testing methods in a district general hospital setting.Methodology. Gastrointestinal pathogens in 159 faecal specimens from hospital inpatients and outpatient clinics were comparatively analysed using the NxTAG GPP assay versus traditional culture, enzyme immunoassay and molecular methods.Results. Positive results were detected in 45 out of 159 specimens (28.3%) by NxTAG GPP, which was a higher positivity rate when compared with traditional diagnostic methods which detected 31 out of 159 (19.5%) positive infections (P=0.087 by Fisher's exact test). Infections were caused by a single organism in 40 out of 45 (88.9%) cases, but 5 out of 45 (11.1%) infections detected were due to coinfections. No coinfections were detected by traditional methods. Campylobacter Group was the most common enteropathogen detected with 15 out of 52 (28.9%) infections. Viruses caused 26.9% of infections, including 15.4% being norovirus. Overall sensitivity, specificity and accuracy for the NxTAG GPP assay were 97.6%, 99.7% and 99.5%, respectively, for enteropathogenic bacteria and viruses detected during this study. No parasites were detected during this study and were not included in comparisons.Conclusions. The NxTAG GPP assay demonstrated high sensitivity and specificity for identifying gastrointestinal pathogens, with comparable accuracy as more resource-intensive and time-consuming standard diagnostic approaches. The NxTAG GPP has the potential to enhance patient diagnosis, reduce turnaround time and improve clinical outcomes compared to routine diagnostic methods.

Introduction. Peri-implantitis is a prevalent and challenging complication in implant dentistry, primarily induced by biofilm-associated pathogens. Among these, Porphyromonas gingivalis and Filifactor alocis have emerged as key contributors, with evidence suggesting their potential synergistic role in exacerbating peri-implant inflammation and tissue destruction.Hypothesis/Gap Statement. While P. gingivalis is a well-characterized periopathogen, the specific role of F. alocis, alone or in combination with P. gingivalis, in peri-implantitis remains underexplored. This study addresses the gap in quantifying their presence in diseased versus healthy peri-implant sites.Aim. To assess the prevalence and microbial load of P. gingivalis and F. alocis in peri-implantitis and healthy peri-implant sites using quantitative real-time PCR (qPCR) and to investigate their correlation with clinical parameters.Methodology. This cross-sectional study included 110 participants: 52 diagnosed with peri-implantitis and 58 with healthy peri-implant tissues. Clinical examination recorded probing depth (PD), clinical attachment level (CAL) and bleeding on probing (BOP). Submucosal biofilm samples were collected and analysed using species-specific qPCR. Statistical analysis employed the Mann-Whitney U test for intergroup comparisons and Spearman's rank correlation for associations between microbial levels and clinical indices.Results. Both P. gingivalis and F. alocis were significantly elevated in peri-implantitis sites compared to healthy controls. Mean P. gingivalis levels were 4.80×10⁶ ± 4.78×10⁶ copies µl^-1 in peri-implantitis and 2.09×10³ ± 1.26×10³ copies µl^-1 in healthy sites (P<0.001). F. alocis levels averaged 4.58×10⁵ ± 3.40×10⁵ copies µl^-1 in peri-implantitis and 2.45×10³ ± 1.64×10³ copies µl^-1 in healthy sites (P<0.001). P. gingivalis showed strong positive correlations with PD, CAL and BOP, while F. alocis correlated moderately with PD and CAL but not significantly with BOP.Conclusion. The significant elevation of P. gingivalis and F. alocis in peri-implantitis supports their potential synergistic involvement in disease pathogenesis. These findings underscore the need for antimicrobial strategies that target both organisms and disrupt their cooperative biofilm behaviour. Further research should clarify their pathogenic interplay and inform the development of precise therapeutic interventions.

Introduction. The cagA and vacA genes encode the CagA and VacA proteins, which are the two main toxins of Helicobacter pylori. Regardless of whether the illness is benign or malignant, the majority of Asian H. pylori strains are cagA (+) and vacA s1 (vacA signal region 1 allele); hence, these genotypes cannot account for the severity of gastroduodenal disease.Gap statement. The babA2 gene encodes the important adhesin BabA of H. pylori, which is crucial for persistent colonization and facilitates the translocation of CagA into host gastric epithelial cells. The synergic interaction of toxins, including CagA, VacA and BabA, could significantly contribute to the pathogenesis of H. pylori. The investigation of cagA, vacA and babA2 genes in clinical H. pylori isolates in Asian nations, particularly Vietnam, is insufficient.Aim. To investigate the cagA, vacA and babA2 genotypes to further understand their synergistic interaction in the development of gastroduodenal disease in Vietnamese populations.Methodology. A cross-sectional study was conducted on 169 H. pylori strains isolated from patients with gastroduodenal disease. The PCR assays were performed to determine the cagA, vacA and babA2 genotypes on DNA extracted from cultured H. pylori isolates.Results. The research showed that the percentage of the cagA(+), babA2(+), vacA s1m1 and vacA s1m2 was 87.6%, 73.4%, 52.1% and 44.4%, respectively. The frequencies of cagA(+)/babA2(+)/vacAs1m1 and cagA(+)/babA2(+)/vacAs1m2 combinations were 44.4% and 28.4 %, respectively. The cagA(+)/babA2(+)/vacAs1m2 combination was associated with peptic ulcer disease [adjusted odds ratio (aOR)=5.53, 95 % confidence interval (CI) 1.09-28.16, P=0.039] in male patients and chronic gastritis with precancerous lesions (aOR=5.31, 95 % CI 1.23-22.89, P=0.025) in female patients.Conclusion. The cagA(+)/babA2(+)/vacAs1m1 and cagA(+)/babA2(+)/vacAs1m2 combinations were found to be quite prevalent among Vietnamese H. pylori strains. The synergistic effect of cagA(+), babA2(+) and vacA s1m2 in increasing the odds of both peptic ulcer disease and gastric precancerous lesions has been observed.

Introduction. In antibiotic chemotherapy, an antimicrobial agent is selected based on MIC, which is determined by a test method using the principle of the broth microdilution. However, it does not provide a viable count in the mutant selection window. In this study, we used turbidimetry and visual judgement to examine the validity of the selection of various antibiotics to treat Pseudomonas aeruginosa based on MIC determination after 24 h of incubation.Methods. The antibiotics used in this study were piperacillin (PIPC), imipenem (IPM), meropenem, ciprofloxacin and amikacin (AMK). The strains used were 30 P. aeruginosa strains clinically isolated that were susceptible to all the antibiotics used, and the standard PAO1 strain. The viable count was measured after exposure for 3 and 24 h to therapeutic concentrations of various antibiotics, at which time turbidity was examined visually or by transmittance. In addition, the MPCs of IPM and PIPC were measured.Results. In this study, 10²-10⁸ c.f.u. ml^-1 of P. aeruginosa survived exposure to PIPC, IPM and AMK at concentrations 2.5-80 times the MIC despite high drug concentrations. No turbidity was observed in the culture medium. Furthermore, both IPM and PIPC showed high mutant prevention concentration (MPC), with 64.5% of strains in IPM and 10% of strains in PIPC showing intermediate or resistance after 24 h.Conclusions. Choosing an appropriate antibiotic based on exceeding the MIC may be insufficient. While the PK/PD theory focuses on MIC, measuring MPC alongside MIC is urgent in clinical practice for optimal antibiotic selection.

Introduction. Six to seven million individuals are infected with Trypanosoma cruzi, the causative agent of Chagas disease. With 12,000 deaths annually, chronic Chagas disease remains a significant global health challenge due to persistent vector transmission, increasing non-vector transmission and limited therapeutic options. Chronic Chagas cardiomyopathy is a leading cause of morbidity and mortality, yet the underlying mechanisms remain poorly understood.Gap Statement. Since its initial description more than 100 years ago, research efforts into the cardiomyopathy found in chronic Chagas disease have primarily focused on the contributions of immune cells, cardiomyocytes and cardiac fibroblasts, leaving a significant gap in understanding the role of microvascular endothelial dysfunction in disease progression.Aim. The aim of this study was to identify any morphological or functional changes to cardiac microvascular endothelial cells induced by T. cruzi infection with the potential to contribute to the pathologies found in chronic Chagas disease.Methodology. We cultured primary cardiac microvascular endothelial cell monolayers in vitro and infected them with T. cruzi trypomastigotes or exposed them to conditioned media collected from control or infected endothelial cells. Cells were analysed for changes in morphology and proliferation, by wound healing assays for measurements of migratory capacity and by tube-forming assay to characterize their ability to form capillary-like structures.Results. We show that T. cruzi infection leads to the development of hypertrophic multinuclear cells, inhibits endothelial proliferation, increases endothelial migration and results in changes in several aspects of angiogenesis.Conclusion. We present data to demonstrate morphological and functional changes in cardiac endothelial cells that occur as a result of T. cruzi infection and propose that these changes may contribute to endothelial dysfunction and the development of chronic Chagas cardiomyopathy.

Introduction. Candida glabrata is a pathogenic yeast in humans, recognized for its genomic plasticity and increasing prevalence of antifungal resistance, including multidrug-resistant phenotypes, especially in the US and European countries.Hypothesis. This study hypothesizes that the resistance mechanisms in clinically resistant strains of C. glabrata differ from laboratory-generated resistant strains.Aim. This study aims to understand the resistance mechanism in Indian clinical isolates of C. glabrata. Methodology. A total of 240 clinical isolates of C. glabrata were tested for antifungal susceptibility and one resistant strain was artificially synthesized in the laboratory. Both clinical and lab-generated resistant strains were analysed for antifungal resistance using methods such as phenotypic assays, real-time quantitative PCR, Fluorescence-activated cell sorting (FACS) analysis and targeted gene sequencing. Mechanisms involving drug efflux pumps, mismatch repair pathways, ergosterol biosynthesis pathway and biofilm formation were systematically studied.Results. Among clinical isolates, one susceptible-dose dependent strain and three fluconazole-resistant strains were identified. Both clinical and lab-generated resistant strains demonstrated antifungal resistance phenotypically, with increased expression of CDR1. Targeted gene sequencing revealed novel mutations in PDR1, while mutations in MSH2 served as genotypic markers for resistance. Overexpression of ERG11 was seen in a lab-generated resistant strain where a specific mutation was identified. Biofilm activity contributed to resistance in one of the clinical strains.Conclusion. This study reports for the first time the fluconazole resistance mechanism in C. glabrata from India. The findings underscore the diversity of resistance mechanisms among clinical and lab-generated isolates, emphasizing the need for novel antifungal therapies to address these emerging resistance profiles effectively.

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.