Journal of medical microbiology最新文献

Introduction. Nosocomial infections, particularly those caused by Gram-negative bacilli, indeed pose significant challenges in healthcare settings. Hospital staff can act as carriers of these infections, potentially transmitting them to patients and colleagues. Propolis, a natural resinous substance collected by honeybees, has shown promising antibacterial properties against various microorganisms, including Gram-negative bacteria like Escherichia coli and Klebsiella pneumoniae.Hypothesis/Gap Statement. Despite the documented antibacterial properties of propolis, limited research has evaluated its efficacy against clinical isolates from healthcare workers, particularly in Iran.Aim. To evaluate the in vitro effect of propolis on K. pneumoniae and E. coli isolated from the nose and nails of hospital personnel in Qazvin.Methodology. Fifty Gram-negative bacilli were isolated from the nose and nails of hospital personnel in Qazvin. An antibiotic sensitivity test was conducted using the disk diffusion method based on CLSI 2024 guidelines for various antibiotics. The most common isolated strain was analysed using enterobacterial repetitive consensus PCR (ERIC-PCR). Finally, the microbroth dilution method was used to assess the antibacterial effect of propolis on the isolated strains.Results. The most frequent pathogens were K. pneumoniae (66%) followed by E. coli (34%). Most of the isolates were sensitive to the majority of antibiotics tested, and the highest antibiotic resistance was observed in trimethoprim/sulfamethoxazole (55%), ceftazidime (32%) and tetracycline (26%). Extended-spectrum beta-lactamase production was found in 10% of isolates of all Gram-negative bacteria. Additionally, 24% of the strains were multidrug-resistant. ERIC-PCR analysis revealed high genetic diversity among K. pneumoniae strains, which were the most common strains isolated from personnel. The MIC of propolis for both K. pneumoniae and E. coli was 5%, and the minimum bactericidal concentration was 10% after culturing 100 µl on Mueller-Hinton agar.Conclusion. The present study showed that the isolates from the nose and nails of hospital personnel may pose a serious issue in the field of public health. These findings suggest that Iranian bee propolis has medicinal value as a natural product and was identified as an antimicrobial substance with positive effects on bacterial strains isolated from hospital personnel.

Introduction. Mycoplasma genitalium, a small and slow-growing bacterium, has gained notoriety due to rapidly increasing rates of antibiotic resistance.Gap Statement. M. genitalium is difficult to culture, limiting efforts to understand its biology and the mechanisms of antimicrobial resistance.Aim. To understand factors that influence success in primary isolation of M. genitalium from clinical samples.Methodology. Neat urine or swabs (high vaginal and anal, in universal transport medium) were collected from patients with confirmed or suspected M. genitalium infections attending the Melbourne Sexual Health Centre. The specimens were stored at -80 °C prior to laboratory analysis. Initial diagnosis was by transcription-mediated amplification (TMA) assay, and samples subsequently testing positive by quantitative PCR (qPCR) were washed twice and inoculated into Vero cell monolayers with a selective antibiotic mixture (cycloheximide and Thayer-Martin Medium I). Cultures were incubated at 37 °C with 5% CO₂ for 8 weeks and observed daily, with qPCR used to monitor growth.Results. In total, 127 TMA-positive samples were subjected to qPCR, and M. genitalium genomic DNA (gDNA) was detected in 53.5% (68/127) of these samples. An isolate was obtained from 26.5% (18/68) of the gDNA-positive samples following co-culture with Vero cells. The isolation rate varied between sample types, with growth detected in 12.5% (3/24) of the high vaginal swabs and 37.5% (15/40) of the urine samples. No isolates were obtained from anal swabs. The proportion with a successful culture was influenced by the initial M. genitalium load in the sample, which translated into the inoculum size for the Vero cell monolayer. Isolation was unsuccessful with low inoculum (<2,000 genome equivalents, geq), partially successful (13.3%) with a moderate inoculum (2,500-9,500 geq) and highly successful (100%) in samples with a high inoculum (>10,000 geq).Conclusion. The initial bacterial load emerged as a critical determinant of isolation success. This emphasizes the importance of optimizing sample collection and M. genitalium isolation procedures.

Introduction. Since 2005, the leading cause of death for western chimpanzees (Pan troglodytes verus) at Tacugama Chimpanzee Sanctuary (TCS) in Sierra Leone has been epizootic neurologic and gastroenteric syndrome (ENGS), associated with the bacterium Sarcina troglodytae (family Clostridiaceae).Gap Statement. The prevalence of S. troglodytae at TCS in clinically normal chimpanzees and the environment remains unknown, as does its distribution in other captive and wild chimpanzee populations and their environments across Africa.Aim. The aim of this study was to determine the distribution and prevalence of Sarcina bacteria in sanctuary and wild chimpanzee populations across Africa and to identify demographic and ecological risk factors for S. troglodytae in chimpanzees and the environment.Methodology. We conducted a prospective, multi-season epidemiological investigation of S. troglodytae in chimpanzees and the environment at TCS and a parallel study at a sanctuary in the Republic of Congo. We also describe the results of surveys of chimpanzees at a sanctuary in Uganda and wild chimpanzee populations in Sierra Leone and Uganda for S. troglodytae. In total, we tested 637 chimpanzee and environmental samples using a species-specific PCR for S. troglodytae and a pan-Sarcina PCR.Results. S. troglodytae was more prevalent in chimpanzees at TCS (n=60) during the dry season (96.7%) than during the rainy season (55.2%). Soil was the most common environmental source of the bacterium (54% dry season vs. 4.8% rainy season). Notably, we did not detect S. troglodytae in faecal samples from sanctuary chimpanzees in the Republic of Congo (n=79) or in wild chimpanzees in Sierra Leone (n=18). We did detect the bacterium in East African chimpanzees (n=84) but at low prevalence (2.6%-10.9%). In contrast, we found the genus Sarcina to be ubiquitous in all chimpanzee populations with a higher prevalence in sanctuary chimpanzees (93.1%-100%) than in wild chimpanzees (66.7%-68.4%).Conclusion. S. troglodytae is markedly more prevalent at TCS, the only location affected by ENGS, than at any other location tested, and soil is a likely reservoir of S. troglodytae. These findings strengthen the association between S. troglodytae and ENGS and have implications for sanctuary management and conservation of western chimpanzees.

Introduction. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS for rapid identification of risk group 3 (RG3) bacteria is impeded by the following two main limitations: (a) equipment and maintenance costs for instruments placed within containment and (b) lack of a validated inactivation protocol to move RG3 material to a lower containment level. A validated inactivation method would improve operations of public health laboratories by allowing safe triage of potential RG3 agents. Albeit a validated, zero-risk inactivation protocol is unlikely, scientific interrogation of methods to identify and mitigate procedural biosafety risks is vital for institutional risk assessment.Gap. To investigate the effect of a standard MALDI-TOF chemical extraction, hypothesized to alter cells, allowing passage through a filter and maintaining ability to replicate, this study paired visualization using a scanning electron microscope (SEM) with extended viability testing.Aim. This work is intended to support risk assessments for the removal of material from a containment laboratory for MALDI-TOF MS.Methodology. A standard set of Bacillus cereus and Bacillus anthracis vegetative and spore preparations was treated with a formic acid:acetonitrile extraction, with or without filtration, and plated on five types of media to monitor growth over 14 days. SEM images were taken of treated and untreated preparations, prior, during and after filtration across two filters. Reference beads provided accurate pore size measurements.Results. SEM demonstrated no difference in treated and untreated cells but did indicate the ineffectiveness of cellulose filters compared to PVDF filters. Growth was observed in preparations that did not include PVDF filtration, whereas all preparations (n=60) that included PVDF filtration were 100% non-viable. Although non-viability was observed, an important finding was the passage of 0.262 and 0.173 µm microspheres through the 0.1 µm PVDF filter. Growth of unfiltered preparations was detected between 1 and 7 days.Conclusions. This investigation demonstrates the value of interrogating materials used for bacterial inactivation, highlighting significant issues in the application of filters for exclusion purposes. Visual examination via SEM was key to providing evidence towards a low-risk inactivation method. These findings, with an understanding of limitations identified herein, can be used to inform risk assessments for the removal of RG3 bacteria from containment.

Introduction. Healthcare-associated infections (HAIs) significantly contribute to the burden of antimicrobial resistance. A major factor in HAIs is the colonization of indwelling medical devices by biofilm-forming opportunistic pathogens such as Candida albicans and Staphylococcus aureus. These organisms frequently co-infect, resulting in synergistic interactions with enhanced virulence and resistance to treatment.Hypothesis/Gap statement. C. albicans and S. aureus readily form dual-species biofilms on silicone elastomers, a commonly used medical device material, yet the colonization phenotypes of these organisms on such surfaces remain poorly understood.Aim. We aimed to develop a simple, optically tractable model to mimic the colonization of indwelling medical devices to investigate C. albicans and S. aureus biofilm formation.Methodology. The system utilizes discs of a silicone elastomer embedded in agar, reflecting device-associated conditions and enabling high-resolution imaging of biofilms formed by C. albicans and S. aureus co-cultures.Results. Initial results using the silicone elastomer colonization model reveal robust biofilm formation. These biofilms exhibited morphological differences between dual-species biofilms formed by S. aureus co-cultures with either yeast- or hyphal-form C. albicans, indicating the impact of differing C. albicans cell morphotypes in biofilm-associated medical device colonization on silicone elastomers. Quantification of biofilm formation by crystal violet staining provided further validation of the system.Conclusion. These findings underscore the importance of developing tools for biofilm study which more closely resemble the infectious microenvironment, with our work detailing such a system which can be employed in further study to improve strategies against device-related HAIs.

Introduction. Urinary tract infections (UTIs) are a significant global health concern, with Escherichia coli being the predominant pathogen responsible for uncomplicated and complicated cases. Fosfomycin has emerged as a promising oral treatment option for multidrug-resistant UTIs, particularly those caused by extended-spectrum β-lactamase (ESBL)-producing E. coli. However, fosfomycin resistance has been paralleled by its irrational use and the emergence of enzymes that modify fosfomycin in ESBL-producing Enterobacteriaceae, especially in Asia.Hypothesis/Gap Statement. There is limited data on the prevalence of fosfomycin resistance among UTI patients in Northern Haryana, India. We hypothesize that demographic factors such as age, gender and patient type (inpatient vs. outpatient) may influence the prevalence of fosfomycin resistance and also provide insights into the effectiveness of fosfomycin in combating ESBL-producing E. coli infections in a tertiary care setting.Aim. This study aimed to investigate the prevalence of fosfomycin resistance among ESBL-producing E. coli among UTI patients in a tertiary care hospital.Methodology. Between March 2023 and February 2024, 7,348 urine samples were received from patients suspected of UTIs. The samples were subjected to screening using wet film examination and standard microbiological methods. Antibiotic susceptibility testing was done by VITEK-2 Compact (using an N-235 card), and ESBL production was confirmed using the combination disc diffusion test.Results. Out of 7,348 urine samples, 1,176 (16%) were culture-positive, with E. coli accounting for 57% of the isolates. Among the 385 E. coli isolates, 224 (58%) were ESBL producers. Fosfomycin demonstrated high efficacy, with 95% susceptibility among ESBL-producing E. coli and 96% among non-ESBL producers. However, 5% of ESBL-producing E. coli isolates were resistant to fosfomycin. Resistance to other antibiotics, such as nalidixic acid (98%) and ampicillin (93%), was notably high. No significant associations were found between ESBL production and demographic factors such as age, gender or patient type (outpatient vs. inpatient).Conclusion. Fosfomycin remains a highly effective treatment option for ESBL-producing E. coli UTIs in Northern Haryana, India, with low resistance rates observed. However, the emergence of fosfomycin resistance, albeit minimal, highlights the need for continuous surveillance and rational use of antibiotics to combat the growing threat of antimicrobial resistance.

Introduction. This study underscores the critical role of identifying heteroresistant infections of Mycobacterium tuberculosis (Mtb) in enhancing the diagnostics of tuberculosis (TB). These conditions complicate diagnostics and treatment, underlining the need for advanced techniques to detect and characterize resistant populations effectively.Hypothesis/Gap statement. Current diagnostics may fail to identify heteroresistance and mixed infections, limiting the understanding of their impact on treatment outcomes.Aim. This pilot study aimed to phenotypically and genotypically characterize rifampicin-heteroresistant clinical isolates and assess their genetic diversity and resistance patterns.Methodology. A retrospective analysis of 2,917 Mtb genomes from Peru (1999-2020) was conducted using MTBseq and TB-Profiler. Techniques included indirect microscopic observation drug susceptibility, MIC determination via tetrazolium microplate assay, agar proportion method and sequencing. From each clinical isolate, three colonies were isolated from both rifampicin-supplemented (1 µg mL^-1) and drug-free media for subsequent phenotypic and genotypic characterization, including rpoB sequencing.Results. Of the 2,917 genomes analysed, 14.6% were classified as mixed infections, 3.8% exhibited heteroresistance to at least 1 drug between 21 antibiotics analysed and 0.79% were rifampicin-heteroresistant. Colonies from rifampicin-supplemented media displayed high resistance (MIC >1 µg mL^-1) with mutations such as S450L in the RpoB protein. In contrast, those from drug-free media exhibited sensitivity to rifampicin (MIC <1 µg ml^-1), harbouring other RpoB mutations including D435Y, L452P and L430P. Notably, some colonies retained WT RpoB sequences, suggesting a diversity of subpopulations within isolates.Conclusion. Whole-genome sequencing and phenotypic analysis confirmed the coexistence of rifampicin-susceptible and rifampicin-resistant Mtb populations within single clinical isolates. Subculturing in drug-free media favoured the selection of sensitive strains, emphasizing the critical need for advanced diagnostic tools to accurately detect and characterize heteroresistant and mixed infections. These findings pave the way for more targeted treatment strategies to combat antimicrobial resistance in TB.

Introduction. Pneumocystis jirovecii pneumonia (PJP, formerly known as Pneumocystis carinii pneumonia), an opportunistic fungal infection caused by the fungus P. jirovecii, is a severe pulmonary infection that primarily affects immunocompromised patients, including those with lung cancer. Traditional diagnostic methods for PJP, such as Grocott-Gomori's methenamine silver staining and real-time PCR, have limitations, including low positivity and high missed diagnosis rates.Gap Statement. Despite the critical need for accurate and sensitive diagnostic tools for PJP, especially in immunocompromised populations, existing methods fall short in providing the necessary reliability and efficiency.Aim. This study aims to evaluate the efficacy of nanopore-based metagenomic third-generation sequencing in diagnosing P. jirovecii infection in lung cancer patients, hypothesizing that this approach may offer superior sensitivity and specificity.Methodology. A prospective observational study was conducted on 118 lung cancer patients with suspected pulmonary P. jirovecii infection at the Sixth Hospital of Nantong City, China, from January 2021 to December 2023. The identification of pathogens in bronchoalveolar lavage fluid samples was performed using both metagenomics and traditional tests.Results. Metagenomics showed a significantly higher detection rate of P. jirovecii (33.0%) compared to methenamine silver staining (4.2%) and real-time PCR (30.5%). The sensitivity, specificity and accuracy of metagenomics detection were all 100%, which is markedly superior to traditional methods. Furthermore, metagenomics also identified mixed infections with other pathogens, such as Cytomegalovirus and Epstein-Barr virus.Conclusion. Metagenomics technology demonstrates high sensitivity and specificity in diagnosing P. jirovecii infection, including mixed infections with other pathogens, in lung cancer patients. It provides a clear direction for clinical treatment and is a powerful tool for diagnosing PJP, contributing to improved diagnostic efficiency and accuracy, reducing misdiagnosis and missed diagnosis rates and improving clinical outcomes in these patients.

Introduction. Sexually transmitted infections (STIs) are a worldwide health issue with a high number of asymptomatic cases and the possibility of multiple infections.Gap statement. New multiplex real-time PCR kits targeting pathogens involved in nonviral STIs are regularly launched, but only some of them have been evaluated in comparative studies.Aim. This study evaluated the clinical performance of two multiplex real-time PCR commercial kits for the detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium and Trichomonas vaginalis: the Bosphore STD Urethritis Mini Bundle Kit (BK; Anatolia Geneworks) and the Viasure Sexually Transmitted Disease Real-Time PCR Detection Kit (VK; CerTest BIOTEC).Methodology. A total of 240 clinical specimens were evaluated. The results were compared with those of the Cobas CT/NG and TV/MG kits (Roche Diagnostics), used as reference methods.Results. Positive agreement ranged between 83.3% and 87.8% for the detection of C. trachomatis, N. gonorrhoeae and T. vaginalis using validated specimen types. For M. genitalium detection, positive agreement was 83.0% for the BK and 68.1% for the VK, which missed 31.9% of M. genitalium-positive specimens. Negative agreement ranged between 98.4% and 100% across the targeted micro-organisms. Both kits were easy to use and compatible with several DNA extraction and PCR thermal cyclers. The VK also detected the genital commensal bacteria Ureaplasma spp. and Mycoplasma hominis, which should not be targeted in STI detection kits.Conclusion. Both kits are convenient methods and showed good performance for the detection of nonviral STIs, but users should be aware of a lower sensitivity of the VK for the detection of M. genitalium.