Local Prevalence Research Articles

Species specificity and specificity diversity (SSD) framework: a novel method for detecting the unique and enriched species associated with disease by leveraging the microbiome heterogeneity

BackgroundDifferentiating the microbiome changes associated with diseases is challenging but critically important. Majority of existing efforts have been focused on a community level, but the discerning power of community or holistic metrics such as diversity analysis seems limited. This prompts many researchers to believe that the promise should be downward to species or even strain level—effectively and efficiently identifying unique or enriched species in diseased microbiomes with statistical rigor. Nevertheless, virtually, all species-level approaches such as differential abundance and differential network analysis methods exclusively rely on species abundances without considering species distribution information, while it can be said that distribution is equally, if not more, important than abundance in shaping the spatiotemporal heterogeneity of community compositions.ResultsHere, we fill the gap by developing a novel framework—species specificity and specificity diversity (SSD)—that synthesizes both abundance and distribution information to differentiate microbiomes, at both species and community scales, under different environmental gradients such as the healthy and diseased treatments. The proposed SSD framework consists of three essential elements. The first is species specificity (SS), a concept that reincarnates the traditional specialist-generalist continuum and is defined by Mariadassou et al. (Ecol Lett 18:974-82, 2015). The SS synthesizes a species’ local prevalence (distribution) and global abundance information and attaches specificity measure to each species in a specific habitat (e.g., healthy or diseased treatment). The second element is a new concept to introduce here, the (species) specificity diversity (SD), which is inspired by traditional species (abundance) diversity in community ecology and measures the diversity of specificity (a proxy for metacommunity heterogeneity, essentially) with Renyi’s entropy. The third element is a pair of statistical tests based on the principle of permutation tests.ConclusionsThe SSD framework can (i) identify and catalogue lists of unique species (US), significantly enriched species (ES) in each treatment based on SS and specificity permutation (SP) test and (ii) measure the holistic differences between assemblages (or treatments) based on SD and specificity diversity permutation (SDP) test. Both capacities can be enabling technologies for general comparative microbiome research including risk assessment, diagnosis, and treatment of microbiome-associated diseases.

Bacteriological Profile and Antimicrobial Resistance Patterns in Pediatric Urinary Tract Infections: A Cross-Sectional Study at Dhaka Shishu Hospital

Urinary tract infections (UTIs) are a prevalent concern in pediatric healthcare, causing distress to children, raising parental concerns, and potentially leading to lasting kidney damage. The highest incidence of first-time symptomatic UTIs occurs in infants during the first year of life, with a subsequent marked decrease. Febrile infants under 2 months, presenting with unexplained fever, constitute a critical subset requiring particular attention. Knowledge of the bacteriological profile and antimicrobial resistance patterns in specific regions is crucial for guiding effective treatment strategies. Methods: A cross-sectional study was conducted at 250 Bedded General Hospital, Jamalpur, Bangladesh from Feb 2016 to Aug 2016 to assess the bacteriological profile and antibiotic resistance patterns in pediatric UTIs. A total of 147 culture-positive UTI patients were included. Bacterial isolates were identified, and colony counts for samples with ≥105 CFU/mL bacteria were considered positive. Antimicrobial susceptibility testing was performed using twelve agents, and resistance patterns were analyzed. Results: Among the 147 culture-positive UTI patients, Escherichia coli (E-coli) was the predominant isolate (70%), followed by Klebsiella spp. (13.6%), Pseudomonas (5.44%), Enterobacter spp (3.40%), Staphylococcus Aureus (3.40%), Proteus (2.72%), and Enterococcus (1.36%). Antimicrobial resistance analysis revealed varying patterns, with Cefradine (79.59%), Co-trimoxazole (SXT) (69.39%), Nalidixic acid (NA) (66.67%), and Ceftazidime (CTM) (48.98%) showing higher resistance rates. No drug exhibited 100% resistance against urinary pathogens, indicating a dynamic resistance landscape. Conclusion: This study highlights the importance of understanding local prevalence and resistance patterns in guiding empirical antibiotic selection for pediatric UTIs. The observed decrease in antimicrobial resistance underscores the need for continuous surveillance and tailored antibiotic strategies. Clinicians should base their treatment decisions on the specific epidemiological context rather than relying solely on universal or national guidelines.

Performance of Risk Models for Antimicrobial Resistance in Adult Patients With Sepsis

The results of prediction models that stratify patients with sepsis and risk of resistant gram-negative bacilli (GNB) infections inform treatment guidelines. However, these models do not extrapolate well across hospitals. To assess whether patient case mix and local prevalence rates of resistance contributed to the variable performance of a general risk stratification GNB sepsis model for community-onset and hospital-onset sepsis across hospitals. This was a retrospective cohort study conducted from January 2016 and October 2021. Adult patients with sepsis at 10 acute-care hospitals in rural and urban areas across Missouri and Illinois were included. Inclusion criteria were blood cultures indicating sepsis, having received 4 days of antibiotic treatment, and having organ dysfunction (vasopressor use, mechanical ventilation, increased creatinine or bilirubin levels, and thrombocytopenia). Analyses were completed in April 2024. The model included demographic characteristics, comorbidities, vital signs, laboratory values, procedures, and medications administered. Culture results were stratified for ceftriaxone-susceptible GNB (SS), ceftriaxone-resistant but cefepime-susceptible GNB (RS), and ceftriaxone- and cefepime-resistant GNB (RR). Negative cultures and other pathogens were labeled SS. Deep learning models were developed separately for community-onset (patient presented with sepsis) and hospital-onset (sepsis developed ≥48 hours after admission) sepsis. The models were tested across hospitals and patient subgroups. Models were assessed using area under the receiver operating characteristic curve (AUROC) and area under precision recall curve (AUPRC). A total of 39 893 patients with 85 238 sepsis episodes (43 207 [50.7%] community onset; 42 031 [48.3%] hospital onset) were included. Median (IQR) age was 65 (54-74) years, 21 241 patients (53.2%) were male, and 18 830 (47.2%) had a previous episode of sepsis. RS contributed to 3.9% (1667 episodes) and 5.7% (2389 episodes) of community-onset and hospital-onset sepsis episodes, respectively, and RR contributed to 1.8% (796 episodes) and 3.9% (1626 episodes), respectively. Previous infections and exposure to antibiotics were associated with the risk of resistant GNB. For example, in community-onset sepsis, 375 RR episodes (47.1%), 420 RS episodes (25.2%) and 3483 of 40 744 (8.5%) SS episodes were among patients with resistance to antimicrobial drugs (P < .001). The AUROC and AUPRC results varied across hospitals and patient subgroups for both community-onset and hospital-onset sepsis. AUPRC values correlated with the prevalence rates of resistant GNB (R = 0.79; P = .001). In this cohort study of 39 893 patients with sepsis, variable model performance was associated with prevalence rates of antimicrobial resistance rather than patient case mix. This variability suggests caution is needed when using generalized models for predicting resistant GNB etiologies in sepsis.

External Validation of an Electronic Health Record-Based Diagnostic Model for Histological Acute Tubulointerstitial Nephritis.

Accurate diagnosis of acute tubulointerstitial nephritis (AIN) often requires a kidney biopsy. We previously developed a diagnostic statistical model for predicting biopsy-confirmed AIN by combining four laboratory tests after evaluating over 150 potential predictors from the electronic health record. Here, we validate this diagnostic model in two biopsy-based cohorts at Johns Hopkins Hospital (JHH) and Yale, which were geographically and temporally distinct from the development cohort, respectively. We analyzed patients who underwent kidney biopsy at JHH and Yale University (2019-2023). We assessed discrimination (AUC) and calibration using previously derived model coefficients and recalibrated the model using an intercept correction factor that accounted for differences in baseline prevalence of AIN between development and validation cohorts. We included 1982 participants: 1454 at JHH and 528 at Yale. JHH (5%) and Yale (17%) had lower proportions of biopsies with AIN than the development set (23%). The AUC was 0.73 (0.66-0.79) at JHH and 0.73 (0.67-0.78) at Yale, similar to the development set (0.73 (0.64-0.81)). Calibration was imperfect in validation cohorts, particularly at JHH, but improved with application of an intercept correction factor. The model increased AUC of clinicians' prebiopsy suspicion for AIN by 0.10 to 0.77 (0.71-0.82). An AIN diagnostic model retained discrimination in two validation cohorts but needed recalibration to account for local AIN prevalence. The model improved clinicians' ability to predict AIN.

Elucidating the influence of wild boar density on African swine fever spread in wild boar populations, Italy, 2022–2023

Abstract Wild boar density has been suggested to play a role in shaping African swine fever (ASF) transmission patterns. To provide quantitative estimates of the influence of wild boar density on ASF spread, a spatially‐explicit detection‐delay SIR mechanistic model of ASF transmission among density‐explicit wild boar habitat was developed and parameterised to observed epidemic data in northern Italy from January 2022 through September 2023. Wild boar density estimates were generated by the ENETWILD consortium. Infectious periods, local prevalence at time of first detection, detection rates, and seasonal recovery rates were estimated directly from surveillance data. Eight models were constructed utilizing static and seasonal transmission rates along with linear relationships between habitat susceptibility/infectivity and wild boar density. Transmission rate, relative susceptibility, and relative infectivity were estimated by fitting each model to the observed epidemic using sequential Monte Carlo approximate Bayesian computation. The model that most closely fit the full data used a seasonal transmission rate but did not support a wild boar density effect on ASF spread across the entire study period. However, further analyses of the model outputs suggest that wild boar density likely played a role in shaping ASF transmission patterns during the second wave only (October 2022 – September 2023). This observation could be due to a lack of power in the first wave, lower surveillance rates in that period, or be from density estimates no longer reflecting the true wild boar density distributions upon the start of the second wave. These results demonstrate that wild boar density impacted ASF propagation in northern Italy. Further investigation by estimating parameters for individual epidemic waves could be beneficial to better characterise the wave‐specific impact of wild boar density. The model developed here could be used in other contexts to evaluate if the influence of wild boar density is present across epidemic scenarios.

An updated phylogeography and population dynamics of porcine circovirus 2 genotypes: are they reaching an equilibrium?

Porcine circovirus 2 (PCV2) emerged more than three decades ago as one of the most impactful pathogens in the swine industry. Despite being a DNA virus, one of the hallmarks of PCV2 is its high evolutionary rate, which has led to the emergence of different genotypes, each exhibiting varying degrees of evolutionary success. Current knowledge suggests the occurrence of three main waves of genotype dominance, alternating over time (i.e., PCV2a, PCV2b, and PCV2d), alongside less prevalent genotypes. However, although PCV2d is currently the most common genotype nowadays, the others continue being circulating in the pig population. The present study reconsidered the epidemiological and evolutionary patterns of PCV2 genotypes using phylodynamic analyses, benefiting from an almost 10-fold increase in ORF2 sequence availability compared to previous studies. Additionally, a phylogeographic analysis was performed to investigate viral dispersal patterns and frequency, and the selective pressures acting on the capsid protein were estimated and compared among genotypes. While successive emergence of major genotypes was confirmed, this study extends previous findings by revealing subsequent prevalence fluctuations of PCV2a and PCV2b after their initial decline. This evolutionary process may represent an example of balancing selection, specifically negative frequency-dependent selection, where a genotype fitness diminishes as it becomes more common, and vice versa. Variations in genotype- or clade-specific immunity-affected by the local prevalence of viral groups-combined with the periodic introduction of strains that have independently evolved in different regions, may have led to fluctuations in the population dynamics of major genotypes over time. These fluctuations were associated with ongoing evolution and variations in the capsid amino acid profile. These findings have profound implications for future control strategies. Although PCV2d remains the most prevalent and widespread genotype, other genotypes should not be neglected. Control strategies should thus target the entire PCV2 population, with a focus on fostering broader and more cross-protective immunity.

Opt-out HIV screening in adults attending the Emergency Department of a London teaching hospital

BackgroundOpt-out Emergency Department blood borne virus (EDBBV) screening was introduced at the Royal Free Hospital under the NHSEI (NHS England and NHS Improvement) programme to expand opt-out testing in local authority areas with high HIV prevalence. This initiative was part of the “Toward Zero” policy towards ending HIV transmission in England by 2030. MethodsAll patients attending the Royal Free Hospital Emergency Department (ED) aged 16 and over were screened for blood borne viruses (HIV/HBV/HCV) unless they opted out. We looked at HIV data from patients seen in ED between the initiation of EDBBV testing on the 12th of April and 12th of August 2022. Hepatitis B and C data was reviewed in a separate study. OutcomeA total of 12,208 samples from 10,641 patients were screened for HIV. Amongst these samples there were 88 which were positive, giving a seroprevalence of 0.84 %. There were 48 patients who were already known to local HIV services, 35 were known to HIV services outside of our Trust and 5 were new diagnoses. ConclusionOur results confirmed our local HIV prevalence to be very high, as per the UK Health Security Agency and supports the need for HIV testing. Opt-out ED BBV screening has been a highly effective method for identifying people living with HIV who are unaware of their status.

8620 Prevalence of Osteopenia of Prematurity and Risk Factors in Neonatal of Maternity Hospital

Abstract Disclosure: D.M. Bastos: None. J.G. Bastos: None. A.C. Bastos: None. Introduction: The osteometabolic disease of prematurity (ODP), formerly known as osteopenia of prematurity, corresponds to a disorder of bone mineralization in the neonatal period in very low birth weight premature newborns. The estimated prevalence is about 30% when the birth weight is less than 1,500 grams and around 60% when it is less than 1,000 grams. There is no specific clinical picture, and it can present with mild manifestations, growth deficit, or even evolve with severe rickets and fractures. To qualify the care of premature newborns (NB) in our Service, we question what is the local prevalence of ODP and what are the clinical, biochemical, or imaging risk factors that are potentially related to a greater predisposition to this condition. Objective: Evaluate the prevalence of ODP and recognize potential risk factors in NBs in a neonatal ICU of a reference maternity hospital in Curitiba/ PR. Method: Retrospective longitudinal study, with analysis of medical records of patients born with a gestational age less than 34 weeks and birth weight less than 1,500 grams, born between January/2013 to August/2016. Discussion: Prematurity is the significant factor, followed by low birth weight, for osteopenia. Newborns (NB) with a birth weight below 1500g should receive 40mg/Kg of calcium and 50 mg/Kg of phosphorus. Supplementation of human milk should be started from 15 days of life or when oral intake reaches 100ml/Kg per day (1g/20 ml of milk). In this study, the classification of the growth curve and prevalence by sex were divergent with the literature. The most vulnerable are those with parenteral nutrition or prolonged fasting, as the adequate diet is the basis of prevention and treatment, similar data being found, as well as association with prolonged use of diuretic, presence of sepsis diagnosis and bronchopulmonary dysplasia. However, there is still a lack of specific and sensitive markers for early diagnosis and treatment. Conclusion: The prevalence of Osteopenia of Prematurity was lower than that found in the literature. The risk factors bronchopulmonary dysplasia and use of diuretics were statistically significant when evaluated in patients with osteopenia. However, no relationship was found between ODP and sepsis, as well as a relationship between ODP and Necrotizing Enterocolitis. Regarding the days kept fasting, use of TPN and Use of antibiotics, a longer duration of use was obtained when compared with the group that did not develop the disease. Presentation: 6/3/2024

8812 Incidence And Clinical Experience Of Immune Checkpoint Inhibitors-Induced Endocrine Side Effects Among Filipino Cancer Patients: A Single-Center Retrospective Study

Abstract Disclosure: N.B. Luna: None. E. Mendoza: None. S.A. Kho: None. Incidence And Clinical Experience Of Immune Checkpoint Inhibitors-Induced Endocrine Side Effects Among Filipino Cancer Patients: A Single-Center, Retrospective Study Immune checkpoint inhibitors (ICIs) serve as immunomodulatory antibodies, which enhance the immune system and substantially improve the prognosis for patients with advanced malignancies [1]. Referral to endocrinology have been increasing because ICIs were associated with endocrine-related adverse effects including hypothyroidism, hyperthyroidism, diabetes, hypophysitis and adrenalitis. Hence, the study aimed to retrospectively determine the local prevalence and profile of Filipino patients who developed endocrinopathies during ICI therapy at the University of Santo Tomas Hospital (USTH), Manila, Philippines from 2013-2019. A single-center retrospective study of ICI-treated cancer patients with serial biochemical and/or radiologic monitoring of endocrine adverse effects was done upon approval by the Research Ethics Committee. A total of 27 subjects were included with a median age of 60 years and male predominance. Pembrolizumab consisted 93% of the ICIs given. The incidence of thyroid dysfunction was 36% (18% overt hypothyroidism, 9% subclinical hypothyroidism, and 9% subclinical hyperthyroidism). The median time at risk for development of overt hypothyroidism is 4 weeks with median TSH level of 9.05 uIU/mL from baseline level of 3.77 uIU/mL. All patients who had baseline hypothyroidism worsened with increase from baseline levothyroxine dose by 50 to 230% in order to achieve euthyroidism (p 0.037). Serial monitoring was done every 2 weeks until euthyroidism. ICIs were temporarily put on hold in 75%. Diabetes (p 0.05), renal carcinoma (p 0.001) and dose of 200mg (p 0.42) were associated to developing overt hypothyroidism. Checking of glycemic levels was not routine among non-diabetic patients. Fifteen percent of diabetic patients had worsening of control (median HbA1c 8.5% [8-9] and 23% were newly diagnosed pre-diabetes (median fasting glucose 114mg/dL [104-120]). With the available imaging results, there were no abnormal adrenal metabolic uptake on PET scan and no evidence of hypophysitis in pituitary MRI. In conclusion, overt hypothyroidism is a common occurrence during ICI therapy (18%). Worsening occurred among all patients with hypothyroidism at baseline. New-onset pre-diabetes and worsening of glycemic control were seen in 15 and 23%, respectively. Serial clinical and biochemical monitoring is important and referral to endocrinology should be made if deemed necessary. [1] L Agrawal, A Bacal, S Jain, V Singh, N Emanuele, Ma Emanuele &amp; F Meah (2020) Immune checkpoint inhibitors and endocrine side effects, a narrative review, Postgraduate Medicine, 132:2, 206-214, DOI: 10.1080/00325481. 2019. 1709344 Presentation: 6/1/2024

Parental knowledge and attitudes toward food allergies: a cross-sectional study on determinants and educational needs

BackgroundFood allergy (FA) may often lead to fatal consequences if it is treated promptly. Parents of children with FA should have adequate knowledge to improve health outcomes and reduce the associated burden. This study aimed to examine the knowledge and attitudes regarding FA among parents of children with FA.MethodsThis was a cross-sectional study conducted among parents attending a primary healthcare center using convenience sampling. The minimum sample size of 280 was calculated using an equation based on the local prevalence of FA among children, and was increased to account for missing data. The data were collected using a four-section questionnaire that collected data about the parents and their children and included questions about knowledge and attitudes regarding FA. The knowledge score was calculated by summing the number of correct answers, with a maximum of 15 points. The Mann–Whitney and Kruskal–Wallis tests were used to examine the associations between the knowledge score and other variables. Spearman’s correlation was employed to test the correlations between the knowledge score and other variables.ResultsA total of 381 parents completed the questionnaires, of whom 71.9% were mothers and 28.1% were fathers. The prevalence of food allergies was 14.22%. Almost one-third had children who had one or more types of FA (32.8%). Most of those patients had received a professional diagnosis of FA (75.3%). The median knowledge score was 7.0 (IQR = 6–8), with variable proportions of correct answers across and within topics. A higher knowledge score was significantly associated with parenting a child with FA (p = 0.006), comorbid asthma or eczema (p = 0.012), the preference to acquire information from professional health agencies (p < 0.001), and higher educational (p = 0.002) and income (p = 0.001) levels. Moreover, the number of discussions held with a healthcare professional regarding FA was significantly correlated with the knowledge score (r = 0.210, p = 0.019). Online resources were the most commonly reported source of information (65.4%). Parents believed that having a child with FA can cause stress in the family (76.1%) and impact siblings’ daily lives (66.7%), while only a minority viewed FA as stigmatizing. Additionally, the majority encouraged governmental spending on FA research (92.9%).ConclusionsParenting a child with FA, comorbid asthma or eczema, number of discussions held with healthcare professionals, and education and income levels were significantly associated with a higher knowledge score. Educational interventions targeting parents should blend emotional regulation, medical information, and management skills to increase knowledge about FA and alleviate associated stress.

Impact of risk information on health beliefs and behaviours: experimental evidence

ABSTRACT The local prevalence of infections and the severity of their consequences are among the key determinants of the adoption of preventive behaviours against infectious diseases. In Bangladesh, where local COVID-19 infection statistics were not readily accessible, I found that most people underestimated the local prevalence of COVID-19 infections while overestimated the fatality rate. In a randomized experiment, the treatment group was provided with information about the coronavirus case numbers in their districts, along with the case fatality rate in Bangladesh and globally. Immediately after receiving this information, the treatment group perceived a higher infection risk. Nine to fifteen days post-intervention, those who received information were less likely to underestimate the local prevalence and, consequently, still perceived a higher infection risk. They also updated their belief about the fatality rate downward. Potentially due to this countervailing update of risk beliefs, the information had no effect on self-reported preventive behaviours.

Parasite Abundance‐Occupancy Relationships Across Biogeographic Regions: Joint Effects of Niche Breadth, Host Availability and Climate

ABSTRACTAimChanging biodiversity and environmental conditions may allow multi‐host pathogens to spread among host species and affect prevalence. There are several widely acknowledged theories about mechanisms that may influence variation in pathogen prevalence, including the controversially debated dilution effect and abundance‐occupancy relationship hypotheses. Here, we explore such abundance‐occupancy relationships for unique lineages of three vector‐borne avian blood parasite genera (the avian malaria parasite Plasmodium and the related haemosporidian parasites Parahaemoproteus and Leucocytozoon) across biogeographical regions.LocationNearctic‐Neotropical and Palearctic‐Afrotropical regions.MethodsWe compiled a cross‐continental dataset of 17,116 bird individuals surveyed from 46 bird assemblages across the Nearctic‐Neotropical and Palearctic‐Afrotropical regions and explored relationships between local parasite lineage prevalence and host assemblage metrics in a Bayesian random regression framework.ResultsMost lineages from these three genera infected ≥ 5 host species and exhibited clear phylogenetic or functional host specificity. Lineage prevalence from all three genera increased with host range, but also with higher degrees of specialisation to phylogenetically or functionally related host species. Local avian community features were also found to be important drivers of prevalence. For example, bird species richness was positively correlated with lineage prevalence for Plasmodium and Leucocytozoon, whereas higher relative abundances of the main host species were associated with lower prevalence for Plasmodium and Parahaemoproteus but higher prevalence for Leucocytozoon.ConclusionsOur results broadly support several of the leading hypotheses about mechanisms that influence pathogen prevalence, including the niche breadth hypothesis in that higher avian host species diversity and broader host range amplify prevalence through increasing ecological opportunities and the trade‐off hypotheses in that specialisation among subsets of available host species may increase prevalence. Furthermore, the three studied avian haemosporidian genera exhibited different abundance‐occupancy relationships across the major global climate gradients and in relation to host availability, emphasising that these relationships do not strictly follow common rules for vector‐borne parasites with different life histories.

Possibilities and limitations of magnetic resonance imaging in the diagnostics of endocervical adenocarcinomas

BACKGROUND: In recent decades, the incidence of cervical adenocarcinomas has increased from 5% to 20%. Endocervical adenocarcinomas are characterized by a more aggressive course and early metastasis. Owing to the difficulties in the cytological diagnosis of cervical adenocarcinoma, early radiation diagnostics and staging subsequently play a key role. Very few studies have examined the use of magnetic resonance imaging in diagnosing cervical adenocarcinomas. AIM: To determine the diagnostic informativeness of magnetic resonance imaging in the staging of cervical adenocarcinomas according to the T-criterion and assessing the depth of tumor invasion into the stroma of the cervix and clarify the semiotic signs of adenocarcinoma and features of tumor growth in the uterus. MATERIALS AND METHODS: In total, 123 patients diagnosed with cervical cancer (C53), who underwent diagnosis and treatment between 2020 and 2023, were examined. The examination results of 22 (18%) patients with cervical adenocarcinoma were analyzed. The average patient age was 56 years. A multiparametric magnetic resonance examination of the pelvic organs was performed on 22 patients using tomographs with a magnetic field strength of 1.5 T. Moreover, 14 (64%) patients underwent surgery including extirpation of the uterus and appendages with pelvic lymphadenectomy. The information value of magnetic resonance imaging was evaluated in 11 patients, whose first stage was surgical treatment. RESULTS: In this study, cervical adenocarcinoma was detected in 18% among all cases of cervical cancer. The information value of magnetic resonance imaging in assessing the local prevalence of endocervical adenocarcinoma according to the T-criterion was as follows (main value with the corresponding 95% confidence interval): sensitivity, 77.78% (39.99%–97.19%); specificity, 50.00% (1.26%–98.74%); positive predictive value, 87.50% (62.64%–96.69%); negative predictive value, 33.33% (7.30%–76.04%); and accuracy, 72.73% (39.03%–93.98%). The information value of magnetic resonance imaging in assessing the depth of tumor invasion into the cervical stroma was as follows: odds ratio, 3.500 (0.145%–84.694%); sensitivity, 85.7% (0.757%–0.993%); specificity, 33.3% (0.018%–0.0648%); positive predictive value, 75% (0.673%–0.883%); negative predictive value, 50% (0.027%–0.972%). CONCLUSIONS: The results of this study showed that magnetic resonance imaging is a good tool with high diagnostic informativeness in detecting endocervical cervical adenocarcinoma. The four macrostructures of tumor growth in endocervical adenocarcinoma identified during magnetic resonance imaging data analysis indicate locally aggressive tumor growth and a high frequency of endometrial dropouts. This finding will allow radiologists to structure a descriptive picture, including the verified cervical adenocarcinoma, to enhance methods of developing a treatment plan for the patient.

Prevalence, risk factors, and characterisation of extended-spectrum β-lactamase -producing Enterobacterales (ESBL-E) in horses entering an equine hospital and description of longitudinal excretion

BackgroundExtended-spectrum β-lactamase -producing Enterobacterales (ESBL-E) are important zoonotic pathogens that can cause serious clinical infections, also in horses. Preventing the spread of ESBL-E, especially in the equine hospital environment, is key to reducing the number of difficult-to-treat infections. Estimating the local prevalence of ESBL-E in horses is crucial to establish targeted infection control programs at equine hospitals. We conducted a prevalence and risk factor study in equine patients on admission to an equine teaching hospital in Finland through a rectal ESBL-E screening specimen of the horse and a questionnaire.ResultsThe prevalence of ESBL-E in admitted horses was 3% (5/161, 95% CI 1–7%); none of the tested factors remained statistically significant in multivariate analysis, although antimicrobial treatment within three months was borderline significant (p = 0.052). Extended-spectrum β-lactamase -producing Klebsiella pneumoniae ST6179:CTX-M-15 was detected in three horses using whole-genome sequencing, which in combination with patient records suggested nosocomial transmission. Escherichia coli isolates were ST1250:CTX-M-1 (n = 1), ST1079:CTX-M-1 (n = 1), and ST1245:CTX-M-14 (n = 1). Multiple virulence genes were detected in the ESBL-E isolates. In the ESBL-E positive horses enrolled in a one-year follow-up study, ESBL-E were unlikely to be isolated in rectal screening specimens after the initial positive specimen.ConclusionsThe prevalence of ESBL-E in horses visiting a veterinary teaching hospital in Finland is low, indicating an overall low prevalence estimate in the country’s equine population. No statistically significant risk factors were identified, likely due to the low number of cases. The duration of ESBL-E carriage is likely to be very short in horses.

Establishment and Application of a Triplex Real-Time Reverse-Transcription Polymerase Chain Reaction Assay for Differentiation of PEDV, TGEV and PKV.

The pathogens responsible for porcine viral diarrhea are diverse, causing significant economic losses to the pig industry. PEDV and TGEV are well-known pathogens causing diarrheal diseases in pigs, leading to significant economic losses in the breeding industry. In contrast, the newly identified diarrhea virus, PKV, has not garnered as much attention. However, co-infection of PKV with PEDV results in more severe symptoms in piglets, such as acute gastroenteritis, and promotes increased replication of PEDV. Rapid and accurate diagnosis of viral diarrhea is essential for farms to identify pathogens early and mitigate economic losses. This study describes the development of a triplex real-time fluorescent quantitative RT-qPCR technique that can simultaneously detect three RNA viruses associated with porcine viral diarrhea: PEDV, TGEV, and PKV. To establish the triplex RT-qPCR method for the simultaneous detection and identification of the above three diarrhea viruses, conserved regions of the M gene of TGEV, the N gene of PEDV, and the 3D gene of PKV were selected to design specific primers and probes. After optimizing the reaction conditions, the method's specificity, sensitivity, and reproducibility were evaluated. The triplex RT-qPCR method did not show a significant difference in PCR efficiency compared to the single RT-qPCR method. The method is specific to TGEV, PKV, and PEDV, exhibits no cross-reactivity with other pathogens, and demonstrates satisfactory sensitivity and reproducibility; the limit of detection (LOD) of PEDV, TGEV, and PKV is 11.42 copies/μL. Furthermore, the performance of the triplex RT-qPCR assay was compared with the Chinese standard single-assay method for detecting TGEV, PKV, and PEDV, showing complete consistency between the two methods (100% compliant). Subsequently, 1502 clinical diarrhea samples were collected from the Guangxi Zhuang Autonomous Region to investigate the local prevalence of TGEV, PKV, and PEDV and the positive rates were 16.38% (246/1502), 1.46% (22/1502), and 45.14% (678/1502), respectively. Co-infection of PEDV and PKV were most common, with a rate of 12.12% (182/1502). This study presents a valuable method for the rapid and simultaneous identification of PEDV, TGEV, and PKV in clinical animal farming practices, and provides a reassessment of the epidemiology of these diarrhea-causing viral pathogens in the Guangxi Zhuang Autonomous Region.

Shelf-to-basin shuttle of highly fractionated chromium isotopes in the Arctic Ocean

The oceanic chromium (Cr) cycle is mainly governed by the interconversion and the distribution of Cr(VI) and Cr(III) species and their stable isotopic ratios (δ53Cr) in the water column. As a result, the Cr cycle generates a strong correlation between the natural logarithm of its dissolved concentration and δ53Cr regardless of the location of sampling. A few studies have reported the Cr composition of certain regions falling off the global Cr array, highlighting the local prevalence of underlying mechanisms participating in the Cr cycle in the oceans. In an effort to better constrain the global Cr array, this study presents an extensive dataset for total dissolved Cr concentration ([Cr]T) and δ53Cr in the Arctic Ocean in regions meeting the environmental conditions where Cr was observed to fall off the global Cr array (e.g. continental shelves, restricted water circulation, sea ice melting). We find that more than 70% of the Arctic seawater collected plot below the global Cr array due to a small addition of highly fractionated Cr (−2.8 ‰ to −1.1 ‰) and its transport across all the Arctic regions sampled. We identify the Chukchi Shelf as the region where highly fractionated Cr is produced, from where a Cr shuttle could work in tandem with the Arctic Fe and Mn shuttles to explain the production and widespread export of isotopically light Cr in the Arctic waters. We identify a second non-reductive release of highly fractionated Cr in the Canadian Arctic Archipelago, Baffin Bay and potentially the Labrador Sea via sediment resuspension, alongside addition of isotopically light Cr originating from crustal rocks. These findings demonstrate that the Arctic-modified outflow signature of Cr isotopes modify the Cr isotopic signature of the North Atlantic waters, and that the North Atlantic waters may deviate from the global Cr array depending on whether the isotopically light Cr added to the Arctic Ocean is Cr(III) that has not been scavenged or Cr(III) that has oxidized to Cr(VI).

Mycoplasma genitalium retrospective audit of Northern Territory isolates from 2022.

The Northern Territory (NT) has the highest rates of sexually transmitted infections (STI) in Australia; however, the local prevalence of Mycoplasma genitalium (M. genitalium) has not been previously determined. This study was designed to review M. genitalium detection, to determine the regional NT prevalence and macrolide resistance rates. In our study the NT background prevalence of M. genitalium is 13%, with the highest detection rates occurring in central Australia and in correctional facility inmates. Symptomatic patients attending sexual health clinics have a positivity rate of 12%, but very high macrolide resistance. The decision to screen for M. genitalium should be based on several factors, including the prevalence of the infection in the local population; the availability of effective treatments; and the potential benefits and risks of detection and therapy.

Phenotypic and genotypic characterization of methicillin resistant Staphylococcus aureus associated with pyogenic infections.

Staphylococcal infections are one of the major infectious diseases affecting globally in spite of advances in development of antimicrobial agents. Knowledge and awareness about the local pattern and prevalence of MRSA infections plays a key role in treatment. The aim of this study was to identify MRSA strains by phenotypic and genotypic methods and to analyze the antibiotic susceptibility pattern of MRSA strains from patients attending a tertiary care hospital. This study was conducted over a period of 1 year, where 296 isolates of Staphylococcus aureus were isolated from various clinical specimens. The isolated strains were examined for antibiotic susceptibility by the modified Kirby Bauer disc diffusion method. Methicillin resistance was detected by cefoxitin disk diffusion test. A total of 104 isolates were found to be MRSA and 192 were found to be MSSA. Among the 104 MRSA isolates, 10 strains that were multidrug resistant were subjected to 16S rRNA gene sequencing analysis. All the 10 strains had a 99% match with S. aureus strains that were responsible for causing some serious biofilm mediated clinical manifestations like cystic fibrosis and device mediated infections. The biofilms were quantified using crystal violet staining and their ability to produce biofilms was analyzed using scanning electron microscopy and matched with the Genbank. Hence these phylogenetic analysis aid in treating the patients and combating resistance to antibiotics.

Clinical Presentation of Enterovirus D68 in a Swiss Pediatric University Center.

Enterovirus D68 (EV-D68) is responsible for millions of infections. In the last decade, there has been an increase in the number of children requiring hospital or critical care admission due to severe respiratory illness. Nevertheless, the epidemiological and clinical importance of EV-D68 infections remains unclear. We aimed to determine the local prevalence of EV-D68 infection in pediatric patients and to characterize its clinical presentation and disease burden compared with non-EV-D68 enterovirus and human rhinovirus (RV) infections. We performed a retrospective single-center study of children presenting with respiratory symptoms and positive respiratory panel polymerase chain reaction for EV/RV from November 2018 to December 2019. We tested EV/RV positive specimens with an EV-D68-specific polymerase chain reaction to discriminate EV-D68, non-EV-D68 and RV and compared their respective clinical presentation, outcomes and treatment. We identified 224 patients (median age 21 months), of which 16 (7%) were EV-D68 positive. They presented with cough (88%), wheezing (62%) and dyspnea (75%). EV-D68 infection had an odds ratio regarding pediatric respiratory severity-score of 11.6 relative to non-EV-D68 [confidence intervals (CI): 3.51-41.14], and of 9.9 (CI: 3.75-27.95) relative to RV. The fitted logistic regression showed that the odds of intensive care were 5 times more likely with EV-D68 than RV infection (CI: 1.32-19.28; P = 0.001). Patients with EV-D68 infections were more likely to receive medical support in the form of supplementary oxygen, antibiotics and steroids. EV-D68 infection is associated with higher morbidity and a higher likelihood of intensive care treatment than non-EV-D68 and RV infections.

Closing the Gaps in Hepatitis C Knowledge Among Internal Medicine Residents in the United States

BackgroundThe introduction of direct-acting antivirals (DAA) has revolutionized hepatitis C virus (HCV) treatment but has not translated into an appreciable decline in HCV prevalence, which is estimated to be 2.4 million in the United States. Efforts are thought to be limited by the lack of experience among nonspecialist providers in managing HCV. However, there have been no comprehensive surveys assessing HCV knowledge among medical trainees to determine if trends have shifted since the discovery of DAAs. MethodsWe performed a retrospective observational study of internal medicine (IM) residents in the United States (n = 1763) who completed the Physician Education and Assessment Center HCV learning module between 2021 and 2022. Participant pre- and post-test performance was compared with further stratified analysis by training year, geography, training program type, and local HCV prevalence using ANOVA and Chi-squared tests of proportions, respectively. ResultsIM residents universally lacked baseline HCV knowledge (average score ± standard deviation, 43% ± 19%); less than 50% of participants answered correctly in the majority of tested domains. There were no consistent trends in performance regardless of resident characteristic used to stratify the participants. Knowledge gaps improved after completing an online educational training module (P < .001). ConclusionsHCV knowledge remains limited among IM residents despite expansion of treatment options. Addressing these gaps during clinical training may substantially increase the availability of HCV treatment in the community, and online modules may be one means by which to integrate these efforts into medical training.