The effect of the transition to molecular diagnosis on the epidemiology and the clinical characteristics of bacterial gastroenteritis in Northern Israel

BACKGROUND

The transition to PCR-based diagnosis of bacterial gastroenteritis (BGE) can increase the sensitivity but might reduce the clinical specificity. The aims of this study were (1) to compare the effect of the change from culture to PCR-based diagnostics on the reported incidence and positivity rates of BGE due to Salmonella, Shigella and Campylobacter species and (2) to compare the demographics, medical background, clinical characteristics and pre-analytic variables between cases with PCR-positive, culture-negative samples to cases with PCR-positive, culture-positive samples.

METHODS

The study was performed at the Emek Medical Centre that serves a population of 0.5 million people in Northern Israel. The study included two parts: (1) a retrospective cohort study, comparing the incidence and positivity rates of laboratory-diagnosed BGE from January 2016 until December 22nd, 2019 when culture was the sole method to January 2020 until April 2023 when PCR was used; (2) a prospective cohort study, conducted between November 2020 until April 2023 that compared the demographics and clinical characteristics of BGE cases that were diagnosed by PCR alone versus cases that were diagnosed by both PCR and culture.

RESULTS

The incidence rate between-periods comparability ratio was only 113% since the incidence rate did not increase during 2020, the first year of the COVID-19 pandemic. The sample positivity rate increased since 2020, with between-periods comparability ratio of 159%. In the second period, the sample positivity rates of culture vs. PCR alone differed between the pathogens and were 90.2%, 63.8% and 54.2% for Salmonella, Campylobacter and Shigella species, respectively (p < 0.001). The following variables were identified as independent predictors of culture positivity: (1) Salmonella infection (O.R. = 10.6, 95% C.I. 3.6-31.1, p < 0.001); (2) Shigella infection (O.R. = 0.46, 95% C.I.0.23-0.93, p = 0.032); (3) time from sample submission to culture (O.R.=0.73, 95% C.I. 0.58-0.92, p = 0.008); (4) the presence of abdominal pain (O.R. = 1.98, 95% C.I. 1.04-3.79, p = 0.038) and the PCR mean Ct value (O.R. = 0.89, 95% C.I.0.85-0.94, p < 0.001).

CONCLUSIONS

The use of PCR had led to improved sensitivity, without noticeable decrease in the clinical specificity. This was especially important in the case of the more fastidious organisms.

Community-acquired pneumonia - use of chest x-rays for diagnosis in family practice

Background

According to guidelines, the diagnosis of pneumonia should be confirmed by chest x-ray, ensuring appropriate management and wise use of antibiotics. Our study aimed to describe use of x-rays by family doctors and patients following diagnosis of pneumonia in primary care practices in the north of Israel.

Methods

This was a retrospective database study including adults diagnosed with pneumonia, assessing rates of referral and actual use of chest x-rays. We examined rates of referral for chest x-rays and rates of adherence to the referral, according to age, gender, smoking status, comorbidities and distance of residence from the radiology facility.

Results

During one year there were 4,230 diagnosed cases of pneumonia in the practice, of which 2,503 were referred for chest x-rays, and 1,920 adhered to the referral (45% of those diagnosed with pneumonia). The rate of referral was higher when the radiology facility was located in the same city as the family doctor compared to outside the city (69.7% and 53.2%, p < 0.001). Patients aged 40–64 were referred more than patients aged 18–39 or 65+ (61.5% vs. 56.5% and 58.3%, p = 0.03). Actual use of chest x-rays (considering both referral and adherence) was more likely when the radiology facility was in the same health centre or city than when it was outside the city [OR = 2.4; 95% CI: 2.1–2.8]; patients aged 65 + or 40–64 were more likely to adhere to the referral for x-ray than those aged 18–39 [OR = 1.3; 95% CI: 1.1–1.6, OR = 1.2; 95% CI: 1.0–1.4, respectively].

Conclusion

Accessibility of radiology facilities seems to be an important factor associated with both doctors’ decisions and patients’ adherence to the referral for chest x-rays.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12875-022-01872-y.

Seroprevalence of SARS-CoV2 among Healthcare Workers: A Prospective Study

BACKGROUND

Healthcare workers (HCWs) have close interaction with confirmed or suspected coronavirus disease 2019 (COVID-19) patients. Infection rates reported among HCWs is between 3% and 17%, and asymptomatic HCWs are a potential source of nosocomial transmission to vulnerable patients and colleagues. Universal mask use and good supply of personal protective equipment was implemented early at our institution.

OBJECTIVES

To determine the rate of infection by the serologic status of HCWs during first three COVID-19 waves, based on occupation and risk of exposure, compared to Israeli general population.

METHODS

We conducted a prospective cohort study at Emek Medical Center from April 2020 to April 2021. A total of 101 HCWs volunteered to be followed at six time points by a serology test and a questionnaire.

RESULTS

A total of 101 HCWs completed six serologic tests. All participants were seronegative at the four initial tests. The cumulative seropositivity rate for COVID-19 in HCWs was 9.9% (10/101). Only three seropositive HCWs (2.97%) were hospital-acquired.

CONCLUSIONS

Seroprevalence and seroconversion dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 101 HCWs during COVID-19 outbreaks at Emek Medical Center were similar to the epidemiological curve of positive polymerase chain reaction results of the Israeli population, as published by the Israeli Ministry of Health, at each time point. Universal mask use and infection control measures may have contributed to a low hospital infection rate.

First case of imported Capillaria philippinensis in Israel

This is the first case report of human Capillaria philippinensis imported from Thailand and diagnosed in Israel by PCR in biopsy material. Capillariasis can be fatal if untreated and should be suspected among returning travelers or foreign workers with protein-losing enteropathy and long standing diarrhea.

Candida Bloodstream Infection, a Dire Complication in Hospitalized COVID-19 Patients: Three Cases from a Single Center in Northern Israel

BACKGROUND

Patients with severe coronavirus disease-2019 (COVID-19) are susceptible to superimposed infections.

OBJECTIVES

To describe COVID-19 patients who presented with complications due to Candida bloodstream co-infection (candidemia) and their outcome in a single center in northern Israel (Emek Medical Center) during the second outbreak of COVID-19 in Israel (15 June 2020 to 20 September 2020).

METHODS

A retrospective study of COVID-19 patients presenting with candidemia was conducted, including clinical and laboratory data. The incidence of candidemia among hospitalized COVID-19 patients was compared to a historical cohort of non-COVID-19 controls.

RESULTS

Three COVID-19 patients complicated with candidemia were documented. All three patients died shortly after the detection of candidemia. Three different Candida sp. were isolated from the blood cultures: C. albicans, C. parapsilosis, and C. glabrata. The incidence of candidemia among COVID-19 patients was 0.679 episodes per 1000 hospital days.

CONCLUSIONS

Our small sample suggests a much higher incidence of candidemia among COVID-19 patients compared to a historical cohort of non-COVID-19 controls. All clinicians treating COVID-19 patients in GICU should be aware of this complication.