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.

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 POINT

We 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.

Spotted Fever Group Rickettsioses in Israel, 2010-2019

In a multicenter, nationwide, retrospective study of patients hospitalized with spotted fever group rickettsiosis in Israel during 2010-2019, we identified 42 cases, of which 36 were autochthonous. The most prevalent species was the Rickettsia conorii Israeli tick typhus strain (n = 33, 79%); infection with this species necessitated intensive care for 52% of patients and was associated with a 30% fatality rate. A history of tick bite was rare, found for only 5% of patients; eschar was found in 12%; and leukocytosis was more common than leukopenia. Most (72%) patients resided along the Mediterranean shoreline. For 3 patients, a new Rickettsia variant was identified and had been acquired in eastern, mountainous parts of Israel. One patient had prolonged fever before admission and clinical signs resembling tickborne lymphadenopathy. Our findings suggest that a broad range of Rickettsia species cause spotted fever group rickettsiosis in Israel.

Screening asymptomatic households for Streptococcus pyogenes pharyngeal carriage as a part of in-hospital investigation of puerperal sepsis

BACKGROUND

Invasive group A streptococcal (iGAS) infection in the peripartum setting is a rare but devastating disease occasionally occurring as a health care-associated infection (HAI). Current guidelines suggest enhanced surveillance and streptococcal isolate storage after a single case of iGAS, as well as a full epidemiological investigation that includes screening health care workers (HCWs) from several sites after 2 cases. Current guidelines do not recommend routine screening of household members of a patient with iGAS.

METHODS

We conducted studies of 3 patients with iGAS puerperal sepsis and related epidemiologic and molecular investigations.

RESULTS

Identical GAS emm gene types were found in pharyngeal cultures of 3 asymptomatic spouses of patients with iGAS puerperal sepsis. HCWs screened negative for GAS, and emm typing indicated that other iGAS cases from this hospital were sporadic and not related to the puerperal cases.

CONCLUSIONS

The concurrent presence of the same emm type in a household member practically excludes the option of an inadvertent HAI or facility outbreak. Hence, we suggest that screening close family members for asymptomatic GAS carriage should be performed early as a part of infection prevention measures, as doing so would have significant utility in saving time and resources related to a full epidemiological inquiry.

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.

Characteristics of hospitalized adult patients with laboratory documented Influenza A, B and Respiratory Syncytial Virus - A single center retrospective observational study

Introduction

The epidemiology, clinical features and outcomes of hospitalized adult patients with Influenza A (FluA), Influenza B (FluB) and Respiratory Syncytial Virus (RSV) have not been thoroughly compared. The aim of this study was to describe the differences between these viruses during 3 winter seasons.

Methods

A retrospective observational study was conducted consisting of all the polymerase chain reaction (PCR)-based diagnoses of FluA, FluB and RSV among adults during 2015–2018, in one regional hospital. Epidemiology, clinical symptoms and outcome-related data were comparatively analyzed.

Results

Between November 2015 and April 2018, 759 patients were diagnosed with FluA, FluB or RSV. Study cohort included 539 adult patients (306 FluA, 148 FluB and 85 RSV). FluB was predominant during the winter of 2017–18. RSV caused 15.7% of hospitalizations with diagnosed viral infection and in comparison to influenza, had distinct epidemiological, clinical features and outcomes, including older age (74.2 vs 66.2, p = 0.001) and higher rates of co-morbidities; complications including bacterial pneumonia (31 vs 18%, p = 0.02), mechanical ventilation (20 vs 7%, p = 0.001), and viral-related death (13 vs 6.6%, p = 0.04). FluA and FluB had similar epidemiology, clinical symptoms and outcomes, but vaccinated patients were less prone to be hospitalized with FluB as compared with FluA (3 vs 14%, p = 0.001). Paroxysmal atrial fibrillation and falls were common (8.7 and 8.5% respectively).

Conclusions

FluA and FluB had similar epidemiological, clinical features and contributed equally to hospitalization burden and complications. RSV had a major impact on hospitalizations, occurring among the more elderly and sick populations and causing significantly worse outcomes, when compared to influenza patients. Vaccination appeared as a protective factor against hospitalizations with FluB as compared with FluA.

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

Genetic sequencing should be used to confirm cases because purpura fulminans is a rare finding.

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.

Disseminated "Haemophilus quentini" infection in a patient with multiple myeloma - a case report and review of the literature

We describe a case report of a 56-year-old male with undiagnosed multiple myeloma who had severe sepsis associated with pneumonia, meningitis, polyarthritis, and osteomyelitis related to invasive "Haemophilus quentini" infection. The genus was misidentified as H. influenzae by the common bacterial identification systems including newly introduced syndromic PCR-based methods. We review the epidemiological, clinical, and laboratory aspects of this rare, cryptic species of Haemophilus.

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.

Cryptococcosis as a cause of nephrotic syndrome? A case report and review of the literature

We present a case of a 74 years old male with cutaneous cryptococcosis of the right forearm. Cryptococcus neoformans var. neoformans was cultivated from the skin and from the bloodstream. He was diagnosed with nephrotic syndrome (focal segmental glomerulosclerosis) 21 months prior to admission, which was steroid-dependent. He was treated with prednisone and cyclosporine A. Concurrently with his renal disease he was also diagnosed as having disseminated severe tinea mannum, tinea corporis and tinea cruris; onychomycosis, skin eczema and psoriasis. After a prolonged course of anti-fungal therapy, his skin lesions as well as his nephrotic syndrome recovered completely. Follow up after 7 months without any anti-fungal or immunosuppression showed no skin or renal recurrence. We assume that the renal disease was related to the pre-existing cutaneous cryptococcosis, aggravated by immunosuppression, and discuss the close association between cutaneous cryptococcosis and nephrotic syndrome, as well as similar case reports in the literature.

Long-term outcomes of inappropriate antibiotic therapy for upper urinary tract infections caused by extended-spectrum beta-lactamase-producing Enterobacteriaceae: a retrospective cohort study

BACKGROUND

To evaluate the short- and long-term outcomes of different antimicrobial treatment options for upper urinary tract infections (UTIs) caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae.

METHODS

We retrospectively analyzed patients with a first episode of febrile UTI and positive urine culture with ESBL-producing E. coli or K. pneumoniae during 2012-2015. We compared outcomes among patients who received: (1) definitive treatment with a carbapenem (CP), (2) a microbiologically appropriate intravenous non-carbapenem agent (NCA), (3) a non-appropriate antimicrobial (NAA), and (4) an intravenous NAA followed by an oral NCA (NAA-PO).

RESULTS

The majority of patients received empirical therapy with NAA (165/178, 93%), and definitive treatment with NCA (n=43), NAA (n=50), and NAA-PO (n=59). The NCA group had significantly higher SIRS score than the NAA-PO group (2.18 versus 1.76, P=0.018), but no differences were found between the NCA and NAA groups (2.18 and 1.92, P=0.15). Clinical cure at discharge from the index hospitalization was high (97-100%) in all 3 groups. The NCA group had longer length of stay as compared with the NAA-PO and NAA groups (8.7days versus 5.39 and 5.24days, P<0.0001) and a lower rate of early (48-72h) improvement (79% versus 96-100%, P=0.0002). Among re-admitted patients, re-admission with ESBL-related bloodstream infection was significantly higher in the NAA group as compared to the NAA-PO and NCA groups (33% versus 4% and 0%, respectively, P=0.02). Death rate within 60days was also higher in the NAA and NCA groups as compared with the NAA-PO group (P=0.048).

CONCLUSIONS

Inappropriate antimicrobial therapy for febrile non-bacteremic UTI with ESBL-producing enterobacteriaceae is associated with favorable short-term outcomes, but also with a long-term risk of relapsed bacteremic UTI. Definitive treatment with appropriate carbapenem-sparing antimicrobial agents effectively prevents late relapses.

Water faucets as a source of Pseudomonas aeruginosa infection and colonization in neonatal and adult intensive care unit patients

We investigated the occurrence of Pseudomonas aeruginosa in our neonatal and adult intensive care units. Using enterobacterial repetitive intergenic consensus polymerase chain reaction, we showed spatial and temporal associations with clonal identity between patients' and adjacent faucets' clones. Both units' taps were highly colonized with P aeruginosa and with other waterborne bacteria. In the neonatal intensive care unit, strict use of sterile water for bathing neonates may have contributed to a reduction in clinical isolation of P aeruginosa postintervention.

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.