Identification Of Pathogens Research Articles

Plastic bronchitis associated with human bocavirus 1 infection in children.

Plastic bronchitis (PB) is a clinical-pathological syndrome characterized by the abnormal accumulation of endogenous substances in the bronchial airways, causing partial or complete obstruction and resulting in impaired lung ventilation. In this retrospective analysis, we aim to summarize the clinical manifestations, imaging characteristics, diagnostic methods, and treatment approaches to enhance clinicians' ability to detect children who are infected withhuman bocavirus 1(hBoV 1) and develop PB. In the period from January 2021 to January 2024, a total of six hBoV 1 infection children were diagnosed with PB through bronchoscopy. The onset of the condition was mainly concentrated between June and December. The detection methods used included metagenomic next-generation sequencing for pathogen identification (three cases) and respiratory pathogen nucleic acid 13-plex detection (oropharyngeal swab) (three cases), both of which confirmed the presence of hBoV 1. Out of the six children with PB, two were girls and four were boys. Their ages ranged from 10 months to 4 years old. Common symptoms reported by all patients included fever, cough,and wheezing. Chest high-resolution computed tomography scans revealed atelectasis in six cases, in addition to pneumonia. After the removal of the plastic bronchi via bronchoscopy, the airway obstruction symptoms in the children were relieved, and no recurrence was observed during the follow-up period. Pathological findings indicated cellulose exudation and inflammatory cell infiltration, consistent with nonlymphatic PB. When children infected with hBoV 1 exhibit persistent or worsening symptoms such as cough, fever, and wheezing despite treatment, clinicians should remain highly vigilant for the potential occurrence of PB. Bronchoscopy plays a crucial role not only in diagnosing the presence of a plastic bronchus but also in effectively treating PB.

Clinical Performance of the LiquidArray® Gastrointestinal VER 1.0 Assay in Patients with Suspected Gastroenteritis

Background/Objectives: Rapid and accurate pathogen identification is essential for the proper management of patients with infectious gastroenteritis, as well as for a better control of disease outbreaks. This observational, non-interventional, single-site study evaluated the diagnostic accuracy of LiquidArray® Gastrointestinal VER 1.0, a multiplex PCR syndromic panel capable of detecting up to 26 clinically relevant enteropathogens. Methods: Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and likelihood ratio (LR) were evaluated using stool samples from 1512 patients with suspected gastroenteritis and were compared to seven competitor assays. Results: LiquidArray® Gastrointestinal VER 1.0 showed a very low invalid rate (0.5% at initial testing, down to 0% after repeat) and high sensitivity (>90% for most detected targets) and specificity (>99% for all detected targets). Accordingly, the PPV and NPV were high (>90% for most targets and >99% for all targets, respectively). The analytical performance of LiquidArray® Gastrointestinal VER 1.0 was also excellent as to co-amplification capability, cross-reactivity and assay precision. Conclusions: This study demonstrates the excellent clinical performance of LiquidArray® Gastrointestinal VER 1.0 and its suitability for implementation in clinical routine for the rapid and accurate diagnosis of infectious gastroenteritis.

First report of Alternaria leaf spot caused by Alternaria brassicae on broccoli in North Carolina, United States.

In September 2023, broccoli (Brassica oleracea var. italica) 'Sweet Bunch' plants on an organic farm in Buncombe County, North Carolina (NC), displayed symptoms of Alternaria leaf spot. Disease affected 10 to 20% of leaf area on all (approximately 30) plants. Lesions were dark brown with chlorotic halos, irregular in shape, and ≤3 cm in diameter. Leaf samples were incubated in a humidity chamber for 24 h, and the pathogen was putatively identified as Alternaria brassicae based on conidial morphology (Rimmer et al. 2007; Supplemental Fig. 1). Leaf pieces (2 x 2 mm) spanning lesion edges were surface-disinfested (1% sodium hypochlorite solution) for 1 min, rinsed in sterile distilled water, embedded in potato dextrose agar, and incubated at 22°C with a 12-h photoperiod. A pure culture was obtained by transferring a hyphal tip onto 20% V8 juice agar and incubated as above. After 10 d, colonies consisted of concentric zones of white to brown mycelia with white, aerial mycelia. Within 7 d, conidia measuring 80 to 150 µm long with 0 to 3 longitudinal septa, 6 to 15 transverse septa, and a long beak were observed, and the isolate was putatively identified as A. brassicae (Rimmer et al. 2007). To confirm identification, DNA was extracted from mycelia and subjected to PCR using primers to amplify a portion of the internal transcribed spacer of rDNA (ITS: ITS1/ITS4) (White et al. 1990), the transcription elongation factor-1 (tef1: EF1-728F/EF1-986R) (Carbone and Kohn 1999), and the glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH: gpd1/gpd2) (Berbee et al. 1999). Amplicons were sequenced at Eton Bioscience (Durham, NC) and subjected to BLAST analysis in NCBI GenBank. Sequences matched (99.5 to 100% identity) A. brassicae CBS 116528 accessions KC584185 (ITS), KC584641 (tef1), and KC584102 (GAPDH) (Woudenberg et al. 2013). All sequences were deposited in NCBI GenBank (accessions PP584506, PP584507, PP584508). To confirm pathogenicity on broccoli and kale (B. oleracea var. sabellica), 5-week-old plants of broccoli 'Sweet Bunch', 'Eastern Crown', and 'Green Magic' and kale 'Winterbor', 'Darkibor', and 'Oldenbor' grown in 10-cm-diameter pots were separated by crop type and arranged in four randomized complete blocks by cultivar. Each block contained single-plant replicates of each cultivar that were either inoculated or non-inoculated. Conidia of A. brassicae obtained from 10-d-old cultures (3.5 x 103 conidia/ml) were sprayed onto each inoculated plant until run-off. Non-inoculated plants were sprayed with distilled water. Plants were incubated in a humidity chamber alternated with ambient greenhouse conditions every 48 h for 10 d, with average greenhouse temperatures ranging from 15 to 28°C. The experiment was conducted twice. Dark brown to gray lesions measuring 1 to 3 mm in diameter were observed on leaves of all inoculated plants within 5 d of inoculation (Supplemental Fig. 2), and non-inoculated plants remained healthy. On broccoli plants, lesions expanded in concentric rings, and sporulation of the pathogen was observed on leaf tissue and petioles 10 d after inoculation. Lesions remained small (< 3 mm) on kale plants, and sporulation was not observed. Alternaria brassicae was re-isolated from leaf tissue of all inoculated cultivars using methods described above. Pathogen identity was confirmed via colony and conidial morphology. The larger impact of A. brassicae on brassicas is unknown, but finding this less common Alternaria species in the eastern United States could have implications for host resistance development and fungicide efficacy (Nieto-Lopez et al. 2023).

Contemporary Methods and Novel Approaches in the Identification and Quantification of Foodborne Pathogens

Foodborne pathogens are a continuous problem attracting the attention of public health institutions, microbiologists and food producers globally. The scientific community has therefore been focused for years on finding “new” and “better” methods, all in an effort to detect foodborne pathogens in the timeliest manner possible. It should be emphasized that the development of molecular genetics – the use of genetic information of biological macromolecules in routine testing in particular – has led to a revolutionary turn in biological science research. Almost all procedures detect different bacterial genetic footprint or biomarkers, which makes bacterial isolation unnecessary. However, these recent studies of “fast microbiological methods”, which require only a fewhours, rather than a few days, have not supplanted the classic way of microbiological food testing, i.e. the classic microbiological methods and the gold standard. The new methods are therefore faced with high requirements such as great detection limits, speed of analysis, relatively low costs and high sensitivity to identify various foodborne pathogens. Some of them provide the possibility of monitoring the pathogens, which is an important part of establishing a pathogen control network in the agri-food production chain at the international level. In this comprehensive literature review the authors present and review identification and quantification methodswith emphasis on the most important EU foodborne pathogens (Salmonella, Campylobacter, Escherichiacoli – STEC, Yersinia and Listeria). Methods have been divided into two large groups – Contemporary methods (Immunoassays and Polymerase Chain Reaction) and Novel approach methods (Biosensors, Bacterial typing, and Omics), and assessed by their functionality, advantages and disadvantages.

Molecular identification and antimicrobial resistance patterns of enterobacterales in community urinary tract infections among indigenous women in Ecuador: addressing microbiological misidentification

BackgroundAntibiotic resistance of Enterobacterales poses a major challenge in the treatment of urinary tract infections (UTIs). In low- and middle-income countries (LMICs), standard microbiological (i.e. urine culture and simple disk diffusion test) methods are considered the “gold standard” for bacterial identification and drug susceptibility testing, while PCR and DNA sequencing are less commonly used. In this study, we aimed to re-identifying Enterobacterales as the primary bacterial agents responsible for urinary tract infections (UTIs) by comparing the sensitivity and specificity of traditional microbiological methods with advanced molecular techniques for the detection of uropathogens in indigenous women from Otavalo, Ecuador.MethodsA facility-based cross-sectional study was conducted from October 2021 to February 2022 among Kichwa-Otavalo women. Pathogens from urine samples were identified using culture and biochemical typing. Morphological identification was doble-checked through PCR and DNA sequencing of 16S, recA, and rpoB molecular barcodes. The isolates were subjected to antimicrobial susceptibility-testing using disk diffusion test.ResultsThis study highlighted a 32% misidentification rate between biochemical and molecular identification. Using traditional methods, E. coli was 26.19% underrepresented meanwhile Klebsiella oxytoca was overrepresented by 92.86%. Furthermore, the genera Pseudomonas, Proteus, and Serratia were confirmed to be E. coli and Klebsiella spp. by molecular method, and one Klebsiella spp. was reidentified as Enterobacter spp. The susceptibility profile showed that 59% of the isolates were multidrug resistant strains and 31% produced extended spectrum beta-lactamases (ESBLs). Co-trimoxazole was the least effective antibiotic with 61% of the isolates resistant. Compared to previous reports, resistance to nitrofurantoin and fosfomycin showed an increase in resistance by 25% and 15%, respectively.ConclusionsCommunity-acquired UTIs in indigenous women in Otavalo were primarily caused by E. coli and Klebsiella spp. Molecular identification (16S/rpoB/recA) revealed a high rate of misidentification by standard biochemical and microbiological techniques, which could lead to incorrect antibiotic prescriptions. UTI isolates in this population displayed higher levels of resistance to commonly used antibiotics compared with non-indigenous groups. Accurate identification of pathogens causing UTIs and their antibiotic susceptibility in local populations is important for local antibiotic prescribing guidelines.

Rapid and precise identification of cervicothoracic necrotizing fasciitis caused by Prevotella and Streptococcus constellatus by using Nanopore sequencing technology: a case report

IntroductionCervicothoracic necrotizing fasciitis (CNF) is one form of necrotizing soft-tissue infections, which could lead to patient demise during short course. Therefore, early recognition and immediate treatment contribute to promising prognosis of patients.Case presentationA 58-year-old diabetic patient presented with a sore throat and progressive irritation of the neck and chest for 4 days. The initial diagnosis was considered to be soft-tissue infection and the clinician gave empirical anti-infectious medication for expectant treatment. During the course of disease, surgical incision was performed to relieve suffocation and shortness of breath. The drainage fluids were detected with microbiological culture and molecular sequencing. Nanopore sequencing technology (NST) helped to identify the coinfection of Streptococcus constellatus and Prevotella spp., which was not recognized during the original period of 15 days. The precise identification of pathogen supported to guide the pharmacologic treatment with meropenem and linezolid. Ultimately, combined with the surgical observation and post-surgical pathological examination, the patient was diagnosed as CNF, which could be much more acute and serious than normal soft-tissue infections. The patient has been successfully treated with prompt antimicrobial medication and appropriate surgical debridement.ConclusionThis case presented a CNF patient with type 2 diabetes, successfully recovered after prompt microbial detection, precise anti-infectious treatment, and appropriate surgical intervention. It highlights the importance of recognizing pathogen by applying rapid microbiological detection, including NST, in acute and serious infectious disease.

Surveillance of Food and Waterborne Pathogens in North-East India: Protocol for a Laboratory-Based Sentinel Surveillance Study.

Food safety is a global concern, which is often underestimated owing to challenges in investigating foodborne diseases. These challenges arise from the increased globalization of the food trade, advancements in agricultural practices, and shifts in environmental factors. In North-East India, common diarrheal outbreaks from fermented foods pose significant health risks. Despite these challenges, systematic data on foodborne pathogens is lacking in India, highlighting a crucial gap in understanding food safety issues. The aim of this research protocol is to establish an integrated surveillance system to identify enteric pathogens circulating within humans, food animals, and the environment through a health approach in North-East India, and to conduct outbreak investigations. The Indian Council of Medical Research (ICMR) initiated a surveillance study across all 8 North-East states in India, employing a centralized digital database for data collation. The project aims to enhance theinfrastructure for microbial culture, antibiotic sensitivity testing, and molecular epidemiological studies. The study involves laboratory-based surveillance of foodborne pathogens in market foods, hospitalized diarrheal patients, poultry and animal farms, slaughterhouses, butcher shops, and diarrheal outbreaks. A standardized case report form ensures consistent data collection of age, sex, signs, symptoms, and admission dates for diarrheal cases. Stool and rectal swabs will undergo testing for pathogen identification and antimicrobial resistance. Similarly, samples of market foods, food animals, and the environment will be collected. Outbreaks confirmed by the Integrated Disease Surveillance Project (IDSP) will be thoroughly investigated following standardized guidelines. In phase I, 5 surveillance centers were established across 4 states (ie, Assam [Dibrugarh and Guwahati], Tripura, Sikkim, and Arunachal Pradesh) in 2020. Following an interim phase I data assessment and the successful establishment of a streamlined system for data procurement, investigation, recording, and analysis, along with the implementation of regular training and monitoring programs, phase II expansion was initiated in 2023-24. This includes the addition of 7 more centers (including 3 veterinary centers) in the remaining 4 states (ie, Manipur, Meghalaya, Mizoram, and Nagaland), eventually covering the entire North-Eastern Region of India. Food and waterborne diseases are a constant public health problem in many countries. Key challenges to the enhancement of food safety policy include the paucity of systematic data and awareness. With this background, ICMR's initiative is the first systematic surveillance study in the country to adopt a single health approach. Data obtained from this project will help to understand the risk of acquiring food and waterborne pathogens, their transmission pathways, and antimicrobial resistance patterns. The scientific evidence generated through this project will be helpful in formulating and strengthening food safety policy and in initiating government programs to protect the health of the nation. DERR1-10.2196/56469.

Principal Component Analysis (PCA) of MALDI-TOF for the Identification of Waterborne Pathogenic Bacteria

The study focuses on the application of Principal Component Analysis (PCA) combined with MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry) for the identification of waterborne pathogenic bacteria in urban water networks. In this comprehensive research, 168 bacterial strains were meticulously isolated from the water networks of Abidjan, Côte d'Ivoire, a region known for its inadequate wastewater treatment infrastructure. The analysis aimed to rapidly and precisely identify these bacterial pathogens, leveraging the power of MALDI-TOF MS and the sophisticated data reduction capabilities of PCA. This approach not only accelerates the identification process but also enhances the accuracy of detecting various pathogens. The study identified a diverse range of pathogens, including Pseudomonas aeruginosa, Escherichia coli, Salmonella, Shigella, Vibrio cholerae, Morganella morganii, Proteus mirabilis, Acinetobacter baumannii, Klebsiella pneumoniae, Providencia rettgeri, Providencia stuartii, Aeromonas hydrophila, Bacillus cereus, Lysinibacillus fusiformis, Lysinibacillus sphaericus, and Staphylococcus aureus. These findings underscore the critical public health risks posed by microbial contamination in water networks, particularly in areas with deficient waste management systems. This study highlights the necessity for improved wastewater management practices, robust public health strategies, and regular monitoring to mitigate the risks associated with waterborne pathogens. Moreover, the integration of PCA with MALDI-TOF MS proves to be a powerful tool for enhancing the efficiency and accuracy of pathogen identification in environmental water samples, offering a promising solution for better public health protection and water quality management in urban settings.

Promise and Peril of a Genotype-First Approach to Mendelian Cardiovascular Disease.

Precision medicine, which among other aspects includes an individual's genomic data in diagnosis and management, has become the standard-of-care for Mendelian cardiovascular disease (CVD). However, early identification and management of asymptomatic patients with potentially lethal and manageable Mendelian CVD through screening, which is the promise of precision health, remains an unsolved challenge. The reduced costs of genomic sequencing have enabled the creation of biobanks containing in-depth genetic and health information, which have facilitated the understanding of genetic variation, penetrance, and expressivity, moving us closer to the genotype-first screening of asymptomatic individuals for Mendelian CVD. This approach could transform health care by diagnostic refinement and facilitating prevention or therapeutic interventions. Yet, potential benefits must be weighed against the potential risks, which include evolving variant pathogenicity assertion or identification of variants with low disease penetrance; costly, stressful, and inappropriate diagnostic evaluations; negative psychological impact; disqualification for employment or of competitive sports; and denial of insurance. Furthermore, the natural history of Mendelian CVD is often unpredictable, making identification of those who will benefit from preventive measures a priority. Currently, there is insufficient evidence that population-based genetic screening for Mendelian CVD can reduce adverse outcomes at a reasonable cost to an extent that outweighs the harms of true-positive and false-positive results. Besides technical, clinical, and financial burdens, ethical and legal aspects pose unprecedented challenges. This review highlights key developments in the field of genotype-first approaches to Mendelian CVD and summarizes challenges with potential solutions that can pave the way for implementing this approach for clinical care.

Economic impact, pathogen identification and management of blossom and peduncle blight in tuberose: A review

In the global floriculture industry, tuberose [Agave amica (Medik.) Thiede &amp; Govaerts syn. Polianthes tuberosa L.] holds significant economic and cultural value, particularly in regions like Tamil Nadu, India. However, the cultivation of this valuable flower is increasingly threatened by diseases such as blossom blight and peduncle blight. This review examines the economic importance of tuberose and the severe impact of these blights, caused by Fusarium equiseti and Lasiodiplodia theobromae respectively, which canresult in crop losses of up to 43 %. The identification and morphological characteristics of these pathogens are discussed, emphasizing the need for accurate detection and diagnosis to manage these diseases effectively. This article also reviews current management strategies, including chemical fungicides, biocontrol agents and cultural practices, highlighting the efficacy of carbendazim and tebuconazole against L. theobromae and the potential of Aimcozim and organic amendments against F. equiseti . Climate change exacerbates the impact of these diseases, necessitating adaptive management practices. Despite progress, research gaps remain in developing integrated disease management strategies and understanding the long-term effects of climate change on disease epidemiology. This review aims to provide a comprehensive overview of the current knowledge and to encourage further research, with the goal of enhancing the sustainability of tuberose cultivation in the face of these increasing challenges.

Can bone SPECT/CT determine optimal sites for microbiological identification in post-traumatic or chronic osteomyelitis of extremities?

IntroductionAccurate microbiological identification is crucial when managing chronic osteomyelitis (COM) and post-traumatic osteomyelitis (PTO). Although bone single photon emission computed tomography/computed tomography (SPECT/CT) has helped in localizing osteomyelitis lesions, its effectiveness in guiding microbiological sampling remains unclear. This study aimed to determine whether bone SPECT/CT can improve microbiological identification rates in COM or PTO of the extremities. Patients and methodsFrom February 2020 to August 2024, 53 patients with suspected COM or PTO in the extremities were retrospectively analyzed. All patients underwent bone SPECT/CT, followed by microbiological sampling during surgery. Tissue samples were taken from the areas of high SPECT/CT uptake or based on intraoperative findings where no uptake was observed. Microorganism identification rates were analyzed, including a sub-group analysis based on antibiotic discontinuation. ResultsOf the 53 patients, 42 had positive bone SPECT/CT scan findings, with pathogen identification in 30 patients (71.4 %). In contrast, pathogen identification occurred in one out of twelve patients (9.1 %) with negative findings (odds ratio 25, p< 0.001). Bone SPECT/CT demonstrated a sensitivity of 96.8 % and an overall accuracy of 75.5 %. When antibiotics had been discontinued for ≥2 weeks, the pathogen identification rate increased to 90 %, compared with 50 % for <2 weeks of discontinuation (odds ratio 10.0, p= 0.006). In a sub-group of 30 patients with adequate antibiotic discontinuation duration, a positive bone SPECT/CT scan yielded a pathogen identification rate of 90.1 % (odds ratio 60.0, p= 0.001). ConclusionBone SPECT/CT effectively identifies optimal sites for microbiological sampling in COM and PTO of the extremities, particularly when antibiotics have been discontinued for ≥2 weeks, enhancing pathogen detection rates.

Toscana Virus in Wild-Caught Sand Flies in Portugal, Findings from the National Vector Surveillance Network, 2023.

Phlebotomine sand flies play a crucial role in both human and veterinary medicine, acting as vectors for Leishmania parasites and most known phleboviruses. In Portugal, the REVIVE program, a comprehensive national surveillance network under the Ministry of Health, has included sand fly surveys since 2016. REVIVE aims to identify existing sand fly species in the country, determine which pathogens are circulating among them, and provide actionable insights for prevention and control measures when necessary. In this way, annually, from May to October, health technicians collect sand flies across mainland Portugal with CDC light traps. The collected sand flies are sent to the Centre for Vectors and Infectious Diseases Research for species identification and molecular screening of pathogens. On 21 September 2023, Toscana virus (TOSV), a well-known phlebovirus in the Mediterranean region due to its capacity to cause neurological disease, was detected in a pool of 30 sand flies collected in Algarve, the southernmost region of Portugal. A 668 bp partial sequence of the nucleoprotein gene shows similarity with TOSV strains from Spain. To our knowledge, this is the first detection of TOSV in its vector in this country, having previously only been reported in vertebrate hosts. These findings highlight the important role of ongoing surveillance efforts in monitoring and understanding the dynamics of sand fly-borne diseases in Portugal.

Enteric Pathogen Detection Using Multiplex PCR Assay in Kidney Transplant Recipients with Diarrhea-Retrospective Before-After Study.

Diarrhea is a frequent complication after kidney transplantation, however the etiology is often not identified. Multiplex PCR assays may increase the detection of diarrheal pathogens among kidney transplant recipients (KTRs), leading to improved management. This was a retrospective before-after study, conducted in a high-volume transplant center. In September 2017, multiplex PCR assay was introduced. We reviewed all hospitalized KTRs with diarrhea during 1/2015-8/2017 (pre-GI PCR, n = 111) and 9/2017-12/2021 (GI PCR, n = 159) and followed them for 3years. We performed univariate and multivariate analysis for predictors of pathogen identification, introducing the study period as an independent variable. Among 270 hospitalized KTRs with diarrhea, 64 (24%) had an identified diarrheal pathogen. The proportion of KTRs with an identified pathogen increased from 20% (13/64) in the pre-GI PCR to 80% (51/64) post GI PCR (p < 0.01). Of 51 KTRs with an identified pathogen in the post GI PCR, 44 (86%) were diagnosed using GI PCR. GI PCR was more likely used in younger KTRs with more recent transplantation and higher creatinine level at admission. The most common non-C. difficile diarrheal pathogens in the post-GI PCR cohort were enteropathogenic Escherichia coli (n = 23, 58%), norovirus (n = 11, 28%), and Campylobacter (n = 11, 28%). Implementing GI PCR significantly increased the detection and identification of GI pathogens (odds ratio [OR] = 21, CI 95% 10-44; p < 0.001). Infectious etiologies of diarrhea were identified in a higher proportion of KTRs after the implementation of GI PCR. This emphasizes the importance of integrating this diagnostic tool into diarrhea workup in KTRs.

Clinical Utility of a Multiplex PCR Panel (BioFire Joint Infection®) in the Adjustment of Empiric Antimicrobial Therapy: Experience in Pediatric Osteoarticular Infections.

This study aims to evaluate the impact of the PCR multiplex panel (BioFire JI®) on the diagnosis and management of pediatric osteoarticular infections. This retrospective study analyzed data from pediatric patients diagnosed with osteoarticular infections between January 2023 and April 2024. The effectiveness of the PCR multiplex panel in identifying pathogens was compared with traditional culture methods. In total, 50 patients were identified (66.6% male, 74% under 3 years of age). They were diagnosed as follows: septic arthritis in 46%, osteomyelitis in 26%, and septic osteoarthritis in 22%. An identifiable agent was isolated by conventional culture in 22 cases (44%). Kingella kingae was the predominant pathogen identified, accounting for 50% of cases (11/22), followed by Staphylococcus aureus (9/22). The BioFire JI® Panel PCR demonstrated a sensitivity of 93%, with a specificity of 63% when evaluated against synovial fluid culture as the reference standard. The panel identified seven additional pathogens not detected by conventional culture methods: 2/9 MSSA (22%), 1/1 S. pyogenes (100%), and 4/11 K. kingae (37%), increasing the yield by 14%. The rapid identification of pathogens facilitated timely and targeted therapeutic interventions. The PCR multiplex panel (BioFire JI®) improved the diagnosis of pediatric osteoarticular infections.

Surveillance on antimicrobial Resistance pattern of Third Generation Cephalosporins at the Benjamin Mkapa Tertiary Hospital in Tanzania

Abstract Background Antimicrobial resistance is a burden in Tanzania and the world economy, resulting in financial losses from lower production brought on by illness due to greater treatment expenses and death. Second- and third-line antibiotics like third generations of cephalosporins should be used rather than first-line, which is an expensive option, due to AMR. The direct effects of AMR include severe prolonged illnesses, prolonged hospital stays death, and (Global Action Plan on Antimicrobial Resistance., 2015) Methodology The retrospective study design was used to review AST to assess the AMR patterns from 2020-2022 for urine, pus, and blood samples as stated in the National Action Plan-Antimicrobial Resistance 2017. Results Three years (2020, 2021, and 2022) of antibiograms based on priority samples, priority pathogens and third generations of cephalosporins for both gram-negative and gram-positive bacteria see Tables 1 and 2. The surveillance identified sensitive (S), intermediate(I), and resistance(R) for tested bacteria. The N is the isolate number. Our antibiograms for third-generation cephalosporins were represented by cefotaxime, ceftazidime and ceftriaxone. The antimicrobial resistance to ceftriaxone for Acinetobacter species was 62.5% while 76% for Citrobacter. E. coli at 60.26%, Enterobacter aerogenes at 67.86%, Klebsiella species at 73.48% at 22.73%, Morganella morganii 65.75% and Staphylococcus aureus at 62.5%, Serratia marcescens 64.56%. Similar resistance trends have been observed in cefotaxime and ceftazidime. Conclusion Antimicrobial susceptibility surveillance, antimicrobial rotation and presentation of findings to clinicians for increased awareness and the promotion of a multi-disciplinary approach to successful AMS programmers is essential. Evidence found will optimize the use of antibiotics. Clinicians, pharmacists, and scientists will use obtained evidence in the development of guidelines and protocols for surgical prophylaxis, setting IPC programs, management of bacterial blood infections (septicemia and sepsis) and managing urinary tract infections by focusing on red flags antibiotics and bacteria such E. coli and K. pneumoniae. Avoiding delay of AST results by enough resources, and technology advancement. This enable identification of the causative pathogens facilitated the correct diagnosis, de-escalation, and use of targeted agents, which are necessary to promote the prudent use of antimicrobials. Antibiograms Table 1: Antibiogram of gram-negative bacteria Table 2: Antibiogram of gram-positive bacteria

A novel ensemble approach with deep transfer learning for accurate identification of foodborne bacteria from hyperspectral microscopy

The detection of foodborne bacteria is critical in ensuring both consumer safety and food safety. If these pathogens are not properly identified, it can lead to dangerous cross-contamination. One of the most common methods for classifying bacteria is through the examination of Hyperspectral microscope imaging (HMI). A widely used technique for measuring microbial growth is microscopic cell counting. HMI is a laborious and expensive process, producing voluminous data and needing specialized equipment, which might not be widely available. Machine learning (ML) methods are now frequently utilized to automatically interpret data from hyperspectral microscopy. The objective of our study is to devise a technique that employs deep transfer learning to address the challenge of limited data and utilizes four base classifiers - InceptionResNetV2, MobileNet, ResNet101V2, and Xception - to create an ensemble-based classification model for distinguishing live and dead bacterial cells of six pathogenic strains. In order to determine the optimal weights for the base classifiers, a Powell's optimization method was utilized in conjunction with a weighted average ensemble (WAVE) technique. We carried out an extensive experimental study to verify the efficiency of our proposed ensemble model on live and dead cell images of six different foodborne bacteria. In order to gain a better understanding of the regions, we performed a Grad-CAM analysis to explain the predictions made by our model. Through a series of experiments, our proposed framework has proven its capacity to effectively and precisely detect numerous bacterial pathogens. Specifically, it achieved a perfect identification rate of 100 % for Escherichia coli (EC), Listeria innocua (LI), and Salmonella Enteritidis (SE), while achieving rates of 96.30 % for Salmonella Typhimurium (ST), 87.13 % for Staphylococcus aureus (SA), and 94.12 % for Salmonella Heidelberg (SH). As a result, it can be considered as an effective tool for the identification of foodborne pathogens, due to its high level of efficiency.

A dataset for developing proteomic tools for pathogen detection via differential cell lysis of whole blood samples

This data descriptor presents a curated dataset for pathogen detection and identification (Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans) directly from whole-blood samples. The dataset was created using differential cell lysis combined with rapid extraction, digestion, and mass spectrometry-based proteomics. Our method offers a rapid diagnostic alternative to traditional culture, enabling timely disease management, such as sepsis. Highlighting our dataset’s uniqueness, it features a three-tier structure: Spectral Libraries of Pathogens for identifying peptide peaks for putative biomarkers; Spiked pathogen in blood MS data for biomarker panel optimization through varied concentration samples; and Parallel Reaction Monitoring (PRM) data from sepsis patients for validating our biomarker panel, achieving 83.3% sensitivity within seven hours without microbial enrichment culture. This dataset serves as a comprehensive reference for bioinformatic tool development and biomarker panel proposals, advancing microbial detection, antimicrobial resistance, and epidemiological studies.

Cases of endophthalmitis caused by Candida albicans and Candida dubliniensis identified via internal transcribed spacer deep sequencing

BackgroundWe report two cases of fungal endophthalmitis induced by Candida species identified based on internal transcribed spacer 1 (ITS1) sequencing.Case presentationIn two cases, endophthalmitis was suspected, and the patients underwent pars plana vitrectomy. Case 1 was a 64-year-old woman with a history of cataract surgery 10 days prior. She had a history of anal primary melanoma, which metastasized throughout the body and subsequently relapsed. Vitreous culture and ITS-1 deep sequencing revealed the presence of the rare fungus, Candida dubliniensis. Case 2 was a 54-year-old man with a history of liver cancer and kidney failure. Culture methods and ITS1 deep sequencing both revealed the presence of Candida albicans. Both patients exhibited good visual prognoses after treatment with topical and systemic antibiotics.ConclusionsWe present two cases of fungal endophthalmitis caused by two Candida species identified by both the culture method and ITS1 deep sequencing. The fungal pathogen was identified by ITS deep sequencing three days after sample submission; the culture method yielded results after 1 week. These findings support the applicability of ITS1 sequencing for timely pathogen identification for cases of fungal endophthalmitis and provide detailed taxonomic information at the species level.

Detection and Characterization of Lasiodiplodia pseudotheobromae Associated with Stem Wilt on Ficus hirta (Vahl) and Its Fungicidal Sensitivity

Ficus hirta Vahl is an important medicinal and edible plant in southern China. Typical green wilting on leaves and brown necrotic spots on the stems were observed since mid-June 2022 in an F. hirta plantation in Danzhou, Hainan (China). The disease rapidly developed, causing stem withering and plant death. The disease incidence varied from 45 to 85% prevalence, and the average disease index was 47 in the period of outbreak during June to December. Relevant hypothetical fungi were isolated from naturally infected wilt tissues, and their pathogens were preliminarily confirmed to be Lasiodiplodia pseudotheobromae through hypothetical fungal culturing, morphological characteristic observations, and pathogenicity testing on F. hirta plants. The phylogenetic tree constructed based on partial ITS, translation elongation factor (TEF1-α), and the β-tubulin gene (TUB2) further confirmed the identity of the pathogen as L. pseudotheobromae. Further research on the biological characteristics of L. pseudotheobromae showed that the optimal temperature for the growth of L. pseudotheobromae was PDA medium, with a temperature of 30 °C and pH of 6. Peptone and fructose were the optimal nitrogen and carbon sources for it. In vitro efficacy testing showed that among eleven fungicides, fluazinam and prochloraz had the highest mycelial growth inhibition, with an EC50 of 0.0477 µg/mL and 0.0996 µg/mL, respectively. And the two fungicides showed significant control on the stem wilt of F. hirta in a pot. To our knowledge, this is the first comprehensive report on the pathogen identification and biological characteristics of L. pseudotheobromae infecting the stem wilt of F. hirta in China. Our results provide important information for developing effective management measures and controlling this disease.

Incidence of an Identifiable Organism in Children Who Underwent a Surgical Procedure for Granulomatous Cervical Lymphadenopathy.

Objectives: The incidence of cervical lymphadenopathy due to nontuberculous mycobacteria is rising in the pediatric population. Our goal with this study was to review the number of pediatric patients with granulomatous cervical adenitis and determine the incidence of identification of a specific organism as both healthcare providers and parents are interested in identifying the causative pathogen. Methods: A retrospective chart review was conducted of patients at a high-volume tertiary care children's hospital between 2017 and 2023. Children were included if they underwent a surgical procedure for lymphadenopathy. Pathology, microbiology, and other laboratory reports were reviewed to document the presence of granulomatous cervical adenitis and the incidence of identification of a specific organism. Additional data collected included patient demographics and type of procedure. Results: Of the 1538 charts reviewed, 163 patients underwent an inclusionary procedure. Mean patient age was 10.7 years (range 2.4 months-20 years), 70 (43%) were female, 25 (15%) had granulomatous cervical adenitis, and a specific organism was identified in 9 of these. Conclusion: Despite the availability of a number of ancillary tests, our data demonstrate that the identification of a specific pathogen in cases of granulomatous cervical lymphadenitis is rare. As a result, physicians should be prepared to rely primarily on the history and physical exam findings to determine a working diagnosis as well as a medical and/or surgical treatment plan.