Polymerase Chain Reaction Test Research Articles

The Effect of Age and Comorbidities: Children vs. Adults in Their Response to SARS-CoV-2 Infection

While children have experienced less severe coronavirus disease (COVID-19) after SARS-CoV-2 infection than adults, the cause of this remains unclear. The objective of this study was to describe the humoral immune response to COVID-19 in child vs. adult household contacts, and to identify predictors of the response over time. In this prospective cohort study, children with a positive SARS-CoV-2 polymerase chain reaction (PCR) test (index case) were recruited along with their adult household contacts. Serum IgG antibodies against SARS-CoV-2 S1/S2 spike proteins were compared between children and adults at 6 and 12 months after infection. A total of 91 participants (37 adults and 54 children) from 36 families were enrolled. Overall, 78 (85.7%) participants were seropositive for anti-S1/S2 IgG antibody at 6 months following infection; this was higher in children than in adults (92.6% vs. 75.7%) (p = 0.05). Significant predictors of a lack of SARS-CoV-2 seropositivity were age ≥ 25 vs. < 12 years (odds ratio [OR] = 0.23, p = 0.04), presence of comorbidities (vs. none, adjusted OR = 0.23, p = 0.03), and immunosuppression (vs. immunocompetent, adjusted OR = 0.17, p = 0.02).

Examination of Pain, Quality of Life, Disability, and Anxiety in Patients Undergoing Lumbar Disc Surgery with and without COVID-19

Aim: This study aims to examine pain, disability, anxiety, and quality of life in patients undergoing lumbar disc herniation (LDH) surgery with and without COVID-19. Material and Method: Eighty patients who were diagnosed with LDH and planned surgery between March and September 2023 were included in the study. 50% of the patients were diagnosed with COVID-19 for at most six months, according to the positive polymerase chain reaction (PCR) test. 50% of the patients had no symptoms of COVID-19, ranging from mild to severe, and the PCR test was negative (-). The patients' pain level, disability, anxiety, and quality of life were evaluated and compared between the groups with and without COVID. Results: The mean scores of physical roles, physical function, mental health, body pain, and social function on the SF-36 quality of life scale in the LDH+COVID-19 (+) patient group were significantly lower than those in LDH+COVID-19 (-) (p

Comparison of clinical characteristics and disease burden of febrile seizures in children with and without COVID-19

BackgroundFebrile seizures (FS) are the most common seizure disorder in children and a common neurologic complication in children with coronavirus disease 2019 (COVID-19). This study aimed to identify differences in clinical characteristics and disease burden between FS with and without COVID-19.Materials and methodsWe conducted a retrospective analysis of medical data at our hospital from December 2019 to July 2023, focusing on hospitalized patients under the age of 14 diagnosed with FS who underwent COVID-19 polymerase chain reaction (PCR) testing. Descriptive statistics and analysis of variance were employed to compare the COVID-19 and non-COVID-19 groups in terms of clinical characteristics and disease burden.ResultsA total of 514 patients were included, with 106 testing positive for COVID-19 and 408 testing negative. Patients with COVID-19 were older (34.87 ± 6.16 vs. 28.61 ± 11.35 months, P < 0.001) and had a higher proportion of males (79.2% vs. 62.3%, P = 0.001). The COVID-19 group had longer seizure durations (4.57 ± 4.38 vs. 3.22 ± 2.91 min, P = 0.006) and more complex FS (25.5% vs. 15.9%, P = 0.022). Laboratory tests showed lower lymphocyte counts in the COVID-19 group (1.87 ± 1.48 vs. 2.75 ± 1.51 × 103/µL, P < 0.001) and higher creatine kinase levels (158.49 ± 82.89 vs. 110.89 ± 56.11 U/L, P < 0.001). No significant differences were found in hospital costs, length of hospitalization, and intensive care unit admissions.ConclusionClinicians should be knowledgeable about the distinct clinical characteristics of FS in children with COVID-19. Despite distinct features, the prognosis remains favorable and does not require excessive intervention. Ongoing monitoring and research are needed to fully understand the impact of COVID-19 on FS and optimize management strategies.

High performance of the DNA methylation-based WID-qEC test for detecting uterine cancers independent of sampling modalities.

Endometrial cancer (EC) is the most prevalent gynaecological cancer in high-income countries and its incidence is continuing to rise sharply. Simple and objective tools to reliably detect women with EC are urgently needed. We recently developed and validated the DNA methylation (DNAme)-based women's cancer risk identification-quantitative polymerase chain reaction test for endometrial cancer (WID-qEC) test that could address this need. Here, we demonstrate that the stability of the WID-qEC test remains consistent regardless of: (i) the cervicovaginal collection device and sample media used (Cervex brush and PreservCyt or FLOQSwab and eNAT), (ii) the collector of the specimen (gynaecologist- or patient-based), and (iii) the precise sampling site (cervical, cervicovaginal and vaginal). Furthermore, we demonstrate sample stability in eNAT medium for 7 days at room temperature, greatly facilitating the implementation of the test into diagnostic laboratory workflows. When applying FLOQSwabs (Copan) in combination with the eNAT (Copan) sample collection media, the sensitivity and specificity of the WID-qEC test to detect uterine (i.e., endometrial and cervical) cancers in gynaecologist-taken samples was 92.9% (95% confidence interval [CI] = 75.0%-98.8%) and 98.6% (95% CI = 91.7%-99.9%), respectively, whilst the sensitivity and specificity in patient collected self-samples was 75.0% (95% CI = 47.4%-91.7%) and 100.0% (95% CI = 93.9%-100.0%), respectively. Taken together these data confirm the robustness and clinical potential of the WID-qEC test.

Assessment of olfactory and gustatory functions in COVID-19 patients

BackgroundOlfactory and gustatory disorders are common problems encountered during the COVID-19 pandemic with a significant impact on the patient’s quality of life: The aim of this study was to assess the olfactory and gustatory functions in COVID-19 patients with correlation between them and clinical and laboratory markers. This was a cross-sectional study conducted on 63 subjects recruited from the COVID-19 clinics at Police Authority and Menoufia University hospitals. The patients were assessed using history taking, anterior rhinoscopy, endoscopic examination, computed tomography, and polymerase chain reaction (PCR) test. Olfactory functions were assessed using the alcohol threshold test. Gustatory functions were assessed using the three-drop method. The olfactory and gustatory functions were correlated with age, gender, and laboratory parameters. Also, the recovery of smell and taste disorders was correlated with our assessed laboratory markers.ResultsThe prevalence of olfactory dysfunction among study participants was 41 patients (65%) of the participants including 12 patients (19.1%) having mild hyposmia, 10 patients (15.8%) having moderate hyposmia, 9 patients (14.3%) having severe hyposmia, and 10 patients (15.8%) having complete anosmia. The prevalence of gustatory dysfunction among study participants was 24 patients (38.1%). Age, gender, and laboratory parameters did not show any statistically significant difference between those who experienced olfactory dysfunction or gustatory dysfunction and those who did not. However, there was a significant positive correlation between the total leucocytic count, serum level of CRP, and serum level of D-dimer and the degree of olfactory dysfunction (0.049, 0.03, and 0.02, respectively). There was a nonsignificant correlation between recovery of olfactory and gustatory dysfunction and laboratory markers.ConclusionOlfactory and gustatory dysfunction are established clinical presentations among COVID-19-positive patients. The laboratory markers had no correlation with the incidence of these dysfunctions or their recovery. However, TLC, serum CRP, and serum D-dimer had a significant positive correlation with the severity of olfactory dysfunction.

Diagnostic Accuracy of Conjunctival Rt-Pcr in Sars-Cov-2: A Systematic Review and Diagnostic Accuracy Meta-Analysis

ABSTRACT Purpose To study the positivity rate of conjunctival realtime polymerase chain reaction (RT-PCR) testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Design Systematic review and diagnostic accuracy meta-analysis. Methods MEDLINE and EMBASE were queried using medical subject headings terms. Diagnostic accuracy meta-analyses and forest plots were obtained using the RevMan software. Results After deduplication, appraisal of abstract titles and full-text analysis of 1441 articles, 42 articles with 3351 COVID-19 patients were included in this review. Of these, 412 conjunctival swabs/Schirmer paper strips tested positive for SARS-CoV-2 by RT-PCR. The pooled sensitivity of the RT-PCR tests across the 24 studies with laboratory-confirmed COVID-19 patients was 10.3%. Conclusions Only 1 in 10 RT-PCR tests performed on conjunctival swabs were positive for SARS-CoV-2. Although this suggests that SARS-CoV-2 is likely present and detectable in the conjunctiva, this detection method has low diagnostic potential.

Identification of unique electromagnetic signatures from GLRaV-3 infected grapevine leaves in different stages of virus development.

Grapevine leafroll associated virus 3 (GLRaV-3) is one of the most common viruses that adversely affect grape production quality around the world. Grapevine virus is usually detected by polymerase chain reaction (PCR) tests, but the main diagnostic challenges with the PCR are uneven distribution of symptoms, low virus titers in early stage, and the tests are time consuming and expensive. In the absence of effective control and treatment for grapevine virus, the recommendation is to remove infected vines before they become a source of transmission and a rapid and early detection method for viruses is urgently needed. This study investigated how GLRaV-3 infection affects spectral behavior of grapevine leaves and the use of remote sensing tools to identify changes caused by the biotic stress. A Real-Time RT-qPCR test was performed to select representative vines with healthy and GLRaV-3 infection, and changes in electromagnetic (EM) spectrum of leaves were observed with a portable hyperspectral spectrometer and a multispectral sensor on a remotely piloted aircraft system (RPAS). The results of this study suggest that foliar EM reflectance may differ depending on the presence or absence of visible symptoms of infected leaves and different stages of virus infection progress could be indicated by changes in the relative rate of reflectance around 700 nm. This research also confirmed that the development of a narrow-band hyperspectral index for the detection of grapevine virus is feasible, further research is recommended in a much more comprehensive investigation including a combination of hyperspectral sensor and chlorophyll fluorescence sensors, interpolation of suspect wavebands into ratios or indices, larger sample sizes and a more controlled study environment.

Detection of Perkinsus sp. in Chionista fluctifraga cultivated in the southeast Gulf of California

Objective. To determine the presence of Perkinsus sp. in the sand clam Chionista fluctifraga cultivated in an intertidal zone of the southeastern Gulf of California, using Ray's thioglycollate fluid medium staining (MFTR) and polymerase chain reaction (PCR). Material and Methods. The prevalence and parasite load of Perkinsus sp. were monthly obtained and correlated with environmental water conditions and clam biometric indicators (n = 540), from May 2018 to September 2019. Results. Presumptive hypnospores of the protozoan were detected in eight months of culture. The prevalence fluctuated from 3.3% to 13.3%, while the average parasite load ranged from 2 to 1286 hypnospores/g of tissue. The intensity of infection varied from negative to light. The prevalence and parasite load were correlated with each other (r=0.61, P˂0.05) but not with the environmental parameters, nor with the biometric indicators of the clam. The PCR test was negative for the MFTR positive cases. Conclusions. Presumptive hypnospores of Perkinsus sp. were detected in C. fluctifraga without clear indications of infection that compromised the clam health in culture. The constant monitoring of Perkinsus sp. in C. fluctifraga is highly recommended to establish possible infections.

Characterization of Post-COVID-19 Definitions and Clinical Coding Practices: Longitudinal Study.

Post-COVID-19 condition (colloquially known as "long COVID-19") characterized as postacute sequelae of SARS-CoV-2 has no universal clinical case definition. Recent efforts have focused on understanding long COVID-19 symptoms, and electronic health record (EHR) data provide a unique resource for understanding this condition. The introduction of the International Classification of Diseases, Tenth Revision (ICD-10) code U09.9 for "Post COVID-19 condition, unspecified" to identify patients with long COVID-19 has provided a method of evaluating this condition in EHRs; however, the accuracy of this code is unclear. This study aimed to characterize the utility and accuracy of the U09.9 code across 3 health care systems-the Veterans Health Administration, the Beth Israel Deaconess Medical Center, and the University of Pittsburgh Medical Center-against patients identified with long COVID-19 via a chart review by operationalizing the World Health Organization (WHO) and Centers for Disease Control and Prevention (CDC) definitions. Patients who were COVID-19 positive with either a U07.1 ICD-10 code or positive polymerase chain reaction test within these health care systems were identified for chart review. Among this cohort, we sampled patients based on two approaches: (1) with a U09.9 code and (2) without a U09.9 code but with a new onset long COVID-19-related ICD-10 code, which allows us to assess the sensitivity of the U09.9 code. To operationalize the long COVID-19 definition based on health agency guidelines, symptoms were grouped into a "core" cluster of 11 commonly reported symptoms among patients with long COVID-19 and an extended cluster that captured all other symptoms by disease domain. Patients having ≥2 symptoms persisting for ≥60 days that were new onset after their COVID-19 infection, with ≥1 symptom in the core cluster, were labeled as having long COVID-19 per chart review. The code's performance was compared across 3 health care systems and across different time periods of the pandemic. Overall, 900 patient charts were reviewed across 3 health care systems. The prevalence of long COVID-19 among the cohort with the U09.9 ICD-10 code based on the operationalized WHO definition was between 23.2% and 62.4% across these health care systems. We also evaluated a less stringent version of the WHO definition and the CDC definition and observed an increase in the prevalence of long COVID-19 at all 3 health care systems. This is one of the first studies to evaluate the U09.9 code against a clinical case definition for long COVID-19, as well as the first to apply this definition to EHR data using a chart review approach on a nationwide cohort across multiple health care systems. This chart review approach can be implemented at other EHR systems to further evaluate the utility and performance of the U09.9 code.

Genetic characterization and pathogenic effects of Hepatozoon canis infection in police dogs in Egypt

BackgroundHepatozoon canis is a protozoan parasite transmitted to dogs through ingesting the arthropod vector (hard ticks), which contains mature protozoal oocysts harboring infectious sporozoites.AimsThis study aims to evaluate the blood parameters, biochemical assays and histopathological appraisal of infected police dogs with Hepatozoon canis, from kennels in the police academy of Egypt during 2020–2021.MethodsRed blood cells count, hemoglobin, hematocrit, blood platelets and white blood cells count from collected blood samples were analyzed, and serum albumin, creatinine, urea, aspartate aminotransferase and alanine aminotransferase were analyzed from serum samples. Polymerase chain reaction amplified the 18S ribosomal RNAgene of the Hepatozoon species for genetic analysis, and the deoxyribonucleic acid products were sequenced and added to GenBank.ResultsThe present study resulted in 5% of the police dog population being infested with Rhipicephalus sanguineus. This study registered the sequences of the Hepatozoon canis 18S ribosomal RNAgene in Egypt for the first time in Genbank (MW362244.1–MW362245.1). The biochemical assay revealed that the parasite severely affected the protein, significantly increasing serum albumin in positive polymerase chain reaction testing dogs.ConclusionA thorough inspection discovered that 100 police dogs had clinical symptoms like fever, emaciation and anemia, while the other 200 were healthy and had no evident clinical indicators.

Ocular manifestations of Monkeypox virus (MPXV) infection with viral persistence in ocular samples – a case series.

ObjectiveWe describe the clinical presentation and ocular viral dynamics in patients with Monkeypox virus-related ophthalmic disease (MPXROD). MethodsIn this case series, we investigated five consecutive patients with confirmed mpox, diagnosed through a positive Monkeypox virus (MPXV) Polymerase Chain Reaction (PCR) test and presenting with ocular symptoms. They were referred from the Reference Center for Sexually Transmitted Infections in São Paulo (CRT) to the Uveitis Sector at the Federal University of São Paulo, between August and December 2022. We performed PCR testing on ocular samples and culture supernatants for MPXV in all patients. Viral sequencing was conducted in one of the cases. ResultsReplicating MPXV was identified in at least one ocular sample of all patients, between day 31 and day 145 after the onset of skin lesions. All patients presented with keratitis, 3 with uveitis (60%) and two exhibited hypopyon (40%). The onset of ocular symptoms occurred at a mean of 21,2 days after the appearance of the first skin lesion and persisted, on average, for 61,6 days, with a worsening trend observed until the initiation of tecovirimat treatment. Tecovirimat treatment was administered to all patients, with initiation occurring between 31 and 145 days after the onset of skin lesions. MPXV genome sequencing of an isolate from one patient classified it as belonging to lineage B1 in clade IIb. ConclusionThis study reveals a late onset and persistence of sight threatening ocular disease, along with potential viral infectivity even after systemic resolution in mpox cases. These findings highlight the risk of ongoing transmission from individuals with prolonged ocular manifestations, particularly through ocular discharge.

Investigation of severe acute respiratory syndrome coronavirus 2 infection status in solid organ transplant recipients treated with tixagevimab/cilgavimab

IntroductionTixagevimab and cilgavimab (T/C) are neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be used to prevent SARS-CoV-2 infection in solid organ transplant (SOT) recipients. However, their neutralizing activity against recent variants was reduced, raising concerns regarding the emergence of breakthrough coronavirus diseases 2019 (COVID-19). This study aimed to investigate the status of the COVID-19 breakthrough after T/C administration. MethodsWe retrospectively investigated breakthrough COVID-19 in SOT recipients administered T/C at Kyoto University Hospital, Japan, from November 2022 to March 2023. Patients were monitored for 6 months after T/C administration. SARS-CoV-2 infection was diagnosed using polymerase chain reaction or antigen tests. The monthly incidence rates of SARS-CoV-2 infection were calculated using the person–time method. ResultsT/C were administered to 67 SOT recipients (liver, 16; lung, 36; and kidney, 15), of whom five were infected with SARS-CoV-2. All five cases were classified as mild, and none of these patients required admission to the intensive care unit (ICU) or died. All infected individuals tested positive for SARS-CoV-2 after March 2023, when T/C-resistant subvariant strains became predominant. The monthly incidence rate of SARS-CoV-2 infection, calculated using the person–time method, suggested an increasing trend. ConclusionsDuring the T/C-resistant variant epidemic, SARS-CoV-2 infections were identified even after T/C administration, suggesting that the prophylactic effects of T/C were invalid. Therefore, emerging variants must be carefully monitored and characterized to determine appropriate antiviral strategies, such as the use of suitable neutralizing antibodies.

The Emergence of Linezolid-Resistant Staphylococcus Epidermidis in the COVID-19 Hospitalized Intubated Patients in North Khorasan, Iran.

The present study aimed to investigate secondary bacterial infections among patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Coagulase-negative Staphylococci can infect immunocompromised patients. Linezolid resistance among Staphylococcus epidermidis is one of the most critical issues. In 2019, 185 SARS-CoV-2-positive patients who were admitted to North Khorasan Province Hospital (Bojnurd, Iran), were investigated. Patients having positive SARS-CoV-2 reverse transcriptase real-time polymerase chain reaction (RT-PCR) test results, who had a history of intubation, mechanical ventilation, and were hospitalized for more than 48 hours were included. After microbiological evaluation of pulmonary samples, taken from intubated patients with clinical manifestation of pneumonia, co-infections were found in 11/185 patients (5.94%) with S. epidermidis, Staphylococcus aureus, and Acinetobacter baumani, respectively. Remarkably, seven out of nine S. epidermidis isolates were linezolid resistant. Selected isolates were characterized using antimicrobial resistance patterns and molecular methods, such as Staphylococcal cassette chromosome mec (SCCmec) typing, and gene detection for ica, methicillin resistance (mecA), vancomycin resistance (vanA), and chloramphenicol-florfenicol resistance (cfr) genes. All of the isolates were resistant to methicillin, and seven isolates were resistant to linezolid. Nine out of 11 isolated belonged to the SCCmec I, while two belonged to the SCCmec IV. It should be noted that all patients had the underlying disease, and six patients had already passed away. The increasing linezolid resistance in bacterial strains becomes a real threat to patients, and monitoring such infections, in conjunction with surveillance and infection prevention programs, is very critical for reducing the number of linezolid-resistant Staphylococcal strains. A preprint of this study was published at https://europepmc.org/article/ppr/ppr417742.

Prevalence of Malaria among Under-5 Children in a Secondary Care Level, Ondo State, Nigeria

Background: Malaria continues to be a leading cause of ill health among children. Globally, this infection remains the major cause of morbidity and mortality especially among the under-five. Aim: The aim of the study was to investigate and document the prevalence of malaria infection among age groups, genders, birth orders, and blood groups of children who attend a secondary health care level, south-west, Nigeria. Subjects and Methods: Blood samples of 500 children whose ages ranged between 1 day and 5 years were collected through venipuncture, and these were tested for malaria parasites through the microscopy method, positivity was confirmed by Polymerase Chain Reaction (PCR) test. It was a hospital-based cross-sectional study. The children were recruited from various points of entry into the hospital which included the emergency room, newborn unit, and outpatient department (OPD). Data analyses were done using the SPSS statistical software and p-value &lt; 0.05 was considered significant. Results: The prevalence of malaria among the neonates (age group 0 to 28 days) was 60.2%, the prevalence of malaria was 49.2% among the infants (aged 29 days to 1 year) while the prevalence was 52.9% among children aged 1 to 5 years (χ2 = 0.004, p &lt; 0.05). The gender prevalence of malaria infection was 30.4% for males and 21.8% for females (χ2 =0.000, p&lt;0.05). The prevalence of malaria infection among birth orders showed that children in the first, second, third, fourth, and fifth birth orders are 41.0%, 28.0%, 22.6%, 5.4%, and 3.1%, respectively (χ2 = 0.0210, p &lt; 0.05). Prevalence of malaria among the blood groups are; A− (1.92%), A+ (13.41%), B− (1.15%), B+ (19.54%), O− (6.51%), O+ (51.73%), AB− (0.38%) and AB+ (5.36%). Conclusion: There is a high prevalence of malaria among the children examined in this study, there is therefore the need to intensify efforts to reduce the burden of the infection in the study area, especially among the children.

The Relationship Between Acute Phase Reactants Levels at the Time of Admission and Comorbid Conditions with Mortality in Patients Diagnosed With Covid-19

Background/aims: The covid-19 pandemic, which is a global problem, is still one of the most important health problems today. Treatment and vaccine studies are as important in predicting prognosis and mortality as early diagnosis and prevention of the disease, which continues unabated. İn this study, it was aimed to evaluate the success of laboratory values, comorbid conditions and intensive care scoring at the time of first admission of patients admitted to intensive care with the diagnosis of Covid-19 in predicting mortality. Methods: The study was conducted in a 3rd step adult emergency deparment. The study included 106 patients who were admitted to the emergency department and subsequently admitted to intensive care, had a positive Covid-19 polymerase chain reaction(PCR) test and met the inclusion criteria. Results: The average age of 10 patients included in the study was 71.85. 65.09 percent of these patients are male and 24.1% are female. While 29 of the patients were survivors, 77 were deceased. İn deceased patients; Procalcitonin, lactate, leukocyte, neutrophil, urea, creatine, asti crpi ferritin, d-dimer values were found to be higher than the other group. Lymphocyte, lymphocyte percentage and pH values were found to be significantly low. Sequential Organ Failure Score(SOFA) and Acute Physiology and Chronic Health Evaluation(APACHE) 2 scores were found to be higher in deceased patients. Conclusion: Ferritin, lactate, urea and pH values, comorbid conditions, Sequantial Organ Failure Score and Acute Sphysiology and Chronic Health Assessment 2 can be used to predict mortality in covid-19 disease.

Novel multiplex-PCR test for Escherichia coli detection.

Detection of E. coli from environmental or clinical samples is important due to the common occurrence of this species of bacteria in all human and animal environments. As commonly known, these bacteria strains can be commensal and pathogenic, causing numerous infections of clinical importance, including infections of the digestive system, urinary, respiratory, and even meninges, particularly dangerous for newborns. The developed multiplex polymerase chain reaction test, confirming the presence of E. coli in samples, can be used in many laboratories. The test provides new opportunities for quick and cheap analyses, detecting E. coli using only three pairs of primers (analysis of the presence of three genes) responsible for metabolism and distinguishing E. coli from other pathogens from the Enterobacteriaceae family. Compared to other tests previously described in the literature, our method is characterized by high specificity and sensitivity.

Utilizing novel Escherichia coli-specific conserved signature proteins for enhanced monitoring of recreational water quality.

Escherichia coli serves as a proxy indicator of fecal contamination in aquatic ecosystems. However, its identification using traditional culturing methods can take up to 24h. The application of DNA markers, such as conserved signature proteins (CSPs) genes (unique to all species/strains of a specific taxon), can form the foundation for novel polymerase chain reaction (PCR) tests that unambiguously identify and detect targeted bacterial taxa of interest. This paper reports the identification of three new highly-conserved CSPs (genes), namely YahL, YdjO, and YjfZ, which are exclusive to E. coli/Shigella. Using PCR primers based on highly conserved regions within these CSPs, we have developedquantitative PCR (qPCR) assays for the evaluation of E. coli/Shigella species in water ecosystems. Both in-silico and experimental PCR testing confirmed the absence of sequence match when tested against other bacteria, thereby confirming 100% specificity of the tested CSPs for E. coli/Shigella. The qPCR assays for each of the three CSPs provided reliable quantification for all tested enterohaemorrhagic and environmental E. coli strains, a requirement for water testing. For recreational water samples, CSP-based quantification showed a high correlation (r > 7, p < 0.01) with conventional viable E. coli enumeration. This indicates that novel CSP-based qPCR assays for E. coli can serve as robust tools for monitoring water ecosystems and other critical areas, including food monitoring.

Surveillance for highly pathogenic avian influenza A (H5N1) in a raptor rehabilitation center-2022.

An ongoing, severe outbreak of highly pathogenic avian influenza virus (HPAI) A H5N1 clade 2.3.4.4b has been circulating in wild and domestic bird populations throughout the world, reaching North America in 2021. This HPAI outbreak has exhibited unique characteristics when compared to previous outbreaks. The global distribution of disease, prolonged duration, extensive number of species and individual wild birds affected, and the large impact on the global poultry industry have all exceeded historical impacts of previous outbreaks in North America. In this study, we describe the results of HPAI surveillance conducted at The Raptor Center, a wildlife rehabilitation hospital at University of Minnesota (Saint Paul, MN, U.S.A.), from March 28th-December 31, 2022. All wild raptors admitted to the facility were tested for avian influenza viruses using polymerase chain reaction (PCR) testing. All non-negative samples were submitted to the United States Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) National Veterinary Services Laboratories for confirmatory HPAI testing and genetic sequencing. During the study period, 996 individual birds representing 20 different species were tested for avian influenza, and 213 birds were confirmed HPAI positive. Highly pathogenic avian influenza surveillance conducted at The Raptor Center contributed 75% of the HPAI positive raptor detections within the state of Minnesota, located within the Mississippi flyway, significantly augmenting state wildlife surveillance efforts. The viral genotypes observed in birds sampled at The Raptor Center were representative of what was seen in wild bird surveillance within the Mississippi flyway during the same time frame. Wildlife rehabilitation centers provide an opportune situation to augment disease surveillance at the human, wildlife and domestic animal interface during ongoing infectious disease outbreaks.

Association between SARS-CoV-2 Infection and Adverse Perinatal Outcomes by Race/Ethnicity in a Large Integrated Health Care System.

Recent studies have reported associations between severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection during pregnancy and adverse perinatal outcomes but the extent to which these associations vary by race/ethnicity remains uncertain. Therefore, we examined how the association between prenatal SARS-CoV-2 infection and adverse perinatal outcomes may be modified by race/ethnicity. A retrospective cohort study was performed using data on 67,986 pregnant women extracted from the Kaiser Permanente Southern California electronic health records between April 6, 2020, and December 31, 2021. Upon admission to labor and delivery, all women were routinely tested for coronavirus disease 2019 (COVID-19) using real-time reverse-transcriptase polymerase chain reaction test. Adjusted odds ratios (aORs) were used to estimate associations. During the study period, COVID-19 was diagnosed in 4,960 (7%) of singleton pregnancies, with the highest rates observed among Hispanics (9.4%) and non-Hispanic Blacks (6.2%). Compared with non-Hispanic Whites, Hispanics (aOR: 1.12, 95% CI: 1.03, 1.21) with SARS-CoV-2 infection had the highest odds of a pregnancy associated with nonreassuring fetal heart rate tracing. Neonates of all races/ethnicities, except for non-Hispanic Blacks, showed significantly increased odds of SARS-CoV-2 infection, with the highest risk observed among Asians/Pacific Islanders (aOR: 10.88, 95% CI: 1.33, 89.04). Non-Hispanic White mothers who tested positive were admitted to intensive care unit (ICU) at a higher rate at delivery and within 7 days of delivery (aOR: 34.77, 95% CI: 11.3, 107.04; aOR: 26.48, 95% CI: 9.55, 73.46, respectively). Hispanics were also at a significantly higher odds of admission to ICU (aOR: 4.62, 95% CI: 2.69, 7.94; aOR: 4.42, 95% CI: 2.58, 7.56, respectively). Non-Hispanic Black, Hispanic, and Asian/Pacific Islander mothers who tested positive for SARS-CoV-2 prenatally, were at increased risk for preeclampsia/eclampsia, and preterm birth as compared to non-Hispanic White mothers. The findings highlight racial/ethnic disparities in the association between SARS-CoV-2 infection and adverse perinatal outcomes. The risk of neonatal SARS-CoV-2 infection was highest for Asian/Pacific Islanders. We also observed a remarkably high risk of ICU admission for non-Hispanic White mothers infected with SARS-CoV-2. · Race/ethnicity influences perinatal outcomes in pregnancies impacted by SARS-CoV-2.. · The risk of neonatal SARS-CoV-2 infection was highest for Asian/Pacific Islanders.. · White mothers had a notably high risk of ICU admission at delivery following SARS-CoV-2 infection..

Whole-Blood PCR Preferred for Timely Diagnosis of Neuroinvasive West Nile Virus Infections: Lessons From the 2021 Arizona Outbreak.

In 2021, the state of Arizona experienced the largest focal outbreak of West Nile virus (WNV) in US history. Timely and accurate diagnostic testing remains a challenge for WNV due to transient viremia and limited immunoassay specificity. Recent studies have identified whole blood (WB) and urine as more sensitive specimen types for the detection of WNV RNA. We evaluated ordering practices, test performance, and patient characteristics of probable and confirmed cases. In total, we identified 190 probable and proven cases, including 127 patients (66.8%) with neuroinvasive disease. Among all cases, only 29.5% had WNV polymerase chain reaction (PCR) testing ordered on WB, of which 80.3% resulted as positive, including 7 cases in which WNV serologic testing was negative and 5 cases for which serologic testing was not ordered. In comparison, only 23.7% of cases that had cerebrospinal fluid (CSF) PCR ordered had a positive result, including 3 cases that were negative by PCR on WB. In contrast, WNV PCR on WB detected 12 neuroinvasive cases that were CSF PCR negative. WNV PCR testing in urine was only ordered on 2 patients, both of whom were positive. Crossing cycle threshold (Ct) values were not significantly different between WB and CSF specimen types, nor was there a correlation between Ct value and days from symptom onset at the time of sample collection; all specimen types and time points had Ct values, with 98% above 30. WB was positive by WNV PCR in several patients for >7 days (range, 7-25 days) after symptom onset, as was the CSF PCR. Taken together, these findings indicate that WNV PCR testing on WB may be the best initial test for timely diagnosis of WNV infection, irrespective of clinical manifestation; however, if negative in patients with suspected neuroinvasive disease, WNV PCR testing on CSF should be ordered.