Preparing for laboratory automation and consolidation-Establishing the validity of pediatric-like low-volume urine samples in boric-acid containing tubes.

Microbiological services consolidation has increased the usage of preservative-containing urine tubes, potentially inhibiting pathogens in low-volume pediatric urine samples, yielding false-negative results. Our study demonstrates comparable growth with 1 ml versus the recommended 3 ml urine, following different shipping intervals. We advocate for regulators to consider similar large-scale validations, ensuring results' consistency.

Optimizing the Yield of In-and-Out Urinary Catheter Cultures by Applying a "Midstream-Like" Approach in Pediatric Patients.

Despite appropriate disinfection, sample contamination during in-and-out urinary catheterization is not uncommon, yielding false-positive and "mixed-culture" interpretations. We implemented a "midstream-like" catheterization technique, and cultured both first- and second-voided urine fractions. Second-fraction cultures exhibited less contaminants and "mixed-culture" interpretations and were better aligned with pyuria, thereby enhancing diagnostic accuracy and minimizing the risk of clinical misdiagnosis and unwarranted antibiotic use.

Respiratory cryptosporidiosis detected by commercial multiplex-PCR in immunosuppressed pediatric patients.

We report the off-label use of a commercial gastrointestinal protozoa multiplex-PCR panel for bronchoalveolar lavage samples, detecting respiratory cryptosporidiosis in 2 immunocompromised pediatric patients. We suggest that implying this readily available assay in cases in which systemic cryptosporidiosis is suspected, may widen our understanding regarding this rarely reported syndrome.

Real-Life Experience and Diagnostic Utility of the BioFire Joint Infection PCR Panel in Bone and Joint Infections: Analysis of a Prospective Validation Study.

INTRODUCTION: Microbiological diagnosis is central for adequate treatment of bone and joint infections. Culture-based methods have a limited diagnostic sensitivity and a long turnaround time (TAT). The objective of this study was to compare the diagnostic performance of BioFire Joint Infection Panel Investigational Use Only version (hereafter BioFire)-a sample-to-result multiplex PCR panel-with culture-based methods and 16S ribosomal RNA (rRNA) PCR and sequencing, when available. METHODS: This study presents a retrospective analysis of a prospective validation study of the BioFire panel. Specimens were obtained from consecutive patients evaluated for suspected bone and joint infections and processed using culture, BioFire, and 16S rRNA PCR and sequencing. Final clinical diagnosis was used as the reference for definition of infection. RESULTS: Samples, including synovial fluid, bone and periarticular tissue, were obtained from 57 patients, 39 of whom were finally diagnosed with a bone or joint infection. Cultures were positive in 27/39 infected patients and in 3/18 uninfected patients (sensitivity 69%, specificity 83%). BioFire was positive in 22/39 infected patients and in none of the uninfected patients (sensitivity 56%, specificity 100%). Sensitivity for PCR panel organisms was 92% (22/24) and sensitivity for organisms identified by any microbiological modality was 69% (22/32). Gram stain results were positive in 13/39 infected patients and in none of the uninfected patients (sensitivity 33%, specificity 100%). 16S rRNA was positive in 20/28 infected patients and in 0/12 uninfected patients (sensitivity 71%, specificity 100%). Net machine time for BioFire-1 h-was shorter than the mean TAT for Gram stain results, which was 4 h. CONCLUSION: BioFire offered equivalent diagnostic performance with superior TAT for bone and joint infections, compared with conventional methods.

What Is Hiding in the Israeli Mediterranean Seawater and Beach Sand.

OBJECTIVE: In the present study, we aimed to investigate the presence of fungi that may affect human health in sand and water on Israeli Mediterranean Sea coast beaches. METHODS: The study included screening of the sand and water of six urban beaches from north to south on the Israeli Mediterranean coast. Sand samples were extracted with water, and the water wash was cultured and quantitated. Water samples were quantitated as well. MALDI-TOF MS analysis and ITS sequencing identified the fungi. RESULTS: The study considered several parameters: 1. Presence of fecal-contamination-related fungi; 2. Presence of dermal-infection-related fungi. 3. Presence of allergy-related fungi; 4. Presence of fungi posing risk for immunocompromised individuals. The screen revealed that about 80% of the isolates were molds and about 20% yeasts. The mold species included opportunistic pathogens and potential allergens: Aspergillus fumigatus and other Aspergillus species, Fusarium, Penicillium, and Mucorales species. Yeast isolates included Candida-including the human commensals Candida albicans and Candida tropicalis-Cryptococcus, and Rhodotorula species. CONCLUSIONS: The results suggest that beaches should be monitored for fungi for safer use, better management, and the benefit of public health.

Persistent abdominal symptoms in returning travellers: clinical and molecular findings.

BACKGROUND: Persistent abdominal symptoms (PAS) are the leading cause of post-travel morbidity although there is a paucity of evidence concerning the aetiology of this condition. Recently molecular methods for protozoa detection in stool have been introduced. Herein, we describe the clinical aspects and the prevalence of gastrointestinal protozoa in returning travellers with PAS. METHODS: From 2017 to 2019, clinical information and stool specimens from returning travellers with PAS were analysed for the presence of parasites using the Allplex-GI-Parasite-assay. Stool findings from symptomatic patients without a travel history were used as a comparator. RESULTS: During the 2-year study, 203 stool specimens from returning travellers were analysed. The median duration of symptoms before seeking care was 6 months, the most common symptoms were fatigue (79.2%), abdominal pain (75.7%) and loose stool (70.8%).Most of travellers had returned from Asia (57.6%), mainly from the Indian-subcontinent and only 52.6% were backpackers. Altogether, 36.9% samples were positive for protozoa, with Blastocystis hominis being the most common (26.6%) in samples, followed by Dientamoeba fragilis (18.7%), Giardia lamblia (3.0%) and Cryptosporidium spp (0.5%). The former two were dominant in all regions. In all cases but one, G. lamblia was acquired, but one were acquired in the Indian subcontinent (odds ratios 16.9; 95% confidence intervals: 1.9-148.3). Entamoeba histolytica was not detected. The demographic characterization of the 1359 non-travellers was comparable with the travellers. Among them D. fragilis was the most common followed by B. hominis, which was significantly less frequent compared among the travellers (16.7% vs 26.6%, P < 0.001). Average Cycle threshold values for each stool parasites were comparable between the two groups. CONCLUSION: Among returning travellers with PAS, more than one-third were positive for gastrointestinal protozoa. A low rate of giardia was found and no E. histolytica while B. hominis followed by D. fragilis were the dominant findings. Further studies are required to better understand the role of these protozoa in PAS.

Viral co-pathogens in COVID-19 acute respiratory syndrome - what did we learn from the first year of pandemic?

OBJECTIVE: This study aimed to describe the distribution of respiratory pathogens and the occurrence of co-pathogens during the first year of the COVID-19 pandemic. METHODS: We used a multiplex polymerase chain reaction (PCR) panel targeting 23 microorganisms to analyze the oro-pharyngeal samples of patients admitted to our hospital with acute respiratory infection (ARI) between March 1, 2020, and February 28, 2021. We matched 40 to 50 patients who were SARS-CoV-2 positive and SARS-CoV-2 negative per month for age and sex. RESULTS: A total of 939 patients with multiplex PCR test results were included in the study. Respiratory pathogens where detected in only 8/476 (1.6%) patients with COVID-19 versus 87/463 (18.7%) patients with non-COVID-19 ARI patients. Diversity and rates of pathogens vastly differed from previous years but showed seasonal variance. CONCLUSION: Patients with SARS-CoV-2 infection presenting with ARI during the first year of the COVID-19 pandemic demonstrated paucity of respiratory co-pathogens.

First reported nosocomial SARS-CoV-2 outbreak in a hospital-based laundry facility.

Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks among health care workers have been scarcely reported so far. This report presents the results of an epidemiologic and molecular investigation of a SARS-CoV-2 outbreak among laundromat facility workers in a large tertiary centre in Israel. Following the first three reported cases of SARS-CoV-2 among laundromat workers, all 49 laundromat personnel were screened by qRT-PCR tests using naso- and oropharingeal swabs. Epidemiologic investigations included questionnaires, interviews and observations of the laundromat facility. Eleven viral RNA samples were then sequenced, and a phylogenetic analysis was performed using MEGAX.The integrated investigation defined three genetic clusters and helped identify the index cases and the assumed routes of transmission. It was then deduced that shared commute and public showers played a role in SARS-CoV-2 transmission in this outbreak, in addition to improper PPE use and social gatherings (such as social eating and drinking). In this study, we present an integrated epidemiologic and molecular investigation may help detect the routes of SARS-CoV-2 transmission, emphasising such routes that are less frequently discussed. Our work reinforces the notion that person-to-person transmission is more likely to cause infections than environmental contamination (e.g. from handling dirty laundry).

The Sheba Medical Center healthcare workers' children's school: can we open schools safely?

OBJECTIVE: The role of school closure in mitigating coronavirus disease 2019 (COVID-19) transmission has been questioned. In our medical centre, during a 9-week national lockdown, an alternative school was opened for health-care workers' (HCW) children with a small number of children per class and strict symptom surveillance. After lockdown was lifted we screened children and their parents for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serology. METHODS: We conducted a cross-sectional study of HCW parents and their children after one teacher contracted COVID-19 following exposure at home and 53 children were exposed, isolated and tested by RT-PCR. We compared families with children attending the alternative school with families whose children who remained at home during the 9-week lockdown. Epidemiological and medical data were collected using a short questionnaire; nasopharyngeal and oropharyngeal swabs were obtained and tested for SARS-CoV-2 by RT-PCR, and blood was collected for SARS-CoV-2 IgA and IgG titres. RESULTS: A total of 435 children attended the Sheba alternative school. Among the 53 children exposed to the infected teacher, none tested positive by RT-PCR. Of these, 18 children-parent pairs were tested for serology and all were negative. A total of 106/435 (24%) children and their 78 parents were recruited for the cross-sectional study; 70 attended the Sheba school and 36 did not. Approximately 16% of children in either group reported symptoms (11/70 in the school group and 6/36 in the 'stay home' group), but SARS-CoV-2 was not detected by PCR in any, and previous exposure, as determined by serological tests, was low and not significantly different between the groups. CONCLUSION: In an alternative school for children of HCWs, active during COVID-19 national outbreak, we found no evidence of increased infection compared with children that stayed home.

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel.

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.

Utilization of machine-learning models to accurately predict the risk for critical COVID-19.

Among patients with Coronavirus disease (COVID-19), the ability to identify patients at risk for deterioration during their hospital stay is essential for effective patient allocation and management. To predict patient risk for critical COVID-19 based on status at admission using machine-learning models. Retrospective study based on a database of tertiary medical center with designated departments for patients with COVID-19. Patients with severe COVID-19 at admission, based on low oxygen saturation, low partial arterial oxygen pressure, were excluded. The primary outcome was risk for critical disease, defined as mechanical ventilation, multi-organ failure, admission to the ICU, and/or death. Three different machine-learning models were used to predict patient deterioration and compared to currently suggested predictors and to the APACHEII risk-prediction score. Among 6995 patients evaluated, 162 were hospitalized with non-severe COVID-19, of them, 25 (15.4%) patients deteriorated to critical COVID-19. Machine-learning models outperformed the all other parameters, including the APACHE II score (ROC AUC of 0.92 vs. 0.79, respectively), reaching 88.0% sensitivity, 92.7% specificity and 92.0% accuracy in predicting critical COVID-19. The most contributory variables to the models were APACHE II score, white blood cell count, time from symptoms to admission, oxygen saturation and blood lymphocytes count. Machine-learning models demonstrated high efficacy in predicting critical COVID-19 compared to the most efficacious tools available. Hence, artificial intelligence may be applied for accurate risk prediction of patients with COVID-19, to optimize patients triage and in-hospital allocation, better prioritization of medical resources and improved overall management of the COVID-19 pandemic.

Delayed diagnosis of colorectal sexually transmitted diseases due to their resemblance to inflammatory bowel diseases.

OBJECTIVE: Sexually transmitted diseases (STDs), mainly lymphogranuloma venereum (LGV), induce colorectal symptoms that may be misdiagnosed as inflammatory bowel disease (IBD). This study describes patients who presented with STDs masquerading as IBD in order to improve understanding of missed diagnosis of colorectal STDs and their association with LGV in Israel. METHODS: This retrospective, descriptive study characterized the clinical, endoscopic, and pathological findings of 16 patients who were diagnosed with a colorectal STD after erroneously being diagnosed with IBD. Molecular genotyping was used to characterize some of the Chlamydia trachomatis isolates. RESULTS: All patients were men who have sex with men (MSM), mostly HIV-1-positive, and had clinical and endoscopic findings compatible with IBD. The STD was diagnosed 1-36 months after the initial diagnosis: 14 were positive for Chlamydia trachomatis, of which three were of the LGV2b (ST58) serotype and one was ST 108 serotype. Five were positive for gonorrhea and four were positive for syphilis. Several pathogens were diagnosed in six episodes. CONCLUSIONS: Colorectal STDs may resemble IBD and therefore their diagnosis may be delayed. IBD symptoms in MSM who engage in non-protected anal sex should prompt at least syphilis and anal PCR for STD testing. If C. trachomatis is diagnosed but LGV subtyping cannot be done, doxycycline 100mg twice daily for 21days should be recommended.

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.

NKX6.1 promotes PDX-1-induced liver to pancreatic ß-cells reprogramming.

Reprogramming adult mammalian cells is an attractive approach for generating cell-based therapies for degenerative diseases, such as diabetes. Adult human liver cells exhibit a high level of developmental plasticity and have been suggested as a potential source of pancreatic progenitor tissue. An instructive role for dominant pancreatic transcription factors in altering the hepatic developmental fate along the pancreatic lineage and function has been demonstrated. Here we analyze whether transcription factors expressed in mature pancreatic ß-cells preferentially activate ß-cell lineage differentiation in liver. NKX6.1 is a transcription factor uniquely expressed in ß-cells of the adult pancreas, its potential role in reprogramming liver cells to pancreatic lineages has never been analyzed. Our results suggest that NKX6.1 activates immature pancreatic markers such as NGN-3 and ISL-1 but not pancreatic hormones gene expression in human liver cells. We hypothesized that its restricted capacity to activate a wide pancreatic repertoire in liver could be related to its incapacity to activate endogenous PDX-1 expression in liver cells. Indeed, the complementation of NKX6.1 by ectopic PDX-1 expression substantially and specifically promoted insulin expression and glucose regulated processed hormone secretion to a higher extent than that of PDX-1 alone, without increasing the reprogrammed cells. This may suggest a potential role for NKX6.1 in promoting PDX-1 reprogrammed cells maturation along the ß-cell-like lineage. By contrast, NKX6.1 repressed PDX-1 induced proglucagon gene expression. The individual and concerted effects of pancreatic transcription factors in adult extra-pancreatic cells, is expected to facilitate developing regenerative medicine approaches for cell replacement therapy in diabetics.

Pancreatic and duodenal homeobox gene 1 induces hepatic dedifferentiation by suppressing the expression of CCAAT/enhancer-binding protein beta.

UNLABELLED: It is believed that adult tissues in mammals lack the plasticity needed to assume new developmental fates because of the absence of efficient pathways of dedifferentiation. However, the well-documented ability of the transcription factor pancreatic and duodenal homeobox gene 1 (PDX-1) to activate pancreatic lineage development and insulin production following ectopic expression in liver suggests a surprising degree of residual plasticity in adult liver cells. This study seeks a mechanistic explanation for the capacity of PDX-1 to endow liver cells with pancreatic characteristics and function. We demonstrate that PDX-1, previously shown to play an essential role in normal pancreatic organogenesis and pancreatic beta-cell function and to possess the potential to activate multiple pancreatic markers in liver, can also direct hepatic dedifferentiation. PDX-1 represses the adult hepatic repertoire of gene expression and activates the expression of the immature hepatic marker alpha-fetoprotein. We present evidence indicating that PDX-1 triggers hepatic dedifferentiation by repressing the key hepatic transcription factor CCAAT/enhancer-binding protein beta. Hepatic dedifferentiation is necessary though not sufficient for the activation of the mature pancreatic repertoire in liver. CONCLUSION: Our study suggests a dual role for PDX-1 in liver: inducing hepatic dedifferentiation and activating the pancreatic lineage. The identification of dedifferentiation signals may promote the capacity to endow mature tissues in mammals with the plasticity needed for acquiring novel developmental fates and functions to be implemented in the field of regenerative medicine.