Papers by Olivier Vandenberg
Nature Communications
Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, e... more Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.
IntroductionWe assessed the usefulness of SARS-CoV-2 RT-PCR cycle thresholds (Ct) values trends p... more IntroductionWe assessed the usefulness of SARS-CoV-2 RT-PCR cycle thresholds (Ct) values trends produced by the LHUB-ULB (a consolidated microbiology laboratory located in Brussels, Belgium) for monitoring the epidemic’s dynamics at local and national levels and for improving forecasting models.MethodsSARS-CoV-2 RT-PCR Ct values produced from April 1, 2020, to May 15, 2021, were compared with national COVID-19 confirmed cases notifications according to their geographical and time distribution. These Ct values were evaluated against both a phase diagram predicting the number of COVID-19 patients requiring intensive care and an age-structured model estimating COVID-19 prevalence in Belgium.ResultsOver 155,811 RT-PCR performed, 12,799 were positive and 7,910 Ct values were available for analysis. The 14-day median Ct values were negatively correlated with the 14-day mean daily positive tests with a lag of 17 days. In addition, the 14-day mean daily positive tests in LHUB-ULB were stron...
Supplemental material, 20130121VR3M_resultats_Viro-CDM_MH_GV_final_CE for Role of Viral Molecular... more Supplemental material, 20130121VR3M_resultats_Viro-CDM_MH_GV_final_CE for Role of Viral Molecular Panels in Diagnosing the Etiology of Fever in Infants Younger Than 3 Months by Cristina Epalza, Marie Hallin, Laurent Busson, Sara Debulpaep, Paulette De Backer, Olivier Vandenberg and Jack Levy in Clinical Pediatrics
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(Abstract D-1292) p. 176info:eu-repo/semantics/nonPublishe
Systematic and Applied Microbiology, 2021
Although at least two genetically distinct groups, or genomospecies, have been well documented fo... more Although at least two genetically distinct groups, or genomospecies, have been well documented for Campylobacter concisus, no phenotype has yet been identified for their differentiation and thus formal description as separate species. C. concisus has been isolated from a variety of sites in the human body, including saliva and stool samples from both healthy and diarrhoeic individuals. We evaluated the ability of a range of whole genome-based tools to distinguish between the two C. concisus genomospecies (GS) using a collection of 190 C. concisus genomes. Nine genomes from related Campylobacter species were included in some analyses to provide context. Analyses incorporating sequence analysis of multiple ribosomal genes generated similar levels of C. concisus GS discrimination as genome-wide comparisons. The C. concisus genomes formed two groups; GS1 represented by ATCC 33237 T and GS2 by CCUG 19995. The two C. concisus GS were separated from the nine genomes of related species. GS1 and GS2 also differed in G+C content with medians of 37.56% and 39.51%, respectively. The groups are consistent with previously established GS and are supported by DNA reassociation results. Average Nucleotide Identity using MUMmer (ANIm) and Genome BLAST Distance Phylogeny generated in silico DNA-DNA hybridisation (isDDH) (against ATCC 33237 T and CCUG 19995), plus G+C content provides cluster-independent GS discrimination suitable for routine use. Pan-genomic analysis identified genes specific to GS1 and GS2. WGS data and genomic species identification methods support the existence of two GS within C. concisus. These data provide genome-level metrics for strain identification to genomospecies level.
SSRN Electronic Journal, 2021
International Journal of Infectious Diseases, 2019
To evaluate the contribution of a multiplex PCR for respiratory viruses on antibiotic and antivir... more To evaluate the contribution of a multiplex PCR for respiratory viruses on antibiotic and antiviral prescription, ancillary test prescription, admission and length of stay of patients. Methods: Two hundred ninety-one adult and pediatric patients visiting the emergency department during the 2015-2016 influenza epidemic were prospectively included and immediately tested 24/7 using the FilmArray Respiratory Panel. The results were communicated to the practitioner in charge as soon as they became available. Clinical and biological data were gathered and analyzed. Findings: Results from the FilmArray Respiratory Panel do not appear to impact admission or antibiotic prescription, with the exception of a lower admission rate for children who tested positive for influenza B. Parameters that account for the clinical decisions evaluated are CRP level, white blood cell count, suspected or proven bacterial infection and, for adult patients only, signs of respiratory distress. Length of stay is also not significantly different between patients with a positive and a negative result. A rapid influenza test result permits a more appropriate prescription of oseltamivir.
European Journal of Clinical Microbiology & Infectious Diseases, 2017
Campylobacter infection is a common cause of diarrhea among international travelers. We studied a... more Campylobacter infection is a common cause of diarrhea among international travelers. We studied antibiotic resistance patterns among Campylobacter isolates obtained from international travelers according to travel destination. Three collections of isolates obtained from international travelers between 2007 and 2014 (Institute of Tropical Medicine, the BLaboratoire Hospitalier Universitaire de Bruxelles Band the Belgian National Reference Centre for Campylobacter) were used. Isolates were tested for minimal inhibitory concentration (MIC) values (E-test m acromethod) for fluoroquinolones, macrolides, tetracyclines, amoxicillinclavulanic acid, and meropenem. Single isolates from 261 travelers were available; median (IQR) age was 25.4 (4-42) years, 85.8% were symptomatic (information for 224 patients available). Overall resistance to ciprofloxacin was 60.9%, ranging from 50.8% in Africa to 75.0% in Asia. Resistance to erythromycin was 4.6%, with the highest rate observed for Southern Asia (15.2%, seven isolates, six of them recovered from patients returning from India). A total of 126 isolates (48.3%) were resistant to tetracycline. No resistance to amoxicillin-clavulanic acid or meropenem was detected. Ciprofloxacin resistance tended to increase over time (53.9% in 2007 versus 72.2% in 2014), erythromycin resistance remained stable (median annual resistance 4.2%). Most (86.2%) ciprofloxacin-resistant isolates had MIC values ≥32 mg/l, and all erythromycin-resistant isolates had MIC values ≥256 mg/l. Co-resistance to ciprofloxacin and erythromycin was observed in 11 (4.2%) isolates, seven of which came from Southern Asia. Among all regions of travel, more than half of Campylobacter isolates were resistant to ciprofloxacin. Overall resistance to erythromycin was below 5% but reached 15.2% in Southern Asia.
Diagnostic microbiology and infectious disease, 2016
chromID™ Salmonella Elite is compared with 3 culture media commonly used for Salmonella isolation... more chromID™ Salmonella Elite is compared with 3 culture media commonly used for Salmonella isolation from stool specimens. As results were equivalent to other chromogenic media (100% sensitivity, 98% specificity), only financial arguments should guide the choice for a medium with respect to another.
Nature microbiology, Oct 3, 2016
In the original version of this Letter, co-author Simon Le Hello's name was coded wrongly resulti... more In the original version of this Letter, co-author Simon Le Hello's name was coded wrongly resulting in it being incorrect when exported to citation databases. This has now been corrected, though no visible changes will be apparent.
Clinical laboratory, 2010
Methicillin-Resistant Staphylococcus aureus (MRSA) is one of the most common and important causes... more Methicillin-Resistant Staphylococcus aureus (MRSA) is one of the most common and important causes of nosocomial infections. Rapid detection of this pathogen is important for conducting good and swift infection control. This prospective study evaluates two chromogenic media for the detection of MRSA. New colony characteristics were noticed during this evaluation: (i) a yellow/golden colouration on a pipette after streaking the colonies of the chromogenic culture could eventually be used as a supplementary identification test to identify the MRSA strains, and (ii) some MRSA strains do not metabolise the chromogens and therefore are not coloured on chromogenic agars. However, they have a typical yellow/golden colony aspect usually observed amongst S. aureus.
Clinical laboratory, 2009
Although Mycobacterium tuberculosis (MTB) can be detected rapidly by means of Nucleic Acid Amplif... more Although Mycobacterium tuberculosis (MTB) can be detected rapidly by means of Nucleic Acid Amplification Techniques (NAT), these NAT tests are expensive and therefore are not used in routine practice or as a screening tool. Although it is generally accepted that clinical and radiological data are important markers for deciding whether to test for MTB using NAT, the optimal combination of markers has not been determined. A prospective study was performed to evaluate NAT using different combinations of clinical, laboratory and radiographic selection criteria. The sensitivity of NAT for detecting MTB in patients with smear negative for acid-fast bacilli was two times higher in patients with radiographic abnormalities and negative routine bacterial culture for respiratory pathogens than those with absence of radiographic abnormalities or positive routine bacterial culture (77.8% vs. 33.3%; p<0.001). Furthermore, a difference of almost 40% can be observed between the positive predicti...
Pediatric Infectious Disease Journal, 2012
Cryptosporidium outbreaks in day-care centers (DCCs) occur commonly. However, controlling spread ... more Cryptosporidium outbreaks in day-care centers (DCCs) occur commonly. However, controlling spread of infection in these settings is difficult, and data about effectiveness of different control strategies are sparse. In this study, a Cryptosporidium outbreak in a large DCC located in Brussels is described with evaluation of hygienic and therapeutic interventions. During a 3-week period, 43 of 130 children attending the DCC developed enteric symptoms. Stools from 122 children were examined for microbial pathogens. Of them, 38 (31%) were diagnosed with Cryptosporidium, 29 of them being symptomatic (76%) and 9 (24%) asymptomatic. Diagnosis was performed by microscopy, antigen tests, and real-time polymerase chain reaction. Strict infection control measures were implemented during the first week after the start of outbreak. After 4 weeks, 27/38 children (71%) were still symptomatic and Cryptosporidium positive. Because of persisting symptoms and fear of further spread of infection, all 27 children were treated with paromomycin. Two weeks later, 18 of 27 children were asymptomatic and were parasitologically negative. The remaining 9 children, still symptomatic and Cryptosporidium positive, were treated with nitazoxanide. Three weeks later, week 9 after the start of outbreak, all 38 children involved in the outbreak were asymptomatic and Cryptosporidium negative. Our study underscores the need to rule out Cryptosporidium etiology in a diarrheal outbreak in a DCC. Rapid implementation of infection control measures can most likely halt the spread of infection. The role of nitazoxanide to limit duration of shedding of oocysts deserves more attention for its use in outbreaks.
Journal of Antimicrobial Chemotherapy, 2013
on behalf of a multicentre study group †
Emerging Infectious Diseases, 2004
Clinical Microbiology and Infection, 2003
Objectives To evaluate the use of the new enzyme-linked immunosorbent assay, the ProSpecT Campylo... more Objectives To evaluate the use of the new enzyme-linked immunosorbent assay, the ProSpecT Campylobacter Microplate Assay (Alexon-Trend, Minneapolis, MN, USA), which allows 2-h detection of both Campylobacter jejuni and Campylobacter coli antigen directly in stool specimens. Methods Over 4 months, all stool samples preserved in Cary±Blair medium, or fresh specimens, from non-hospitalized children and HIV-infected patients (adults and children), submitted to our laboratory were evaluated with the ProSpecT Campylobacter Microplate Assay. Results were compared with those obtained by routine culture methods using both a speci®c medium and a ®ltration method for the recovery of Campylobacter spp. Results Of the 1205 stool specimens cultured, 101 were found to be positive for either C. jejuni or C. coli, giving an overall recovery rate of 8.38%. Ninety samples were positive by both culture and ProSpecT Campylobacter Microplate Assay, and 11 were positive by culture only, giving a sensitivity of 89.1%. In addition, of 1104 samples negative by culture, 25 were initially positive by ProSpecT Campylobacter Microplate Assay. We found no cross-reaction with other bacterial enteropathogens isolated from stool specimens. These results thus con®rm a high speci®city (97.7%) for both C. jejuni and C. coli. The positive and negative predictive values found were 78.3% and 99%, respectively. There was no statistically signi®cant difference in sensitivity and speci®city if the stool was fresh or preserved with Cary±Blair medium. Conclusion These data suggest that the ProSpecT Campylobacter Microplate Assay is a rapid and easy-to-use test for the detection of both C. jejuni and C. coli in stool specimens. It could be used for patients for whom early antibiotic therapy is needed or for epidemiologic studies.
Clinical Microbiology and Infection, 2013
For septic patients, delaying the initiation of antimicrobial therapy or choosing an inappropriat... more For septic patients, delaying the initiation of antimicrobial therapy or choosing an inappropriate antibiotic can considerably worsen their prognosis. This study evaluated the impact of rapid microbial identification (RMI) from positive blood cultures on the management of patients with suspected sepsis. During a 6-month period, RMI by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was performed for all new episodes of bacteraemia. For each patient, the infectious disease specialist was contacted and questioned about his therapeutic decisions made based on the Gram staining and the RMI. This information was collected to evaluate the number of RMIs that led to a therapeutic change or to a modification of the patient's general management (e.g. fast removal of infected catheters). During the study period, 277 new episodes of bacteraemia were recorded. In 71.12% of the cases, MALDI-TOF MS resulted in a successful RMI (197/277). For adult and paediatric patients, 13.38% (21/157) and 2.50% (1/40) of the RMIs, respectively, resulted in modification of the treatment regimen, according to the survey. In many other cases, the MALDI-TOF MS was a helpful tool for infectious disease specialists because it confirmed suspected cases of contamination, especially in the paediatric population (15/40 RMIs, 37.50%), or suggested complementary diagnostic testing. This study emphasizes the benefits of RMI from positive blood cultures. Although the use of this technique represents an extra cost for the laboratory, RMI using MALDI-TOF MS has been implemented in our daily practice.
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Papers by Olivier Vandenberg