Diagnosing COVID-19; towards a feasible COVID-19 rule-out protocol

Introduction: We present the results of the COVID-19 rule-out protocol at Ghent University Hospital, a step-wise testing approach which included repeat NFS SARS-CoV-2 rRT-PCR, respiratory multiplex RT-PCR, low-dose chest CT and bronchoscopy with BAL to confirm or rule-out SARS-CoV-2 infection in patients admitted with symptoms suggestive of COVID-19.

Results: Between 19 March 2020 and 30 April 2020, 455 non-critically ill patients with symptoms suspect for COVID-19 were admitted. The initial NFS for SARS-CoV-2 rRT-PCR yielded 66.9%, the second NFS 25.4% and bronchoscopy with BAL 5.9% of total COVID-19 diagnoses. In the BAL fluid, other respiratory pathogens were detected in 65% (13/20) of the COVID-19 negative patients and only in 1/7 COVID-19 positive patients. Retrospective antibody testing at the time around BAL sampling showed a positive IgA or IgG in 42.9 % of the COVID-19 positive and 10.5% of the COVID-19 negative group. Follow-up serology showed 100% COVID-19 positivity in the COVID-19 positive group and 100% IgG negativity in the COVID-19 negative group.

Conclusion: In our experience, bronchoscopy with BAL can have an added value to rule-in or rule-out COVID-19 in patients with clinical and radiographical high-likelihood of COVID-19 and repeated negative NFS testing. Furthermore, culture and respiratory multiplex PCR on BAL fluid can aid to identify alternative microbial etiological agents in this group. Retrospective analysis of antibody development in this selected group of patients suggests that the implementation of serological assays in the routine testing protocol will decrease the need for invasive procedures like bronchoscopy.

Antimicrobial prescription in severe COVID-19 and CAP: a matched case-control study

BACKGROUND

In severe coronavirus diseases 2019 (COVID-19), a high and potentially excessive use of antimicrobials for suspected bacterial co-infection and intensive care unit (ICU)-acquired infections has been repeatedly reported.

OBJECTIVES

To compare an ICU cohort of community-acquired pneumonia (CAP) with a cohort of severe COVID-19 pertaining to co-infections, ICU-acquired infections and associated antimicrobial consumption.

METHODS

We retrospectively compared a cohort of CAP patients with a cohort of COVID-19 patients matched according to organ failure, ICU length of stay (LOS) and ventilation days. Patient data such as demographics, infection focus, probability and severity, ICU severity scores and ICU and in-hospital mortality, days of antimicrobial therapy (DOT) and number of antimicrobial prescriptions, using an incremental scale, were registered and analysed. The total number of cultures (sputum, urinary, blood cultures) was collected and corrected for ICU LOS.

FINDINGS

CAP patients (n = 148) were matched to COVID-19 patients (n = 74). Significantly less sputum cultures (68.2% versus 18.9%, P < 0.05) and bronchoalveolar lavages (BAL) (73.7% versus 36.5%, P < 0.05) were performed in COVID-19 patients. Six (8.1%) COVID-19 patients were diagnosed with a co-infection. Respectively, 58 of 148 (39.2%) CAP and 38 of 74 (51.4%) COVID-19 patients (P = 0.09) developed ICU-acquired infections. Antimicrobial distribution, both in the number of prescriptions and DOT, was similar in both cohorts.

CONCLUSIONS

We found a low rate of microbiologically confirmed bacterial co-infection and a high rate of ICU-acquired infections in COVID-19 patients. Infection probabilities, antimicrobial prescriptions and DOT were comparable with a matched CAP cohort.

Toilet drain water as a potential source of hospital room-to-room transmission of carbapenemase-producing Klebsiella pneumoniae

BACKGROUND

Carbapenemase-producing Enterobacterales (CPE) have rapidly emerged in Europe, being responsible for nosocomial outbreaks.

AIM

Following an outbreak in the burn unit of Ghent University Hospital, we investigated whether CPE can spread between toilets through drain water and therefrom be transmitted to patients.

METHODS

In 2017, the burn centre of our hospital experienced an outbreak of OXA-48-producing Klebsiella pneumoniae that affected five patients staying in three different rooms. Environmental samples were collected from the sink, shower, shower stretcher, hand rail of the bed, nursing carts, toilets, and drain water to explore a common source. Whole-genome sequencing and phylogenetic analysis was performed on K. pneumoniae outbreak isolates and two random K. pneumoniae isolates.

FINDINGS

OXA-48-producing K. pneumoniae was detected in toilet water in four out of six rooms and drain water between two rooms. The strain persisted in two out of six rooms after two months of daily disinfection with bleach. All outbreak isolates belonged to sequence type (ST) 15 and showed isogenicity (<15 allele differences). This suggests that the strain may have spread between rooms by drain water. Unexpectedly, one random isolate obtained from a patient who became colonized while residing at the geriatric ward clustered with the outbreak isolates, suggesting the outbreak to be larger than expected. Daily application of bleach tended to be superior to acetic acid to disinfect toilet water; however, disinfection did not completely prevent the presence of carbapenemase-producing K. pneumoniae in toilet water.

CONCLUSION

Toilet drain water may be a potential source of hospital room-to-room transmission of carbapenemase-producing K. pneumoniae.

Infrared spectroscopy as a novel tool to diagnose onychomycosis

BACKGROUND

The determination of causative organisms of onychomycosis is still not optimal. There remains a need for a cheap, fast and easy-to-perform diagnostic tool with a high capacity to distinguish between organisms.

OBJECTIVES

To determine whether attenuated total-reflectance Fourier transform infrared (ATR-FTIR) spectroscopy can detect and differentiate causative agents in culture-based, ex vivo nail and in vivo nail models.

METHODS

A methodological study was conducted. Both the ex vivo nail model and in vivo pilot study were carried out in an academic university hospital.

RESULTS

Analysis of cultured fungi revealed spectral differences for dermatophytes (1692-1606 and 1044-1004 cm^-1 ) and nondermatophytes and yeasts (973-937 cm^-1 ), confirmed by dendrograms showing an excellent separation between samples from different genera or species. Exploration of dermatophytes, nondermatophytes and yeasts growing on ex vivo nails exposed prominent differences from 1200 to 900 cm^-1 . Prediction models resulted in a 96·9% accurate classification of uninfected nails and nails infected with dermatophytes, nondermatophytes and yeasts. Overall correct classification rates of 91·0%, 97·7% and 98·6% were obtained for discrimination between dermatophyte, nondermatophyte and yeast genera or species, respectively. Spectra of in vivo infected and uninfected nails also revealed distinct spectral differences (3000-2811 cm^-1 , 1043-950 cm^-1 and 1676-1553 cm^-1 ), illustrated by two main clusters (uninfected vs. infected) on a dendrogram.

CONCLUSIONS

Our data suggest that ATR-FTIR spectroscopy may be a promising, fast and accurate method to determine onychomycosis, including identification of the causative organism, bypassing the need for lengthy fungal cultures.

The resident microflora of voided midstream urine of healthy controls: standard versus expanded urine culture protocols

The workup and interpretation of urine cultures is not always clear-cut, especially for midstream samples contaminated with commensals. Standard urine culture (SUC) protocols are designed in favor of growth of uropathogens at the expense of commensals. In selected clinical situations, however, it is essential to trace fastidious or new uropathogens by expanding the urine culture conditions (EUC). The aim of our study was to map the microflora in midstream urine specimens from healthy controls by means of EUC, in view of the interpretation of bacterial culture results in symptomatic patients. Midstream urine specimens from 101 healthy controls (86 females and 15 males) were examined using both SUC and EUC. Whilst 73 % of samples examined by SUC showed no growth at 10³ colony-forming units (CFU)/mL, 91 % of samples examined by EUC grew bacterial species in large numbers (≥10⁴ CFU/mL). Asymptomatic bacteriuria, as defined by the European guidelines for urinalysis, was detected in six samples with both protocols. EUC revealed 98 different species, mostly Lactobacillus, Staphylococcus, Streptococcus, and Corynebacterium. None of the samples grew Staphylococcus saprophyticus, Corynebacterium urealyticum, or Aerococcus urinae. Samples from females contained higher bacterial loads and showed higher bacterial diversity compared to males. Midstream urine of healthy controls contains large communities of living bacteria that comprise a resident microflora, only revealed by EUC. Hence, the use of EUC instead of SUC in a routine setting would result in more sensitive but less specific results, requiring critical interpretation. In our view, EUC should be reserved for limited indications.

Uropathogen distribution and antimicrobial susceptibility in uncomplicated cystitis in Belgium, a high antibiotics prescribing country: 20-year surveillance

Treatment of cystitis in primary care is usually empirical, guided by the prior probability of causal pathogens and their susceptibility. To re-evaluate empirical treatment guidelines, the actual distribution and susceptibility of uropathogens was examined and compared with two previous surveys in Belgium over the past 20 years. Because of the alarming increase in carriage of extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Escherichia coli, this specific resistance was explored. From May 2014 to December 2015, 120 general practitioners collected midstream urine specimens from adult pre- and postmenopausal female patients with suspected cystitis. A dipslide was inoculated and sent for microbiological analysis. Anal swabs were collected for ESBL and carbapenemase detection. Of 265 enrolled patients, 203 (79.3 %) had a positive culture. Escherichia coli (81.6 %) was the most frequently isolated uropathogen, followed by Staphylococcus saprophyticus (8 %), confirming the results of the 1995 and 2005 surveys. The susceptibility of E. coli remained nearly 100 % for nitrofurantoin and fosfomycin, decreased from nearly 100 % in 1995 to 94.2 % for quinolones, from 73.2 to 55.5 % for ampicillin, and from 83.3 to 76.3 % for trimethoprim-sulfamethoxazole (TMP-SMX). In E. coli present in positive urine cultures, ESBLs were found in 2.5 % and carbapenemases were absent. In fecal specimens, ESBL-producing E. coli were found in 7.9 % and carbapenemases were not detected. Over a 20-year period, the distribution of uropathogens in women with cystitis remained unchanged. Susceptibility remained excellent for nitrofurantoin and fosfomycin. For TMP-SMX, ampicillin, and quinolones, there was a decrease.

PCR-based detection of Aspergillus fumigatus Cyp51A mutations on bronchoalveolar lavage: a multicentre validation of the AsperGenius assay® in 201 patients with haematological disease suspected for invasive aspergillosis

OBJECTIVES

In patients with invasive aspergillosis (IA), fungal cultures are mostly negative. Consequently, azole resistance often remains undetected. The AsperGenius^® multiplex real-time PCR assay identifies clinically relevant Aspergillus species and four resistance-associated mutations (RAMs; TR34/L98H/T289A/Y121F) in the Cyp51A gene. This multicentre study evaluated the diagnostic performance of this assay on bronchoalveolar lavage (BAL) fluid and correlated the presence of RAMs with azole treatment failure and mortality.

METHODS

Stored BAL samples from patients with haematological diseases with suspected IA were used. BAL samples that were galactomannan/culture positive were considered positive controls for the presence of Aspergillus. Azole treatment failure and 6 week mortality were compared in patients with and without RAMs that had received ≥5 days of voriconazole monotherapy.

RESULTS

Two hundred and one patients each contributed one BAL sample, of which 88 were positive controls and 113 were negative controls. The optimal cycle threshold cut-off value for the Aspergillus species PCR was <38. With this cut-off, the PCR was positive in 74/88 positive controls. The sensitivity, specificity, positive predictive value and negative predictive value were 84%, 80%, 76% and 87%, respectively. 32/74 BAL samples were culture negative. Azole treatment failure was observed in 6/8 patients with a RAM compared with 12/45 patients without RAMs (P = 0.01). Six week mortality was 2.7 times higher in patients with RAMs (50.0% versus 18.6%; P = 0.07).

CONCLUSIONS

The AsperGenius^® assay had a good diagnostic performance on BAL and differentiated WT from Aspergillus fumigatus with RAMs, including in culture-negative BAL samples. Most importantly, detection of RAMs was associated with azole treatment failure.

Implementation of a multidisciplinary infectious diseases team in a tertiary hospital within an Antimicrobial Stewardship Program

BACKGROUND

In January 2011, as part of an antimicrobial stewardship program the Antimicrobial Management Team (AMT) at the Ghent University Hospital initiated a multidisciplinary Infectious Diseases Team (MIT) consisting of infectious diseases physicians, clinical microbiologists, and clinical pharmacists. The aim of this study is to describe the type and acceptance rate of recommendations provided by the MIT.

METHOD

Prospective, observational study in a tertiary care, university teaching hospital with 1062 beds in non-consecutive hospitalized adult patients, excluding intensive care units and paediatrics.

RESULTS

The MIT communicated 432 recommendations in 87 days observed. Of the 293 patients for whom a recommendation was made, the median age was 57 years (range: 16-91 years) and 169 (57·7%) were male. Skin or soft tissue infections (14%), respiratory tract infections (13%), infections without known focus (11%), abdominal infections (11%), and bone infections (8%) were most common. Recommendations were made to perform additional clinical investigation(s) [N = 137 (27%)], to adjust the dose of an antimicrobial drug [N = 42 (8%)], to stop an antimicrobial drug [N = 104 (21%)], to switch from a parenteral to an oral drug [N = 39 (8%)] or to initiate an antimicrobial drug [N = 178 (36%)], with an acceptance rate of 73·0%, 83·3%, 81·7%, 76·9%, and 84·0%, respectively.

CONCLUSIONS

The MIT formulated about five recommendations a day primarily focusing on pharmacotherapy, but also on clinical investigations. In both fields, a high acceptance rate was observed.

Therapeutic drug monitoring-based dose optimisation of piperacillin and meropenem: a randomised controlled trial

PURPOSE

There is variability in the pharmacokinetics (PK) of antibiotics (AB) in critically ill patients. Therapeutic drug monitoring (TDM) could overcome this variability and increase PK target attainment. The objective of this study was to analyse the effect of a dose-adaption strategy based on daily TDM on target attainment.

METHODS

This was a prospective, partially blinded, and randomised controlled trial in patients with normal kidney function treated with meropenem (MEM) or piperacillin/tazobactam (PTZ). The intervention group underwent daily TDM, with dose adjustment when necessary. The predefined PK/pharmacodynamic (PK/PD) target was 100% fT>4MIC [percentage of time during a dosing interval that the free (f) drug concentration exceeded 4 times the MIC]. The control group received conventional treatment. The primary endpoint was the proportion of patients that reached 100% fT>4MIC and 100 % fT>MIC at 72 h.

RESULTS

Forty-one patients (median age 56 years) were included in the study. Pneumonia was the primary infectious diagnosis. At baseline, 100% fT>4MIC was achieved in 21% of the PTZ patients and in none of the MEM patients; 100% fT>MIC was achieved in 71% of the PTZ patients and 46 % of the MEM patients. Of the patients in the intervention group, 76 % needed dose adaptation, and five required an additional increase. At 72 h, target attainment rates for 100% fT>4MIC and 100% fT>MIC were higher in the intervention group: 58 vs. 16%, p = 0.007 and 95 vs. 68%, p = 0.045, respectively.

CONCLUSIONS

Among critically ill patients with normal kidney function, a strategy of dose adaptation based on daily TDM led to an increase in PK/PD target attainment compared to conventional dosing.

Musculoskeletal manifestations of lysosomal storage disorders

Lysosomal storage disorders (LSDs), a heterogeneous group of inborn metabolic disorders, are far more common than most doctors presume. Although patients with a severe LSD subtype are often readily diagnosed, the more attenuated subtypes are frequently missed or diagnosis is significantly delayed. The presenting manifestations often involve the bones and/or joints and therefore these patients are frequently under specialist care by (paediatric) rheumatologists, receiving inadequate treatment. Since effective disease-specific treatments, including enzyme replacement therapy and stem cell transplantation, have become available for certain LSDs and timely initiation of these treatments is necessary to prevent the development of severe, disabling and irreversible manifestations, early diagnosis has become essential. The challenge is to raise awareness for better recognition of the presenting signs and symptoms of LSDs by all doctors who may encounter these patients, including rheumatologists.

Determination of the aerobic biodegradability of polymeric material in a laboratory controlled composting test

A laboratory method is presented for investigating the biodegradation of an organic test material in an aerobic composting system based on the evolution of carbon dioxide. In addition to carbon conversion, biodegradation can also be monitored through weight loss and physical disintegration. The test method is different from other biodegradation tests, especially aquatic tests, because of the elevated temperature representative for real composting conditions and also because of enhanced fungal degradation activities. A ring test was run using paper and poly-beta-hydroxybutyrate/valerate as test materials and cellulose powder as a reference material. The test results and the experience gained by the participants showed that the method is suitable and practicable. Experience with real technical-scale composting facilities confirms that the method provides test results of high predictive value. The test is designed to become a European Standard in connection with determining the compostability of packagings and packaging materials.

Source separation, selective collection and in reactor digestion of biowaste

Biowaste or the organic fraction of domestic waste, for instance kitchen, fruit and garden waste, is collected selectively in several European communities. The complementary fraction is called the dry or non recyclable fraction. A Dutch study reported that 92% of the participants that have a weekly collection service of both fractions (biowaste and non recyclable fraction) and 80% of the participants in the alternating collection program (one week biowaste and the next week non recyclable fraction) are pleased with separate collection of biowaste. Dominating problems that arise in case of alternating collection are a repulsive odor and an infestation with flies and maggots. By expanding the definition of biowaste to include non recyclable or soiled paper like dirty newspapers, table napkins and paper handkerchiefs, most of these problems can be overcome without changing the way compostable waste is collected and processed. The expanded definition of biowaste was used in this paper. Over a 12 month period a quality survey of the collected biowaste was conducted by the composting facility Intercompost, Hoeselt, Belgium. A special aspect was the fact that in one participating community baby diapers were included in the soiled paper fraction; this is called "biowaste+". The biowaste+ had a 10% non recyclable paper fraction opposed to only 1-2% of non recyclable paper present in the conventional biowaste. Baby diapers were a rather notable part (more than 80%) of this non recyclable paper fraction of biowaste+ and as a consequence might contribute to a large extent to improve the collection and treatment of biowaste. It was demonstrated that rural districts yielded about 35% more biowaste than more urban districts; resp. +/- 122 kg biowaste/capita. year versus +/- 90 kg biowaste/capita. year. In Hoeselt the biowaste+ yield was about 130 kg/capita.year. Biowaste+ is also separately collected in another Belgium community, namely Brecht. The purity level of the biowaste+ and the amount of non recyclable paper (including diapers) were comparable with the results of Hoeselt. In Hoeselt the biowaste+ fraction is composted aerobically. In Brecht on the other hand, the biowaste+ is processed using the Dry Anaerobic Composting process (DRANCO). The latter process is discussed in more detail. The biological start-up of the dry anaerobic composting installation at Brecht, Belgium, is reported. The reactor has a total volume of 808 m3 and a design capacity of 730 m3. After 2 months of start up, the fermentor was at full loading rate, i.e. 8 kg bVS/m3 reactor.day and the installation was working at full capacity, i.e. 40 ton/day.(ABSTRACT TRUNCATED AT 400 WORDS)

The use of bioluminescence as a reporter to study the adherence of the plant growth promoting rhizopseudomonads 7NSK2 and ANP15 to canola roots

The adherence of the plant growth promoting rhizopseudomonads Pseudomonas aeruginosa 7NSK2 and Pseudomonas fluorescens ANP15 to canola roots (Brassica campestris L. c.v. Tobin) was examined by means of a bacterial bioluminescence system. The bioluminescence broad host range vector pDLUX-I was constructed from pLAFR-I and the lux A–E genes of Vibrio fischerii. This vector was conjugally transferred into the plant growth promoting rhizopseudomonads 7NSK2 and ANP15. The transformed strains were constitutively bioluminescent at an optimal temperature of 21 °C. The measured bioluminescence was directly proportional to the density of the bacteria in suspension and was the same for both planktonic and sessile bacteria adhering to the root surface. The adherence of the plant growth promoting rhizopseudomonads was proportional to the density of the bacterial inoculum, approached saturation at 60 min, and was reversible. The kinetics of the microbial adhesion was described by a Freundlich isotherm suggesting that the adherence of the bacteria to the canola root surface does not involve specific receptors. We conclude that the pDLUX-I vector is an easy and accurate way to study the kinetics of microbial adherence to the rhizoplane.Key words: rhizopseudomonads, bioluminescence, adhesion, plant growth promotion.not available