Evaluation of COVID-19 rapid antigen test against polymerase chain reaction test in immunocompromised patients.

On the 11th of March 2020, the world faced a new global pandemic, COVID-19 which is a disease caused by the novel coronavirus, it had multiple devastating outcomes on multiple sectors along with significant rates of mortality. These challenges encouraged the development of multiple testing methods, as well as anti-viral medications such as Molnupiravir, as well as evaluating the efficacy of available medications against it, like; Azithromycin, Ritonavir and Hydroxychloroquine. Vaccination against COVID-19 forged into a significant challenge, few months ensuing the first case of SARS-CoV-2, which was diagnosed in December 2019, in Wuhan-China, thus, multiple vaccines were approved for use around the world to combat this pandemic. Our study includes a sample of 556 oncology patients at Augusta Victoria Hospital in Jerusalem, all patients were tested using Panbio rapid antigen test and Allplex PCR Assay. The main objective was to study the sensitivity and specificity of Rapid antigen test, which contributes to a faster isolation call and management of infected patients, thus decreasing the risk on spread to other patients and health care. Patients were categorized based on two factors: Ct range and age group and studying their possible effect on false-negative results. Patients with Ct value less than 20, had the highest detection rate which is consistent with other studies in the literature. The sensitivity and specificity of Panbio Rapid Antigen testing were of 69.9% and 100%, respectively. A correlation between age group and false negative results could not be made, but a correlation between Ct value and false negative result was noticed, Ct value was directly related to false negative results. P-value of 0.007 indicated that results were statistically significant where PCR test is considered more sensitive compared to rapid antigen test.

Serotype distribution and drug resistance in Streptococcus pneumoniae, Palestinian Territories.

To determine antimicrobial drug resistance of Streptococcus pneumoniae serotypes, we analyzed isolates from blood cultures of sick children residing in the West Bank before initiation of pneumococcal vaccination. Of 120 serotypes isolated, 50.8%, 73.3%, and 80.8% of the bacteremia cases could have been prevented by pneumococcal conjugate vaccines. Serotype 14 was the most drug-resistant serotype isolated.

Characterization of large mumps outbreak among vaccinated Palestinian refugees.

During a large mumps virus (MuV) outbreak which occurred in the Palestinian refugee camps of the West Bank, 68.1% (2,636/3,871) of the cases were vaccinated with one dose of trivalent measles, mumps, and rubella (MMR) vaccine. Attack rates by camp ranged from less than 1 case per 1,000 people in the population to 43/1,000 (overall, 11/1,000). The outbreak lasted from December 2003 to June 2005, with two peaks, one from April to May 2004 and the other from March to April 2005. To control the outbreak, a mass MMR vaccination campaign was conducted in May 2005. Evaluation of the immune status of cases (n=59) and healthy controls (n=51) revealed high levels of mumps immunoglobulin G (IgG) and a low MuV-specific IgM in clinical cases indicative of a booster immune response. This suggested a secondary rather than a primary infection due to the insufficient protection conferred by the single vaccine dose included in the vaccination program. This prediction was further confirmed by the low seroprevalence (68.6%) found in the healthy control group, which was below the threshold level required for MuV herd immunity. Mumps diagnosis was established mainly by reverse transcription-PCR in clinical samples obtained within 48 h from the onset of disease. Of the parotid fluids and nasopharyngeal aspirates analyzed, 92% were positive for MuV RNA, while only 33% of the urine samples were positive. Phylogenetic analysis of the MuV SH gene identified the outbreak strain as the H genotype, which has been in circulation worldwide at least since 1989.

Comparison between pernasal flocked swabs and nasopharyngeal aspirates for detection of common respiratory viruses in samples from children.

In this prospective study we compared the use of pernasal flocked swab samples with the use of nasopharyngeal aspirate (NPA) samples for the detection of respiratory viruses from 455 children less than 5 years of age. Overall, the sensitivity and the specificity of the pernasal flocked swab samples were 98.5% and 100%, respectively. The excellent sensitivity of the flocked swab samples in combination with the rapid means by which they may be collected makes them an alternative to NPA samples, whose collection is more invasive.

High rate of human bocavirus and adenovirus coinfection in hospitalized Israeli children.

We investigated coinfection of human bocavirus (HBoV) and other respiratory viruses in hospitalized children by real-time PCR. A high rate (69.2%) of adenovirus infection was found among children infected with HBoV. Such high rates of HboV-adenovirus coinfection have not been previously reported, underscoring the need to investigate the contribution of HBoV in patient clinical presentations.

Population Screening Using Sewage Reveals Pan-Resistant Bacteria in Hospital and Community Samples.

The presence of pan-resistant bacteria worldwide possesses a threat to global health. It is difficult to evaluate the extent of carriage of resistant bacteria in the population. Sewage sampling is a possible way to monitor populations. We evaluated the presence of pan-resistant bacteria in Israeli sewage collected from all over Israel, by modifying the pour plate method for heterotrophic plate count technique using commercial selective agar plates. This method enables convenient and fast sewage sampling and detection. We found that sewage in Israel contains multiple pan-resistant bacteria including carbapenemase resistant Enterobacteriacae carrying blaKPC and blaNDM-1, MRSA and VRE. blaKPC carrying Klebsiella pneumonia and Enterobacter cloacae were the most common Enterobacteriacae drug resistant bacteria found in the sewage locations we sampled. Klebsiella pneumonia, Enterobacter spp., Escherichia coli and Citrobacter spp. were the 4 main CRE isolated from Israeli sewage and also from clinical samples in our clinical microbiology laboratory. Hospitals and Community sewage had similar percentage of positive samplings for blaKPC and blaNDM-1. VRE was found to be more abundant in sewage in Israel than MRSA but there were more locations positive for MRSA and VRE bacteria in Hospital sewage than in the Community. Therefore, our upgrade of the pour plate method for heterotrophic plate count technique using commercial selective agar plates can be a useful tool for routine screening and monitoring of the population for pan-resistant bacteria using sewage.

Molecular detection of antibiotic resistance genes from positive blood cultures.

Rapid detection of the bacterial causative agent causing sepsis must be coupled with rapid identification of the antibiotic resistant mechanism that the pathogen might possess. Real-time PCR (qPCR)-based assays have been extensively utilized in the clinical microbiology field as diagnostic tools for the rapid detection of specific nucleic acid (NA) targets. In this chapter, we will discuss the technical aspects of using an internally controlled qPCR assay for the rapid detection of Klebsiella pneumoniae carbapenemase gene (bla KPC) in positive Bactec blood culture bottles. The multiplex qPCR (bla KPC/RNase P) utilizes specific primers and probes for the detection of the bacterial carbapenem resistance mechanism, bla KPC gene, and the internal control RNase P. The internal control of the qPCR assay is vital for detecting any inhibitors that are well known to be present in the blood culture bottles. Rapid detection of the antibiotic resistant mechanism present in the bacterial pathogen causing sepsis can help in better managing patients' infection.

Clinical Microbiology in Pediatrics.

Abstract ABSTRACTThe clinical microbiology laboratory plays a critical role in the diagnosis of infectious diseases in the pediatric population. Children are uniquely susceptible to infectious agents because of immature immunologic and physiologic systems. The etiologies and manifestations of infections in pediatric patients are often distinctly different and more severe than those seen in adults. This requires laboratories to implement unique microbiologic methods for rapid and accurate diagnoses in this population. The broad spectrum of diseases diagnosed in the pediatric period and the growing complexity of pediatric laboratory testing can be challenging. This review discusses key aspects of pediatric clinical microbiology including preanalytic and analytic variables, test selection, performance, and data interpretation. In order to provide comprehensive pediatric clinical microbiology services, laboratories need to be aware of the specific needs of this patient population.

Survival of fastidious and nonfastidious aerobic bacteria in three bacterial transport swab systems.

In the present study, we followed the CLSI procedure M40-A to evaluate three specimen transport systems [the new BD CultureSwab MaxV(+), the new Remel BactiSwab, and the Medical Wire & Equipment Transwab] for the survival of fastidious and nonfastidious organisms for 0, 6, 24, and 48 h at room temperature. BD CultureSwab MaxV(+) outperformed the other two swabs for the recovery of the three fastidious organisms, Haemophilus influenzae, Neisseria gonorrhoeae, and Neisseria meningitidis for up to 48 h. Indeed, BD CultureSwab MaxV(+) maintained a constant number of viable H. influenzae and N. meningitidis for up to 48 h, and only a 2 log reduction was noted for N. gonorrhoeae, fulfilling the requirements of M40-A guidelines. However, unlike Remel BactiSwab and the Medical Wire & Equipment Transwab, which fulfilled the M40-A requirements for maintaining the viability of Streptococcus pneumoniae, BD CultureSwab MaxV(+) could not maintain the viability of S. pneumoniae reference or clinical strains past 6 h. Excellent overall sensitivity (98%) (95% confidence interval, 89.5 to 99.7) was observed when the BD CultureSwab MaxV(+) rectal swabs were compared to the "gold standard" stool cultures. Thus, the BD CultureSwab MaxV(+) rectal swab can be used when investigating gastrointestinal bacterial outbreaks or when health care providers face difficulties in obtaining stool samples, particularly from children.