High rate of bacterial respiratory tract co-infections upon admission amongst moderate to severe COVID-19 patients.

BACKGROUND: The role of bacterial and viral co-infection in the current COVID-19 pandemic remains elusive. The aim of this study was to describe the rates and features of co-infection on admission of COVID-19 patients, based on molecular and routine laboratory methods. METHODS: A retrospective study of COVID-19 and non-COVID-19 patients undergoing Biofire®, FilmArray® Pneumonia Panel, bioMérieux, and routine cultures during the first 3 days from admission, between June 2019 and March 2021. RESULTS: FilmArray tests were performed in 115 COVID-19 and in 61 non-COVID-19 patients. Most (>99%) COVID-19 patients had moderate-critical illness, 37% required mechanical ventilation. Sputa and endotracheal aspirates were the main samples analyzed. Positive FilmArray tests were found in 60% (70/116) of the tests amongst COVID-19 patients and 62.5% (40/64) amongst non-COVID-19 patients. All 70 cases were positive for bacterial targets, while one concomitant virus (Rhinovirus/Enterovirus) and one Legionella spp. were detected. The most common bacterial targets were Haemophilus influenzae (36%), Staphylococcus aureus (23%), Streptococcus pneumoniae (10%) and Enterobacter cloacae (10%). Correlation between FilmArray and cultures was found in 81% and 44% of negative and positive FA tests, respectively. Positive FilmArray results typically (81%) triggered the administration of antibiotic therapy and negative results resulted in antimicrobials to be withheld in 56% of cases and stopped in 8%. Bacterial cultures of COVID-19 patients were positive in 30/88 (34%) of cases. CONCLUSIONS: Bacterial co-infection is common amongst moderate-critical COVID-19 patients on admission while viral and atypical bacteria were exceedingly rare. Positive FilmArray results could trigger potentially unnecessary antibiotic treatment.KEY POINTWe found high rates of on-admission bacterial co-infection amongst hospitalized moderate to severe COVID-19 patients. Molecular tests (Biofire, FilmArray) and routine microbiological tests revealed 60% and 34% bacterial co-infection, respectively, while viral and fungal co-infections were rare.

High Rates of Bacterial Pulmonary Co-Infections and Superinfections Identified by Multiplex PCR among Critically Ill COVID-19 Patients.

BACKGROUND: The role of bacterial co-infection and superinfection among critically ill COVID-19 patients remains unclear. The aim of this study was to assess the rates and characteristics of pulmonary infections, and associated outcomes of ventilated patients in our facility. METHODS: This was a retrospective study of ventilated COVID-19 patients between March 2020 and March 2021 that underwent BioFire®, FilmArray® Pneumonia Panel, testing. Community-acquired pneumonia (CAP) was defined when identified during the first 72 h of hospitalization, and ventilator-associated pneumonia (VAP) when later. RESULTS: 148 FilmArray tests were obtained from 93 patients. With FilmArray, 17% of patients had CAP (16/93) and 68% had VAP (64/93). Patients with VAP were older than those with CAP or those with no infection (68.5 vs. 57-59 years), had longer length of stay and higher mortality (51% vs. 10%). The most commonly identified FilmArray target organisms were H. influenzae, S. pneumoniae, M. catarrhalis and E. cloacae for CAP and P. aeruginosa and S. aureus for VAP. FilmArray tests had high negative predictive values (99.6%) and lower positive predictive values (~60%). CONCLUSIONS: We found high rates of both CAP and VAP among the critically ill, caused by the typical and expected organisms for both conditions. VAP diagnosis was associated with poor patient outcomes.

Streptococcus pyogenes bacteremia and toxic shock syndrome related to Strongyloides stercoralis hyperinfection: a case report.

BACKGROUND: We describe a patient with Strongyloides stercoralis hyperinfection associated with Streptococcus pyogenes and with streptococcal toxic shock syndrome. To the best of our knowledge this association has not been previously described. CASE PRESENTATION: A 78 year-old Israeli man, who was born in Iraq but lived in Israel for 66 years, presented with multi-organ failure including acute kidney and hepatic injury, coagulopathy, and lactic acidosis. He had a medical history including aortic valve replacement, diabetes mellitus, spinal stenosis, and low back pain treated with repeated local steroid injections. Blood cultures were positive for Streptococcus pyogenes and antibiotic treatment was switched to penicillin G, clindamycin, and intravenous immunoglobulins. Repeated physical examinations failed to identify the source of the bacteremia. On day 12 of hospitalization the serology results for Strongyloides stercoralis sent on admission, because of chronic eosinophilia, came back positive. A microscopic stool examination and stool polymerase chain reaction were positive for Strongyloides stercoralis. Ivermectin therapy was commenced and continued for a total of 4 weeks. He was discharged for rehabilitation after 25 days. He had no exposure to endemic countries or to immigrants. During many years he had multiple gastrointestinal symptoms, respiratory symptoms, cutaneous symptoms, chronic eosinophilia, and high immunoglobulin E levels. He underwent several operative procedures and numerous hospitalizations and medical encounters with different experts but a parasitic infection was not considered. His asymptomatic daughter was also found to be serologically positive. CONCLUSIONS: Strongyloides stercoralis hyperinfection associated with Streptococcus pyogenes bacteremia and toxic shock is described for the first time. The case also highlights the importance of history taking and reviewing past laboratory results, the utility of serological tests for Strongyloides stercoralis, and the importance of screening asymptomatic family members of an infected patient. Strongyloides stercoralis hyperinfection must be considered in the differential diagnosis of any patient with Streptococcus pyogenes bacteremia or toxic shock of no clear source as well as in symptomatic patients with chronic or intermittent eosinophilia, even without any epidemiological risk factors.

Case Report: Typhoid Fever and Spotted Fever Group Rickettsiosis Presenting Concomitantly in an Indian Immigrant.

We present a rare case of an Indian immigrant suffering from concomitant infection of Salmonella typhi and spotted fever group Rickettsia. We discuss the scarce reports of dual infections from the developing world and the related diagnostic challenges.

Two Cases of Israeli Spotted Fever with Purpura Fulminans, Sharon District, Israel.

We report a series of 5 case-patients who had Israeli spotted fever, of whom 2 had purpura fulminans and died. Four case-patients were given a diagnosis on the basis of PCR of skin biopsy specimens 3-4 days after treatment with doxycycline; 1 case-patient was given a diagnosis on the basis of seroconversion. Rickettsia spp. from the 2 case-patients who died were sequenced and identified as Rickettsia conorii subsp. israelensis. Purpura fulminans has been described in association with R. rickettsii and R. indica, but rarely with R. conorii subsp. israelensis.

A prospective survey of Pseudomonas aeruginosa colonization and infection in the intensive care unit.

BACKGROUND: Pseudomonas aeruginosa (PA) surveillance may improve empiric antimicrobial therapy, since colonizing strains frequently cause infections. This colonization may be 'endogenous' or 'exogenous', and the source determines infection control measures. We prospectively investigated the sources of PA, the clinical impact of PA colonization upon admission and the dynamics of colonization at different body sites throughout the intensive care unit stay. METHODS: Intensive care patients were screened on admission and weekly from the pharynx, endotracheal aspirate, rectum and urine. Molecular typing was performed using Enterobacterial Repetitive Intergenic Consensus Polymerase Chain reaction (ERIC-PCR). RESULTS: Between November 2014 and January 2015, 34 patients were included. Thirteen (38%) were colonized on admission, and were at a higher risk for PA-related clinical infection (Hazard Ratio = 14.6, p = 0.0002). Strains were often patient-specific, site-specific and site-persistent. Sixteen out of 17 (94%) clinical isolates were identical to strains found concurrently or previously on screening cultures from the same patient, and none were unique. Ventilator associated pneumonia-related strains were identical to endotracheal aspirates and pharynx screening (87-75% of cases). No clinical case was found among patients with repeated negative screening. CONCLUSION: PA origin in this non-outbreak setting was mainly 'endogenous' and PA-strains were generally patient- and site-specific, especially in the gastrointestinal tract. While prediction of ventilator associated pneumonia-related PA-strain by screening was fair, the negative predictive value of screening was very high.