European Journal of Clinical Microbiology & Infectious Diseases最新文献

Purpose

We aimed to determine the changes in the frequency of respiratory pathogens and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during containment of the 2019 coronavirus disease pandemic and elucidate the epidemiological interference that may have occurred after lifting pandemic measures.

Methods

A total of 4,770 Nasopharyngeal swab samples were collected from children with ARTIs from the First People’s Hospital of Yunnan Province between January 2022 and December 2023 and subjected to nucleic acid testing for 13 types of respiratory pathogens and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Results

The frequency of pathogens among children from 2020 to 2022 was in the following order: HRV > Mp > HADV > H3N2 > HMPV and HRV > HRSV > HPIV > H1N1 > H3N2. In weeks 1 to 3 of 2023, the frequency of pathogens significantly declined, and then H1N1 rebounded significantly in 2023. HRV, HRSV, and H3N2 showed a shift in the season of high frequency. Patterns of multi-pathogen infections were more complex in 2023 than in 2022, with HRV having a higher frequency and co-infection rate than other pathogens. These changes may have been associated with interference caused by the resurgence of SARS-CoV-2 prevalence, in addition to being influenced by changes in pandemic containment and lifting measures.

Conclusions

The frequency rate of common respiratory pathogens among children was not significantly different and remained high. The study findings help elucidate the aforementioned unique historical period and effectively control respiratory tract infections to reduce the harm to pediatric health caused by respiratory pathogens.

Purpose

Malaria keeps on being a serious global health threat, especially in many tropical countries, where it is endemic. Also in non-endemic countries, like Spain, malaria is an issue that requires attention due to the presence of imported cases.

Methods

This is a retrospective study, including all patients diagnosed with malaria at Severo Ochoa University Hospital from 2006 to 2022, being classified according to: (I) their type of stay in an endemic area as visiting friends and relatives (VFR), migrants of recent arrival (MRA), or tourism and business (T&B), and (II) the mode of presentation as microscopic (MM) or submicroscopic (SMM) malaria.

Results

In this study, 132 patients (23.7% of all suspected) were diagnosed with malaria. The PCR was the most sensitive technique (99.2%), followed by antigen detection (78.8%) and microscopy (75%), with Plasmodium falciparum being the predominant species (94.7%). VFR was the largest group infected with malaria (69.7%), mostly symptomatic (98.2%) and presenting MM (90.2%). Instead, MRA patients (25%) presented milder (47.4%) or no symptoms (31.6%) and higher cases of SMM (42.4%). Coinfection with another imported pathogen was present in 19 patients (14.4%), being MRA more frequently coinfected (30.3%)

Conclusion

This study shows the need for establishing systems for VFRs to attend pre-travel consultations to reduce malaria imported risk. In the case of MRA, screening for imported diseases should be conducted upon their arrival. Finally, we highlight two cases of co-infection with imported viruses, showing that presence of symptoms resembling malaria from another imported pathogen does not exclude malaria.

This study investigated the molecular characteristics of urinary carbapenemase-producing Klebsiella pneumoniae isolates (n = 194) in Gauteng, South Africa, using simple, cost-effective PCR methodologies. Extensively drug resistant (XDR) ST307 with bla_OXA-181 on IncX3 plasmids was endemic in Gauteng community hospitals leaving limited options for treating in- and outpatient urinary tract infections. High-level ceftazidime/avibactam resistance was detected among isolates harbouring bla_OXA-48-like including bla_OXA-181. These findings highlighted the need for genomic methodologies suitable for lower- and middle-income countries to track XDR clones and plasmids in community hospitals. Such results will aid with treatment and stewardship strategies.

Purpose

Urinary Tract Infections (UTIs) are among the most prevalent infections globally. Every year, approximately 150 million people are diagnosed with UTIs worldwide. The current state-of-the-art diagnostic methods are culture-based and have a turnaround time of 2–4 days for pathogen identification and susceptibility testing.

Methods

This study first establishes an optical density culture-based method for spiking healthy urine samples with the six most prevalent uropathogens. Urine samples were spiked at clinically significant concentrations of 10³-10⁵ CFU/ml. Three DNA extraction kits (BioStic, PowerFood, and Blood and Tissue) were investigated based on the DNA yield, average processing time, elution volume, and the average cost incurred per extraction. After DNA extraction, the samples were sequenced using MinION and Flongle flow cells.

Results

The Blood and Tissue kit outperformed the other kits based on the investigated parameters. Using nanopore sequencing, all the pathogens and corresponding genes were only identified at a spike concentration of 10⁵ CFU/ml, achieved after 10 min and 3 hours of sequencing, respectively. However, some pathogens and antibiotic-resistance genes (ARG) could be identified from spikes at 10³ colony formation units (CFU/mL). The overall turnaround time was five hours, from sample preparation to sequencing-based identification of pathogen ID and antimicrobial resistance genes.

Conclusion

This study demonstrates excellent promise in reducing the time required for informed antibiotic administration from 48 to 72 h to five hours, thereby reducing the number of empirical doses and increasing the chance of saving lives.

Purpose

Loop-mediated isothermal amplification (LAMP) is a simple and rapid nucleic acid method for DNA amplification at a constant temperature. The “gold standard” culture method for yeast detection, has low sensitivity with severe consequences, increasing morbidity and mortality rates. Here, we report the development of a LAMP method for the specific detection of C. glabrata.

Methodology

The specific LAMP primers for C. glabrata detection were designed and evaluated.

Results

The LAMP assay accurately detected C. glabrata with no cross-reactivity with other Candida species.

Conclusion

The developed molecular method would be a promising tool in the management of invasive candidiasis.

Purpose

Predicting infection risk in carbapenem-resistant Acinetobacter baumannii (CRAB) colonized patients may help in improving timely appropriate antibiotic therapy. This study aims to explore risk factors for developing infections in hospitalized patients with previous CRAB colonization.

Methods

We performed an observational retrospective cohort study at ASST Sette Laghi-Varese Hospital between January 2020 and December 2022. All consecutive adult (> 18 years old) hospitalized patients with documented colonization by CRAB at any anatomical site or with CRAB infections preceded by CRAB colonization were included. Univariate and multivariate analyses were performed to investigate infection risk factors.

Results

Overall, 144 patients were included in the study: 104 colonized only and 40 infected patients. Colonization and infection rates significantly changed over the years (2020–2022, p < 0.001). The incidence of infections in CRAB carriers was 27.8% (40/144). Median time from colonization to infection was 4 days (IQR 1-8.5). Overall, inhospital mortality was 32.7% and 55.0% in colonized only and infected patients, respectively. At the multivariable logistic regression cardiovascular disease (OR 5.83, 95% CI 1.12–30.43, p = 0.037), COVID-19 (OR 3.72, 95% CI 1.16–11.91, p = 0.027) and intensive care unit (ICU) admission (OR 8.83, 95% CI 2.94–26.51, p < 0.001) were risk factors independently associated with cardiovascular disease CRAB infection after colonization.

Conclusions

We observed an increased infection risk in patients colonized with CRAB with cardiovascular disease, COVID-19 and admitted in ICU setting. Additional evidence is needed to identify predictors of infection in colonized patients.

Oropouche virus is the aetiological agent of Oropouche fever. At present, this is currently considered one of the most important vector-borne diseases in Latin America. On 27 May 2024, the Ministry of Public Health of Cuba reported the first ever outbreak of Oropouche fever. In this report, we describe three human cases of Oropouche virus infection with symptoms and signs of neurological disease and clinical diagnosis of Guillain-Barré Syndrome. This study offers insights regarding that Oropouche virus is a causal agent of neurological disorders and it could be involved in the etiology of the Guillain-Barré Syndrome.

Mycoplasma pneumoniae, a frequent respiratory pathogen, can cause neurological disease manifestations. We here present a case of M. pneumoniae as cause of meningitis and occurrence of an intracranial abscess as a complication of mastoiditis with septic cerebral venous sinus thrombosis in a patient with multiple sclerosis on anti-CD20 therapy.

Purpose

To describe the long-term effects of an ASP among febrile neutropenia (FN) patients.

Methods

A quasi-experimental study was conducted between 2015 and 2023 at a tertiary care hospital in Istanbul, Türkiye. The ASP was implemented for FN patients, and the effects were assessed before and after the ASP interventions, which included FN clinical pathways and regular multi-disciplinary meetings with relevant healthcare workers.

Results

A total of 489 FN episodes of 290 patients were included, 42% were female, and the mean age was 56 years (SD: 15, range: 18–89 years). After the intervention, the rate of appropriate antimicrobial therapy at the levels of starting (p = 0.005), switching (p < 0.001), and de-escalation/discontinuation, (p < 0.001) significantly increased. Another positive impact of the ASP was a significant reduction in candidemia (from 4.88 to 0.74, p = 0.004), as well as a significant reduction in the 90-day mortality rate (from 19 to 5%, p < 0.001). In multivariate analysis, having a gram-negative bloodstream infection, prolonged days with fever, and a high risk for neutropenia were found to be significant predictors of 90-day mortality, while follow-up with ASP significantly reduced mortality.

Conclusion

Implementation of ASP led to reduced candidemia and LOS without increasing mortality, even in a country with a high rate of antimicrobial resistance. Implementation of sustainable ASP for FN patients is critical in combating antimicrobial resistance.

Purpose

The urinary tract is colonized by microbial communities that impact urinary health. Previous studies have suggested that the bacterial composition of the male urinary microbiota is related to STIs. This study assessed the bacterial composition of the urinary microbiome in South African MSM with and without C. trachomatis.

Methods

This study used urine samples from MSM attending care at the King Edward VIII hospital and the Aurum Institute in Durban, South Africa. A total of 200 samples were tested for C. trachomatis infection using the Applied Biosystems™ TaqMan^® Assays. Urinary microbiomes of 23 samples were characterized using 16 S rRNA (V3 and V4) gene sequencing on the Illumina MiSeq platform.

Results

Bacterial taxonomic analysis showed a high abundance of Streptococcus, Corynebacterium, and Staphylococcus in all the sequenced samples. Moreover, Prevotella and Lactobacillus were detected in urine samples of MSM. Alpha diversity metrics showed a slight increase in microbial diversity in C. trachomatis positive samples; however, this was not significant (ANOVA, P > 0.05). Principal coordinates analysis (PCoA) showed that the microbiome of C. trachomatis infected MSM was not clearly different from those uninfected. Distinct bacterial communities were not detected between positive and negative samples (PERMANOVA F_1,22= 1.0284, R² = 0.047%, P = 0.385).

Conclusion

Most microbiome studies on MSM to date have focused on the gut microenvironment. Few studies, however, have provided data regarding the normal composition of the male urethral microbiomes or if these microbiomes are associated with male STIs. This study adds to the growing body of knowledge highlighting the urinary microbiome in MSM.