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Objectives To study the presence of viral RNA in follicular fluid, cumulus cells and endometrial tissue samples in SARS-CoV-2 positive women undergoing assisted reproductive technologies (ART). Design Prospective, single-center, observational study. Setting Tertiary hospital, University Hospital UZ Brussel, Belgium. Patients Sixteen patients undergoing transvaginal oocyte retrieval who had a positive SARS-CoV-2 RNA test less than 48 hours before the procedure. All cases were done between September 2020 and June 2021 and used in-vitro fertilization or intracytoplasmic sperm injection. All embryos were vitrified to avoid conception during SARS-CoV-2 infection. Intervention Follicular fluid aspirated during oocyte retrieval, cumulus cells and endometrial samples were analyzed for SARS-CoV-2 RNA using RealStar® SARS-CoV-2 RT-PCR-Kit1.0 (Altona-Diagnostics). Main outcome measures The primary outcome parameter was the detection of viral RNA in follicular fluid, cumulus cells and endometrial cells. Fertilization rate, embryo developmental potential and clinical outcome after frozen embryo transfer were secondary outcome parameters. Results Samples from sixteen patients were analyzed. Cycle threshold (Ct) values < 40 were considered positive. All samples were negative for SARS-CoV-2 viral RNA. No inflammatory lesions of the endometrium were identified histologically. Fertilization rate, embryo development and clinical outcomes after embryo transfer were reassuring. Conclusions In women infected with SARS-CoV-2 who underwent ART, viral RNA was undetectable in follicular fluid, cumulus cells and endometrium. Caution is warranted in view of the small sample size, and the risk of SARS-CoV-2 affecting the embryo via ART cannot be ruled out. Adequate counselling of women and couples undergoing ART is crucial in parallel with further research on the effect of exposure of the early human embryo to SARS-CoV-2., In patients with a SARS-CoV-2 infection, viral RNA was undetectable in follicular fluid, cumulus cells and endometrial biopsies. Additionally, embryological data and clinical outcomes are reported.

This study describes, for the first time, the occurrence of an epidemic of enteroaggregative Escherichia coli (EAEC) O111:H21 in a Belgian nursery and describes a practical approach concerning its management. Few data exist in the literature on this type of outbreak. Clinical and microbiological investigations were needed to find a link between the cases and identify the causative agent. The microbiological procedure followed was first based on conventional analyses: isolation using selective cultures, identification by MALDI-TOF MS, antibiogram, determination of the serogroup by agglutination, then whole genome sequencing. A total of 7/21 children were infected with this pathogen. Four cases could be confirmed by a molecular technique, wgMLST, as belonging to the same bacterial clone. The action plan put in place focused on symptomatic case eviction, strict general hygiene precaution as well as specific cleaning and disinfection measures. The epidemic did last only a few days. It appears important, in the context of an epidemic, that clinical laboratories standardize their practice by equipping themselves with molecular techniques such as a multiplex which does not focus only on the serotype O157:H7 and which make it possible to distinguish the different pathotypes of E. coli by targeting several virulence genes (stx, aggR…). However, cost/effectiveness studies are awaited to confirm the interest of a systematic search by molecular method for the pathogen involved in a suspected outbreak occurring in a nursery.

Among Shiga toxin (Stx)-producing Escherichia coli (STEC) strains of various serotypes, O157:H7 and five major non-O157 STEC (O26:H11, O111:H8, O103:H2, O121:H19 and O145:H28) can be selectively isolated by using tellurite-containing media. While human infections by O165:H25 STEC strains have been reported worldwide, their detection and isolation are not easy, as they are not resistant to tellurite. Systematic whole-genome sequencing (WGS) analyses have not yet been conducted. Here, we defined O165:H25 strains and their close relatives, including O172:H25 strains, as clonal complex 119 (CC119) and performed a global WGS analysis of the major lineage of CC119, called CC119 sensu stricto (CC119ss), by using 202 CC119ss strains, including 90 strains sequenced in this study. Detailed comparisons of 13 closed genomes, including 7 obtained in this study, and systematic analyses of Stx phage genomes in 50 strains covering the entire CC119ss lineage, were also conducted. These analyses revealed that the Stx2a phage, the locus of enterocyte effacement (LEE) encoding a type III secretion system (T3SS), many prophages encoding T3SS effectors, and the virulence plasmid were acquired by the common ancestor of CC119ss and have been stably maintained in this lineage, while unusual exchanges of Stx1a and Stx2c phages were found at a single integration site. Although the genome sequences of Stx2a phages were highly conserved, CC119ss strains exhibited notable variation in Stx2 production levels. Further analyses revealed the lack of SpLE1-like elements carrying the tellurite resistance genes in CC119ss and defects in rhamnose, sucrose, salicin and dulcitol fermentation. The genetic backgrounds underlying these defects were also clarified.

It is generally accepted that microorganisms can colonize a non-pathological endometrium. However, in a clinical setting, endometrial samples are always collected by passing through the vaginal–cervical route. As such, the vaginal and cervical microbiomes can easily cross-contaminate endometrial samples, resulting in a biased representation of the endometrial microbiome. This makes it difficult to demonstrate that the endometrial microbiome is not merely a reflection of contamination originating from sampling. Therefore, we investigated to what extent the endometrial microbiome corresponds to that of the vagina, applying culturomics on paired vaginal and endometrial samples. Culturomics could give novel insights into the microbiome of the female genital tract, as it overcomes sequencing-related bias. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy were included. An additional vaginal swab was taken from each participant right before hysteroscopy. Both endometrial biopsies and vaginal swabs were analyzed using our previously described WASPLab-assisted culturomics protocol. In total, 101 bacterial and two fungal species were identified among these 10 patients. Fifty-six species were found in endometrial biopsies and 90 were found in vaginal swabs. On average, 28 % of species were found in both the endometrial biopsy and vaginal swab of a given patient. Of the 56 species found in the endometrial biopsies, 13 were not found in the vaginal swabs. Of the 90 species found in vaginal swabs, 47 were not found in the endometrium. Our culturomics-based approach sheds a different light on the current understanding of the endometrial microbiome. The data suggest the potential existence of a unique endometrial microbiome that is not merely a presentation of cross-contamination derived from sampling. However, we cannot exclude cross-contamination completely. In addition, we observe that the microbiome of the vagina is richer in species than that of the endometrium, which contradicts the current sequence-based literature.

E. coli O157:H7 is a known Shiga toxin-producing Escherichia coli (STEC), causing foodborne disease globally. Cattle are the main reservoir and consumption of beef and beef products contaminated with E. coli O157:H7 is an important source of STEC infections in humans. To emphasize the cattle-to-human transmission through the consumption of contaminated beef in Bishoftu, Ethiopia, whole-genome sequencing (WGS) was performed on E. coli O157 strains isolated from three sources (cattle, beef, and humans). Forty-four E. coli O157:H7 isolates originating from 23 cattle rectal contents, three cattle hides, five beef carcasses, seven beef cuts at retail shops, and six human stools in Bishoftu between June 2017 and May 2019 were included. This study identified six clusters of closely related E. coli O157:H7 isolates based on core genome multilocus sequence typing (cgMLST) by targeting 2513 loci. A genetic linkage was observed among the isolate genomes from the cattle rectal contents, cattle hides, beef carcasses at slaughterhouses, beef at retail shops, and human stool within a time frame of 20 months. All the strains carried practically the same repertoire of virulence genes except for the stx2 gene, which was present in all but eight of the closely related isolates. All the strains carried the mdfA gene, encoding for the MdfA multi-drug efflux pump. CgMLST analysis revealed genetically linked E. coli O157:H7 isolates circulating in the area, with a potential transmission from cattle to humans through the consumption of contaminated beef and beef products. Keywords: E. coli O157:H7; whole-genome sequencing; cgMLST; transmission; virulence genes; antimicrobial resistance, E. coli O157:H7 is a known Shiga toxin-producing Escherichia coli (STEC), causing foodborne disease globally. Cattle are the main reservoir and consumption of beef and beef products contaminated with E. coli O157:H7 is an important source of STEC infections in humans. To emphasize the cattle-to-human transmission through the consumption of contaminated beef in Bishoftu, Ethiopia, whole-genome sequencing (WGS) was performed on E. coli O157 strains isolated from three sources (cattle, beef, and humans). Forty-four E. coli O157:H7 isolates originating from 23 cattle rectal contents, three cattle hides, five beef carcasses, seven beef cuts at retail shops, and six human stools in Bishoftu between June 2017 and May 2019 were included. This study identified six clusters of closely related E. coli O157:H7 isolates based on core genome multilocus sequence typing (cgMLST) by targeting 2513 loci. A genetic linkage was observed among the isolate genomes from the cattle rectal contents, cattle hides, beef carcasses at slaughterhouses, beef at retail shops, and human stool within a time frame of 20 months. All the strains carried practically the same repertoire of virulence genes except for the stx2 gene, which was present in all but eight of the closely related isolates. All the strains carried the mdfA gene, encoding for the MdfA multi-drug efflux pump. CgMLST analysis revealed genetically linked E. coli O157:H7 isolates circulating in the area, with a potential transmission from cattle to humans through the consumption of contaminated beef and beef products.

With the increase in antimicrobial resistance, fast reporting of antimicrobial susceptibility testing (AST) results is becoming increasingly important. EUCAST developed a method for rapid AST (RAST) directly from the broth of positive blood cultures (BC). Inhibition zones are read after 4, 6, and 8 h, with specific breakpoints per time point. We evaluated the RAST method based on EUCAST disk diffusion methodology with inoculation of BC broth using WASPLab® (inclusive Colibrí™ and Radian®). Forty-nine non-duplicate strains were tested: Escherichia coli n = 17, Klebsiella pneumoniae n = 7, Pseudomonas aeruginosa n = 4, Acinetobacter baumannii n = 2, Staphylococcus aureus n = 10, Enterococcus faecalis n = 6, and Enterococcus faecium n = 3. Results were compared to direct AST and standardized AST. Good categorical agreement was obtained at all time points for all groups, except P. aeruginosa. RAST cut-offs for extended-spectrum β-lactamase (ESBL)-producing Enterobacterales enabled the detection of all included ESBL isolates (n = 5) at all time points, except for 1 E. coli ESBL after 4 h. RAST cut-offs for carbapenemase-producing Enterobacterales enabled the detection of only one carbapenemase after 6 h. However, all carbapenemases (n = 3) were correctly detected after 8 h. Two methicillin-resistant S. aureus were included; both were correctly categorized as cefoxitin-resistant at 6 and 8 h. At 4 h, there was insufficient growth for inhibition zone interpretation. EUCAST RAST is a fast supplementary tool for direct AST of positive BC. WASPLab® provides a significant advantage as pictures are made automatically implicating that we are not strictly bound to the time points for inhibition zone interpretation.

Objectives This study reports antimicrobial activity for ceftaroline and comparators against bacterial isolates from patients with skin and skin structure infections (2015–2018). Methods A central laboratory performed susceptibility testing according to CLSI broth microdilution methodology. EUCAST breakpoints were used. Results Isolates were collected in Europe, 14,408 isolates (53.9%); Asia/South Pacific (SP), 5,317 (19.9%); Latin America, 4,268 (16.0%); and Africa/Middle East (ME), 2,753 (10.3%). In all regions, all 7,950 methicillin-susceptible Staphylococcus aureus (MSSA) isolates were susceptible to ceftaroline and vancomycin; susceptibility to daptomycin, linezolid, teicoplanin, and tigecycline was ≥99.6%. Susceptibility of all 9,174 methicillin-resistant S. aureus (MRSA) isolates to daptomycin, linezolid, teicoplanin, tigecycline and vancomycin was ≥97.7%, with 90.8%–96.5% susceptible to ceftaroline. The ceftaroline MIC90 was 0.008 mg/L against Streptococcus pyogenes, 0.015–0.03 mg/L against Streptococcus agalactiae, and 0.008–0.015 mg/L against Streptococcus dysgalactiae. All β-hemolytic streptococci were susceptible to vancomycin. Susceptibility of extended-spectrum β-lactamase (ESBL)-negative Escherichia coli to ceftaroline ranged from 67.0% in Asia/SP to 91.0% in Africa/ME; susceptibility to amikacin, meropenem and tigecycline was ≥96.7% in all regions. Susceptibility of ESBL-negative Klebsiella pneumoniae to ceftaroline ranged from 78.4% in Europe to 83.2% in Africa/ME, and among ESBL-negative Klebsiella oxytoca was 76.3% in Asia/SP, and 89.0%–93.5% in the other regions. Among ESBL-negative K. pneumoniae and ESBL-negative K. oxytoca, susceptibility was highest to amikacin (93.7%–96.4% and 95.7%–100%, respectively) and meropenem (89.7%–97.4% and 98.3%–100%, respectively). Conclusions Ceftaroline was active against the Gram-positive isolates collected; susceptibility of ESBL-negative Gram-negative isolates showed regional variations.

Background: In the period following the declaration of the COVID-19 pandemic, more evidence became available on the epidemiology of bacterial co-/superinfections (bCSs) in hospitalized COVID-19 patients. Various European therapeutic guidelines were published, including guidance on rational antibiotic use. Methods: In this letter to the editor, we provide an overview of the largest meta-analyses or prospective studies reporting on bCS rates in COVID-19 patients and discuss why the reader should interpret the results of those reports with care. Moreover, we compare different national and international COVID-19 therapeutic guidelines from countries of the European Union. Specific attention is paid to guidance dedicated to rational antibiotic use. Results: We found a significant heterogeneity in studies reporting on the epidemiology of bCSs in COVID-19 patients. Moreover, European national and international guidelines differ strongly from each other, especially with regard to the content and extent of antibiotic guidance in hospitalized COVID-19 patients. Conclusion: A standardized way of reporting on bCSs and uniform European guidelines on rational antibiotic use in COVID-19 patients are crucial for antimicrobial stewardship teams to halt unnecessary antibiotic use in the COVID-19 setting.

Simple Summary Enteropathogenic Escherichia coli (EPEC) from cattle receive little attention, although some belong to the most notorious O serotypes of attaching/effacing Shigatoxigenic Escherichia coli (AE-STEC) responsible for the uremic and hemolytic syndrome in humans, such as O26. Nevertheless, the O serotypes and virulotypes of the large majority of bovine EPEC remain unidentified. This study aimed to identify five non-classical O serotypes (O123/186, O156, O177, O182, and O183) by a polymerase chain reaction (PCR) among three collections of bovine EPEC from young diarrheic calves, healthy cattle at slaughterhouses, and healthy calves in dairy farms. The virulotypes and sequence types (STs) obtained after the whole genome sequencing of several O156, O177, and O182 bovine EPEC were closely related or identical to the virulotypes and STs of ten bovine and the human AE-STEC of the same O:H serotype. This study allows us to identify more EPEC O serotypes from cattle and to speculate on their evolution. Enteropathogenic Escherichia coli (EPEC) produce attaching/effacing (AE) lesions and cause non-bloody diarrhea in mammals. A minority of bovine EPEC belong to one of the ten classical serotypes of human and bovine AE-STEC. The purpose of this study was to identify five non-classical O serotypes (O123/186, O156, O177, O182, and O183) among bovine EPEC and to characterize their virulence repertoires by whole genome sequencing. Around 40% of the 307 EPEC from 307 diarrheic calves, 368 EPEC from 47 healthy cattle, and 131 EPEC from 36 healthy calves in dairy farms were analyzed. Serotype O177 was the most frequent among EPEC from diarrheic and healthy calves, while the O156 was the most frequent in healthy cattle. The genomic analysis identified different H serotypes, MLSTypes, and/or eae gene subtypes among the O156 and O177 EPEC, while the O182 was homogeneous. The virulence gene profiles of bovine EPEC were closely related to each other and to the profiles of ten bovine and human AE-STEC. These results emphasize the need for additional studies to identify more O:H serotypes of bovine EPEC and to elucidate their origin and evolution of EPEC with regard to AE-STEC belonging to the same O:H serotypes.

The microbiome of the reproductive tract has been associated with (sub)fertility and it has been suggested that dysbiosis reduces success rates and pregnancy outcomes. The endometrial microbiome is of particular interest given the potential impact on the embryo implantation. To date, all endometrial microbiome studies have applied a metagenomics approach. A sequencing-based technique, however, has its limitations, more specifically in adequately exploring low-biomass settings, such as intra-uterine/endometrial samples. In this proof-of-concept study, we demonstrate the applicability of culturomics, a high-throughput culturing approach, to investigate the endometrial microbiome. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy, as part of their routine work-up at Brussels IVF, were included after their informed consent. Biopsies were used to culture microbiota for up to 30 days in multiple aerobic and anaerobic conditions. Subsequent WASPLab®-assisted culturomics enabled a standardized methodology. Matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS) or 16S rRNA sequencing was applied to identify all of bacterial and fungal isolates. Eighty-three bacterial and two fungal species were identified. The detected species were in concordance with previously published metagenomics-based endometrial microbiota analyses as 77 (91%) of them belonged to previously described genera. Nevertheless, highlighting the added value of culturomics to identify most isolates at the species level, 53 (62.4%) of the identified species were described in the endometrial microbiota for the first time. This study shows the applicability and added value of WASPLab®-assisted culturomics to investigate the low biomass endometrial microbiome at a species level.

Background: Healthcare-associated SARS-CoV-2 infections need to be explored further. Our study is an analysis of hospital-acquired infections (HAIs) and ambulatory healthcare workers (aHCWs) with SARS-CoV-2 across the pandemic in a Belgian university hospital. Methods: We compared HAIs with community-associated infections (CAIs) to identify the factors associated with having an HAI. We then performed a genomic cluster analysis of HAIs and aHCWs. We used this alongside the European Centre for Disease Control (ECDC) case source classifications of an HAI. Results: Between March 2020 and March 2022, 269 patients had an HAI. A lower BMI, a worse frailty index, lower C-reactive protein (CRP), and a higher thrombocyte count as well as death and length of stay were significantly associated with having an HAI. Using those variables to predict HAIs versus CAIs, we obtained a positive predictive value (PPV) of 83.6% and a negative predictive value (NPV) of 82.2%; the area under the ROC was 0.89. Genomic cluster analyses and representations on epicurves and minimal spanning trees delivered further insights into HAI dynamics across different pandemic waves. The genomic data were also compared with the clinical ECDC definitions for HAIs; we found that 90.0% of the ‘definite’, 87.8% of the ‘probable’, and 70.3% of the ‘indeterminate’ HAIs belonged to one of the twenty-two COVID-19 genomic clusters we identified. Conclusions: We propose a novel prediction model for HAIs. In addition, we show that the management of nosocomial outbreaks will benefit from genome sequencing analyses.

Recently, Copan (Italy) introduced the Colibrí instrument for automated colony picking and preparation of matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) target plates. Our study aimed to validate this system for yeasts as such testing has not been performed yet and is a missing link needed to implement the system for routine use. Fifty-five Candida strains were selected to evaluate the accuracy of Colibrí. For each strain, a sheep blood agar plate supplemented with X and V factors (HEM) and a Sabouraud agar plate (SAB) were inoculated and incubated using the WASPlab specimen processing system (Copan). After 18 h and 36 h of incubation, the isolates were spotted in parallel using Colibrí and manually onto MALDI-TOF target plates with the addition of formic acid and identified using MALDI-TOF mass spectrometry. The reproducibility was evaluated using ATCC reference and clinical isolate-derived strains. The cumulative percentage of acceptable identification scores (IDs) after 36 h was 91%for strains cultured on HEM plates using both Colibrí and the manual method. The SAB plates showed inferior results for both Colibrí (76%) and the manual method (78%). We observed an overall agreement of 92% at 18 h for identification of the strains on the HEM plates between Colibrí and the manual method and 94% after 36 h. For the SAB plates, the agreement was 78% after 18 h and 84% after 36 h. Apart from Candida dubliniensis and Candida tropicalis, all Candida species were identified with 100% accuracy using Colibrí on HEM plates. We observed good agreement between Colibrí and the manual reference method. These results demonstrate that Colibrí is a reliable system for MALDI-TOF target preparation for yeast identification, allowing increased standardization and less hands-on time.

Enteropathogenic

As with other pathogens, competitive interactions between Bordetella pertussis strains drive infection risk. Vaccines are thought to perturb strain diversity through shifts in immune pressures; however, this has rarely been measured because of inadequate data and analytical tools. We used 3344 sequences from 23 countries to show that, on average, there are 28.1 transmission chains circulating within a subnational region, with the number of chains strongly associated with host population size. It took 5 to 10 years for B. pertussis to be homogeneously distributed throughout Europe, with the same time frame required for the United States. Increased fitness of pertactin-deficient strains after implementation of acellular vaccines, but reduced fitness otherwise, can explain long-term genotype dynamics. These findings highlight the role of vaccine policy in shifting local diversity of a pathogen that is responsible for 160,000 deaths annually.

As with other pathogens, competitive interactions between Bordetella pertussis strains drive infection risk. Vaccines are thought to perturb strain diversity through shifts in immune pressures; however, this has rarely been measured because of inadequate data and analytical tools. We used 3344 sequences from 23 countries to show that, on average, there are 28.1 transmission chains circulating within a subnational region, with the number of chains strongly associated with host population size. It took 5 to 10 years for B. pertussis to be homogeneously distributed throughout Europe, with the same time frame required for the United States. Increased fitness of pertactin-deficient strains after implementation of acellular vaccines, but reduced fitness otherwise, can explain long-term genotype dynamics. These findings highlight the role of vaccine policy in shifting local diversity of a pathogen that is responsible for 160,000 deaths annually.

BackgroundWorldwide, healthcare-associated SARS-CoV-2 infections are a major problem: they are associated with increased morbidity, mortality, and hospitalization costs. In-depth studies across the pandemic are crucial to understand and prevent transmission in hospital settings. The principal aims of this study were to characterise patients and validate ECDC definitions of healthcare-associated COVID-19 infections.MethodsWe set up a retrospective observational study spanning the first three waves of the COVID-19 pandemic in a Belgian university hospital: it describes the characteristics of COVID-19 patients admitted, with either healthcare- or community-associated infections. We performed a cluster analysis through epidemiological and viral genome analyses of the healthcare-associated infections, in order to validate the ECDC definitions of healthcare-associated COVID-19 infections.ResultsBetween week 10 of 2020 and week 22 of 2021, 168 patients were hospitalized with healthcare-associated COVID-19. The following factors were found more often in symptomatic healthcare- than in community-associated hospitalized patients: older age, increased frailty, smoking habits, and comorbidities. The genome-based cluster analyses showed that different viral lineages predominated in different timeframes. We observed a good correlation of epidemiological data with genome sequencing results in at least 12 different outbreaks in our hospital, thus validating the ECDC definitions. ConclusionsThis in-depth characterization sheds new light on the problem of healthcare-associated COVID-19 infections, in particular on patients’ characteristics, epidemiology, and cluster dynamics. Even though epidemiological evaluation of nosocomial infections is vital, management of nosocomial outbreaks can undoubtedly benefit from genome sequencing analyses to reinforce their strategy.

Shiga toxin (Stx)-producing Escherichia coli (STEC) are foodborne pathogens causing serious diseases, such as haemorrhagic colitis and haemolytic uraemic syndrome. Although O157:H7 STEC strains have been the most prevalent, incidences of STEC infections by several other serotypes have recently increased. O121:H19 STEC is one of these major non-O157 STECs, but systematic whole genome sequence (WGS) analyses have not yet been conducted on this STEC. Here, we performed a global WGS analysis of 638 O121:H19 strains, including 143 sequenced in this study, and a detailed comparison of 11 complete genomes, including four obtained in this study. By serotype-wide WGS analysis, we found that O121:H19 strains were divided into four lineages, including major and second major lineages (named L1 and L3, respectively), and that the locus of enterocyte effacement (LEE) encoding a type III secretion system (T3SS) was acquired by the common ancestor of O121:H19. Analyses of 11 complete genomes belonging to L1 or L3 revealed remarkable interlineage differences in the prophage pool and prophage-encoded T3SS effector repertoire, independent acquisition of virulence plasmids by the two lineages, and high conservation in the prophage repertoire, including that for Stx2a phages in lineage L1. Further sequence determination of complete Stx2a phage genomes of 49 strains confirmed that Stx2a phages in lineage L1 are highly conserved short-tailed phages, while those in lineage L3 are long-tailed lambda-like phages with notable genomic diversity, suggesting that an Stx2a phage was acquired by the common ancestor of L1 and has been stably maintained. Consistent with these genomic features of Stx2a phages, most lineage L1 strains produced much higher levels of Stx2a than lineage L3 strains. Altogether, this study provides a global phylogenetic overview of O121:H19 STEC and shows the interlineage genomic differences and the highly conserved genomic features of the major lineage within this serotype of STEC.

Despite the low rates of bacterial co-/superinfections in COVID-19 patients, antimicrobial drug use has been liberal since the start of the COVID-19 pandemic. Due to the low specificity of markers of bacterial co-/superinfection in the COVID-19 setting, overdiagnosis and antimicrobial overprescription have become widespread. A quantitative and qualitative evaluation of urinary tract infection (UTI) diagnoses and antimicrobial drug prescriptions for UTI diagnoses was performed in patients admitted to the COVID-19 ward of a university hospital between 17 March and 2 November 2020. A team of infectious disease specialists performed an appropriateness evaluation for every diagnosis of UTI and every antimicrobial drug prescription covering a UTI. A driver analysis was performed to identify factors increasing the odds of UTI (over)diagnosis. A total of 622 patients were included. UTI was present in 13% of included admissions, and in 12%, antimicrobials were initiated for a UTI diagnosis (0.71 daily defined doses (DDDs)/admission; 22% were scored as ‘appropriate’). An evaluation of UTI diagnoses by ID specialists revealed that of the 79 UTI diagnoses, 61% were classified as probable overdiagnosis related to the COVID-19 hospitalization. The following factors were associated with UTI overdiagnosis: physicians who are unfamiliar working in an internal medicine ward, urinary incontinence, mechanical ventilation and female sex. Antimicrobial stewardship teams should focus on diagnostic stewardship of UTIs, as UTI overdiagnosis seems to be highly prevalent in admitted COVID-19 patients.

The current routine laboratory practices to investigate food samples in case of foodborne outbreaks still rely on attempts to isolate the pathogen in order to characterize it. We present in this study a proof of concept using Shiga toxin-producing Escherichia coli spiked food samples for a strain-level metagenomics foodborne outbreak investigation method using the MinION and Flongle flow cells from Oxford Nanopore Technologies, and we compared this to Illumina short-read-based metagenomics. After 12 h of MinION sequencing, strain-level characterization could be achieved, linking the food containing a pathogen to the related human isolate of the affected patient, by means of a single-nucleotide polymorphism (SNP)-based phylogeny. The inferred strain harbored the same virulence genes as the spiked isolate and could be serotyped. This was achieved by applying a bioinformatics method on the long reads using reference-based classification. The same result could be obtained after 24-h sequencing on the more recent lower output Flongle flow cell, on an extract treated with eukaryotic host DNA removal. Moreover, an alternative approach based on in silico DNA walking allowed to obtain rapid confirmation of the presence of a putative pathogen in the food sample. The DNA fragment harboring characteristic virulence genes could be matched to the E. coli genus after sequencing only 1 h with the MinION, 1 h with the Flongle if using a host DNA removal extraction, or 5 h with the Flongle with a classical DNA extraction. This paves the way towards the use of metagenomics as a rapid, simple, one-step method for foodborne pathogen detection and for fast outbreak investigation that can be implemented in routine laboratories on samples prepared with the current standard practices.

Two colorimetric broth microdilution antifungal susceptibility tests were compared, Sensititre YeastOne and MICRONAUT-AM for nine antifungal agents. One hundred clinical Candida isolates were tested, representing a realistic population for susceptibility testing in daily practice. The reproducibility characteristics were comparable. Only for fluconazole, caspofungin, 5-flucytosine and amphotericin B, an essential agreement of ≥90% could be demonstrated. Sensititre minimal inhibitory concentrations (MICs) were systematically higher than MICRONAUT MICs for all antifungals, except for itraconazole. CLSI clinical breakpoints (CBPs) and epidemiological cut-off values (ECVs) were used for Sensititre MICs while for MICRONAUT the EUCAST CBPs and ECVs were used. Only fluconazole, micafungin, and amphotericin B had a categorical agreement of ≥90%. For fluconazole, micafungin, and amphotericin B the susceptibility proportions were comparable. Susceptibility proportion of posaconazole and voriconazole was higher using the MICRONAUT system. For itraconazole and anidulafungin, the susceptibility proportion was higher using Sensititre. It was not possible to determine the true MIC values or the correctness of a S/I/R result since both commercial systems were validated against a different reference method. These findings show that there is a significant variability in susceptibility pattern and consequently on use of antifungals in daily practice, depending on the choice of commercial system.

Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are usually fragmented, limiting our understanding of their dynamics. Here, we performed a systematic analysis of 239 draft genomes and 7 complete genomes of Shiga toxin (Stx)-producing Escherichia coli O145:H28, the major virulence factors of which are encoded by prophages (PPs) or plasmids. The results indicated that PPs are more stably maintained than plasmids. A set of ancestrally acquired PPs was well conserved, while various PPs, including Stx phages, were acquired by multiple sublineages. In contrast, gains and losses of a wide range of plasmids have frequently occurred across the O145:H28 lineage, and only the virulence plasmid was well conserved. The different dynamics of PPs and plasmids have differentially impacted the pangenome of O145:H28, with high proportions of PP- and plasmid-associated genes in the variably present and rare gene fractions, respectively. The dynamics of PPs and plasmids have also strongly impacted virulence gene repertoires, such as the highly variable distribution of stx genes and the high conservation of a set of type III secretion effectors, which probably represents the core effectors of O145:H28 and the genes on the virulence plasmid in the entire O145:H28 population. These results provide detailed insights into the dynamics of PPs and plasmids, and show the application of genomic analyses using a large set of draft genomes and appropriately selected complete genomes.

There are different patterns in the COVID-19 outbreak in the general population and amongst nursing home patients. We investigate the time from symptom onset to diagnosis and hospitalization or the length of stay (LoS) in the hospital, and whether there are differences in the population. Sciensano collected information on 14,618 hospitalized patients with COVID-19 admissions from 114 Belgian hospitals between 14 March and 12 June 2020. The distributions of different event times for different patient groups are estimated accounting for interval censoring and right truncation of the time intervals. The time between symptom onset and hospitalization or diagnosis are similar, with median length between symptom onset and hospitalization ranging between 3 and 10.4 days, depending on the age of the patient (longest delay in age group 20&ndash, 60 years) and whether or not the patient lives in a nursing home (additional 2 days for patients from nursing home). The median LoS in hospital varies between 3 and 10.4 days, with the LoS increasing with age. The hospital LoS for patients that recover is shorter for patients living in a nursing home, but the time to death is longer for these patients. Over the course of the first wave, the LoS has decreased.

Highlights • Hydroxychloroquine (HCQ) 2400 mg over 5 days was used in Belgium for COVID-19. • Impact of HCQ on mortality among 8075 patients with COVID-19 was assessed. • Lower mortality in HCQ-treated patients as compared to supportive care. • Lower mortality was irrespective of symptom duration., Hydroxychloroquine (HCQ) has been largely used and investigated as therapy for COVID-19 across various settings at a total dose usually ranging from 2400 mg to 9600 mg. In Belgium, off-label use of low-dose HCQ (total 2400 mg over 5 days) was recommended for hospitalised patients with COVID-19. We conducted a retrospective analysis of in-hospital mortality in the Belgian national COVID-19 hospital surveillance data. Patients treated either with HCQ monotherapy and supportive care (HCQ group) were compared with patients treated with supportive care only (no-HCQ group) using a competing risks proportional hazards regression with discharge alive as competing risk, adjusted for demographic and clinical features with robust standard errors. Of 8075 patients with complete discharge data on 24 May 2020 and diagnosed before 1 May 2020, 4542 received HCQ in monotherapy and 3533 were in the no-HCQ group. Death was reported in 804/4542 (17.7%) and 957/3533 (27.1%), respectively. In the multivariable analysis, mortality was lower in the HCQ group compared with the no-HCQ group [adjusted hazard ratio (aHR) = 0.684, 95% confidence interval (CI) 0.617–0.758]. Compared with the no-HCQ group, mortality in the HCQ group was reduced both in patients diagnosed ≤5 days (n = 3975) and >5 days (n = 3487) after symptom onset [aHR = 0.701 (95% CI 0.617–0.796) and aHR = 0.647 (95% CI 0.525–0.797), respectively]. Compared with supportive care only, low-dose HCQ monotherapy was independently associated with lower mortality in hospitalised patients with COVID-19 diagnosed and treated early or later after symptom onset.

Purpose: Different respiratory sampling methods exist to identify lower airway pathogens in patients with cystic fibrosis (CF), of which bronchoalveolar lavage (BAL), and expectorated sputum are considered the "gold standard." Because BAL cannot be repeated limitless, the diagnosis of lower respiratory tract infections in non-expectorating patients is challenging. Other sampling techniques are nasal swab, cough swab, and induced sputum. The purpose of this study (NCT02363764) was to compare concordance between the microbiological yield of nasal swab, cough swab, and expectorated sputum in expectorating patients; nasal swab, cough swab, and induced sputum in non-expectorating patients; nasal swab, cough swab, induced sputum, and BAL in patients requiring bronchoscopy ("BAL-group"); and to determine the clinical value of cough swab in non-expectorating patients with CF. Methods: Microbiological yield detected by these different sampling techniques was compared between and within 105 expectorating patients, 30 non-expectorating patients and BAL-group (n = 39) in a single CF clinic. Specificity, sensitivity, positive (PPV), and negative (NPV) predictive values were calculated. Results: Overall low sensitivity (6.3-58.0%) and wide-ranging predictive values (0.0-100.0%) indicated that nasal swab was not appropriate to detect lower airway pathogens [Pseudomonas aeruginosa (Pa), Staphylococcus aureus (Sa), and Haemophilus influenzae (Hi)] in all three patient groups. Microbiological yield, specificity, sensitivity, PPV, and NPV of cough swab and induced sputum were largely similar in non-expectorating patients and in BAL-group (except sensitivity (0.0%) of induced sputum for Hi in BAL-group). Calculations for Pa and Hi could not be performed for non-expectorating patients because of low prevalence (n = 2 and n = 3, respectively). In expectorating patients, concordance was found between cough swab and expectorated sputum, except for Hi (sensitivity of 40.0%). Conclusion: Our findings suggest that cough swab might be helpful in detecting the presence of some typical CF pathogens in the lower airways of clinically stable patients with CF. However, in symptomatic patients, who are unable to expectorate and who have a negative cough swab and induced sample, BAL should be performed as it currently remains the "gold standard."

Under the coordination of the European Centre for Disease Prevention and Control (ECDC), the European Legionnaires’ disease Surveillance Network (ELDSNet) conducts surveillance of Legionnaires’ disease (LD) in Europe. Between 2011 and 2015, 29 countries reported 30,532 LD cases to ECDC (28,188 (92.3%) confirmed and 2,344 (7.7%) probable). Four countries (France, Germany, Italy and Spain) accounted for 70.3% of all reported cases, although their combined populations represented only 49.9% of the study population. The age-standardised rate of all cases increased from 0.97 cases/100,000 population in 2011 to 1.30 cases/100,000 population in 2015, corresponding to an annual average increase of 0.09 cases/100,000 population (95%CI 0.02–0.14; p = 0.02). Demographics and infection setting remained unchanged with ca 70% of cases being community-acquired and 80% occurring in people aged 50 years and older. Clinical outcome was known for 23,164 cases, of whom 2,161 (9.3%) died. The overall case fatality ratio decreased steadily from 10.5% in 2011 to 8.1% in 2015, probably reflecting improved reporting completeness. Five countries (Austria, Czech Republic, Germany, Italy, and Norway) had increasing age-standardised LD notification rates over the 2011−15 period, but there was no increase in notification rates in countries where the 2011 rate was below 0.5/100,000 population.

We detected four cfiA – bft1 doubly positive Bacteroides fragilis strains out of 486 B. fragilis isolates analyzed for antibiotic susceptibilities and antibiotic resistance genes from a recent pan-European survey. The prevalence of the enterotoxin bft genes was roughly equal among cfiA -negative and -positive B. fragilis strains. We also demonstrated that the cfiA – bft doubly positive strains had the most common B. fragilis genomic pattern (I.1.). Thus we concluded that the bft -carrying CTn 86 conjugative transposons are mobile accounting for this unexpected simultaneous occurrence of the cfiA and bft genes.

Here we examine the carbapenem and metronidazole resistance mechanisms of 640 Bacteroides strains reported in the 2008-2009 European antibiotic susceptibility survey. Of the 22 strains with elevated imipenem minimum inhibitory concentrations (≥4 μg/mL), 10 were cfiA-positive and out of these 5 carried activating insertion sequence (IS) elements in the upstream regions of the cfiA genes. However, resistant strains with cfiA genes but with no activating IS elements were found (n=2) as well as a resistant strain with no cfiA gene. In the former the resistance phenotypes by Etest were heterogeneous, whilst in the latter no carbapenemase production was seen ; both mechanisms have been rarely observed, examined and characterised. Interestingly, few (n=3) nim-positive strains were found, including one metronidazole-resistant strain harbouring nimE activated by ISBf6, and two susceptible strains harbouring chromosomally located nim genes.

A hybrid strain of enteroaggregative and Shiga toxin 2-producing Escherichia coli (EAEC-STEC) serotype O104:H4 strain caused a large outbreak of haemolytic uraemic syndrome and bloody diarrhoea in 2011 in Europe. Two surveys were performed in the European Union (EU) and European Economic Area (EEA) countries to assess their laboratory capabilities to detect and characterise this previously uncommon STEC strain. Prior to the outbreak, 11 of the 32 countries in this survey had capacity at national reference laboratory (NRL) level for epidemic case confirmation according to the EU definition. During the outbreak, at primary diagnostic level, nine countries reported that clinical microbiology laboratories routinely used Shiga toxin detection assays suitable for diagnosis of infections with EAEC-STEC O104:H4, while 14 countries had NRL capacity to confirm epidemic cases. Six months after the outbreak, 22 countries reported NRL capacity to confirm such cases following initiatives taken by NRLs and the European Centre for Disease Prevention and Control (ECDC) Food- and Waterborne Disease and Zoonoses laboratory network. These data highlight the challenge of detection and confirmation of epidemic infections caused by atypical STEC strains and the benefits of coordinated EU laboratory networks to strengthen capabilities in response to a major outbreak.

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An enteroaggregative Verotoxin (Vtx)-producing Escherichia coli strain of serotype O104:H4 has recently been associated with an outbreak of haemolytic-uremic syndrome and bloody diarrhoea in humans mainly in Germany, but also in 14 other European countries, USA and Canada. This O104:H4 E. coli strain has often been described as an enterohaemorrhagic E. coli (EHEC), i.e. a Vtx-producing E. coli with attaching and effacing properties. Although both EHEC and the German O104:H4 E. coli strains indeed produce Vtx, they nevertheless differ in several other virulence traits, as well as in epidemiological characteristics. For instance, the primary sources and vehicles of typical EHEC infections in humans are ruminants, whereas no animal reservoir has been identified for enteroaggregative E. coli (EAggEC). The present article is introduced by a brief overview of the main characteristics of Vtx-producing E. coli and EAggEC. Thereafter, the O104:H4 E. coli outbreak is compared to typical EHEC outbreaks and the virulence factors and host specificity of EHEC and EAggEC are discussed. Finally, a renewed nomenclature of Vtxproducing E. coli is proposed to avoid more confusion in communication during future outbreaks and to replace the acronym EHEC that only refers to a clinical condition.

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In September-October 2007, a mixed-serotype outbreak of verocytotoxin-producing Escherichia coli (VTEC) O145:H28 and O26:H11 occurred in the province of Antwerp, Belgium. Five girls aged between 2 and 11 years developed hemolytic uremic syndrome, and seven other coexposed persons with bloody diarrhea were iden- tified. Laboratory confirmation of O145:H28 infection was obtained for three hemolytic uremic syndrome pa- tients, one of whom was coinfected with O26:H11. The epidemiological and laboratory investigations revealed ice cream as the most likely source of the outbreak. The ice cream was produced at a local dairy farm using pasteurized milk. VTEC of both serotypes with indistinguishable pulsed-field gel electrophoresis patterns were isolated from patients, ice cream, and environmental samples. Quantitative analysis of the ice cream indicated concentrations of 2.4 and 0.03 CFU=g for VTEC O145 and O26, respectively. Virulence typing revealed that the repertoire of virulence genes carried by the O145:H28 outbreak strain was comparable to that of O157 VTEC and more exhaustive as compared to the O26:H11 outbreak strain and nonrelated clinical strains belonging to these serotypes. Taken together, these data suggest that O145:H28 played the most important role in this outbreak.

AIMS: This study evaluated a typing method of O26:H11 enterohaemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC) based on the variation in genomic location and copy numbers of IS621. METHODS AND RESULTS: Two multiplex PCRs, targeting either the left (5') or right (3') IS/chromosome junction of 12 IS621 insertion sites and one PCR specific of another truncated copy, were developed. Thirty-eight amplification profiles were observed amongst a collection of 69 human and bovine O26:H11 EHEC and EPEC. Seventy-one per cent of the 45 EHEC and EPEC with identical IS621 fingerprints within groups of two, three or four isolates had >85% pulsed field gel electrophoresis (PFGE) profile similarity, including four groups of epidemiologically related EHEC or EPEC, while most of the groups had CONCLUSIONS: The IS621 fingerprinting and the PFGE are complementary typing assays of EHEC and EPEC; though, the former is less discriminatory. SIGNIFICANCE AND IMPACT OF THE STUDY: The IS621 printing method represents a rapid (24 h) first-line surveillance and typing assay, to compare and trace back O26:H11 EHEC and EPEC during surveys in farms, multiple human cases and outbreaks.

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The susceptibilities of 824 Bacteroides fragilis group isolates against nine antibiotics were evaluated in a Europe-wide study involving 13 countries. Species determination, by different methods, was carried out on all but one isolate. Resistance rates were evaluated according to species and geographical areas via CLSI and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. The present data were compared with those obtained 10 and 20 years ago at a European level. High-level resistance (MIC ≥ 64 mg/L) to ampicillin was observed in 44.5% of the strains, which is a significant increase relative to 20 years ago (16%). Piperacillin/tazobactam was more active than amoxicillin/clavulanic acid (3.1% and 10.4% resistance, respectively), again with a resistance increase relative to earlier studies. Dramatic increases in resistance were observed for cefoxitin, clindamycin and moxifloxacin, with rates of 17.2%, 32.4% and 13.6%, respectively. The lowest resistances were found for imipenem, metronidazole and tigecycline (1.2%

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Preliminary evaluation of multiplex PCR-based O157 IS-printing method for subtyping of verocytotoxin-producing Escherichia coli O157 G. Buvens, O. Soetens, S. Lauwers, D. Piérard Belgian Reference Laboratory for VTEC/EHEC, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium Background: Verocytotoxin-producing Escherichia coli (VTEC) are frequent causes of bloody diarrhea (BD) and the hemolytic-uremic syndrome (HUS). Whereas more than 200 serotypes have been described, O157:H7/non-motile are the most commonly associated with BD and HUS. Strong phylogenetic similarity between O157 isolates has been shown by genomic cluster analysis. Only highly discriminative but time-consuming techniques like pulsed-field gel electrophoresis (PFGE) and multilocus variable number of tandem repeats analysis (MLVA) are useful for O157 subtyping. For efficient infection control rapid techniques are needed. Ooka et al. recently described a multiplex PCR-based subtypingmethod based on the variable location of Insertion Sequence 629 (IS629) among VTEC O157 strains (O157 IS-printing) (1). Objectives: To evaluate O157 IS-printing as compared to PFGE. Materials and methods: Thirty-seven VTEC O157 isolates were included. O157 IS-printing was applied as described (1). PFGE was performed according to CDC PulseNet protocol for E. coli. Banding patterns were analyzed using GelCompar II. Results: Using PFGE, indistinguishable band patterns were obtained for 12 O157:H7 isolates associated with an outbreak during the summer of 2008, for 2 isolates from 2 siblings and for 2 O157:H7 recovered from 1 patient, respectively. Twenty-one other epidemiologically unrelated isolates showed distinct band patterns. O157 IS-printing yielded similar clustering as PFGE with the exception of 3 pairs of PFGE distinct isolates that clustered together. Conclusions: O157 IS-printing can be performed within 5 hours while several days are needed for PFGE, reducing the workload dramatically. No specialized equipment is needed, and a large number of strains can be analyzed simultaneously. Although less discriminative, it is a suitable tool for rapid subtyping of VTEC O157 isolates. Acknowledgements: Research funded by grant 2007-29 of "Prospective Research for Brussels" program of the Brussels-Capital Region to G.B. 1. Ooka T, Terajima J, Kusumoto M et al. J Clin Microbiol 2009;47:2888-94

Initial evaluations of the COBAS(R) AmpliPrep/COBAS(R) TaqMan(R) HIV-1 Test (CAP/CTM) showed good performance but afterwards reports about under-quantification became available. The aim of this study was to investigate if the problem is solved with the second version of this assay, the COBAS(R) AmpliPrep/COBAS(R) TaqMan(R) HIV-1 Test, version 2.0 (CAP/CTM v2.0). Remaining plasma of 375 consecutive HIV-1 positive samples with viral load >/=4000 copies/ml was collected in 3 labs. Samples were diluted and retested with our routine method COBAS(R) AmpliPrep/COBAS(R) AMPLICOR(R) HIV-1 MONITOR Test v1.5 in the ultrasensitive mode (CAP/CA PHS) as well as with CAP/CTM and CAP/CTM v2.0 tests. An absolute difference between the results of two methods of >/=0.71 log10 copies/ml (cp/ml) was defined as moderately discrepant and an absolute difference of >/=0.93 log10 cp/ml as severely discrepant. In addition, criteria for considering the new methods equivalent to the routine method were formulated. CAP/CTM compared to CAP/CA PHS: 36 (9.5%) and 20 (5.3%) samples were respectively considered as moderately and severely under-quantified by CAP/CTM. The mean difference between CAP/CTM and CAP/CA PHS was -0.32 log10 cp/ml. Eight out of 19 of the severely under-quantified samples were from patients infected with HIV-1 subtype B strain. CAP/CTM v2.0 compared to CAP/CA PHS: No sample was moderately or severely under-quantified by CAP/CTM v2.0. A mean difference of +0.08 log10 cp/ml was found with CAP/CTM v2.0 compared to CAP/CA PHS. The under-quantification problem of the CAP/CTM kit was clearly demonstrated. Criteria for equivalence of CAP/CTM v2.0 to the routine test CAP/CA PHS were fulfilled.

Accumulating evidence suggests that differences in pathogenic potential of Verocytotoxin-producing Escherichia coli (VTEC) are due to specific virulence characteristics encoded on horizontally acquired pathogenicity islands such as the locus of enterocyte effacement (LEE), and O Island 122 (OI 122). Whereas intimin and enterohemolysin are used in VTEC diagnostics for many years, the prevalence of OI 122 genes in VTEC associated with human disease in Belgium is unknown. In addition to the characterization of a limited number of VTEC O157, we compared the distribution of OI 122 and other virulence genes in non-O157 VTEC isolated from patients with and without the hemolytic uremic syndrome (HUS). One hundred and twenty-nine non-O157 VTEC consecutively isolated from routinely submitted stool samples (2 from HUS patients), seventeen non-O157 VTEC isolates from HUS patients, and twenty-one O157 VTEC (of which 10 from HUS patients) were included in this study. PCR was used for the detection of VT1, VT2, eae, multiple plasmid genes (ehx, saa, espP, katP, and etpD), and 9 ORFs of OI 122. All O157 VTEC isolates (16 O157:H7 and 5 O157:H-) carried VT2, eae, and all plasmid genes, except one sorbitol-fermenting O157:H- isolate which lacked espP and katP. Four isolates were carrying both VT1 and VT2. All O157 VTEC possessed a complete OI 122 (COI 122) with all nine ORFs present. The virulence factors present in 19 non-O157 VTEC isolates recovered from HUS patients were compared to those present in the 127 isolates from patients without HUS. While VT1 was significantly more present in VTEC not associated with HUS (pTwenty-seven out of 146 (18.5%) non-O157 isolates carried a COI 122, 81 (55.5%) had an incomplete OI 122, and in 38 (26%) isolates OI 122 was not detected. Isolates associated with HUS (7/19; 36.8%) carried significantly more often a COI 122 than non-HUS isolates (20/127; 15.7%) (pOur study confirms the association of OI 122 with O157 and with severe disease induced by non-O157. This genomic island could be considered in addition to the toxin type and other virulence factors for determining the pathogenicity of non-O157 clinical isolates. Our data show that the prevalence of COI 122 in non-O157 VTEC in Belgium is lower compared to other reports. * research supported by Brussels-Capital Region grant PRFB 2007-29 allowed to G Buvens

In order to evaluate the prevalence of infections with Verocytotoxin-producing Escherichia coli (VTEC) in the Brussels-Capital Region, clinical stool samples collected by 6 of the 9 hospital laboratories for microbiology were investigated. In addition to routinely submitted stool samples from UZ Brussel, all other participating laboratories were asked to submit ten stools per week for VTEC screening. Samples to include in this study were selected as follows: those from patients with HUS; from patients with a history of bloody diarrhea; from children Stool samples were cultured on sorbitol MacConkey (SMAC) agar and SMAC with cefixime and tellurite. A colony sweep and single colonies were tested for VTEC using a multiplex PCR targeting VT1, VT2, and their subtypes. Isolated VTEC were tested for the presence of the eae and ehx genes, and latex agglutination was used to identify serogroups O157, O26, O103, O111, O121, and O145. A total of 4240 stool samples were screened for VTEC between January and October 2008, with 67 (1.58%) positive PCR results. VTEC were isolated from 46 (68.6%) PCR positive stools. Twenty-four (52.2%) isolates were positive for VT1, 14 (30.4%) for VT2 (including 3 VT2f), and 8 for both VT1 and VT2. The eae and ehx genes were present in 30 (65.2%) out of 46 isolates. Eighteen (39.1%) isolates belonged to the six previously mentioned O serogroups, comprising 8 O157, 5 O26, 3 O111, and 2 O103. The highest prevalence of VTEC was detected in stools from patients with a history of bloody diarrhea (8.8%) followed by stools containing macroscopic blood (2.4%). Prevalence among young children (2.06%) was significantly higher than in random diarrhea samples (0.67%) (pThis surveillance shows an increased prevalence of VTEC compared to previous data collected in our lab. The majority of isolates (82.6%) belonged to non-O157 serogroups. Comparable proportions were recently reported in the Netherlands. Our data show that clinical laboratories should consider testing samples from patients with HUS, bloody diarrhea or a history of bloody diarrhea for the presence of VTEC. Screening of pediatric stool samples can also be considered. * research supported by Brussels-Capital Region grant PRFB 2007-29 to G Buvens

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Bordetella pertussis, the causative agent of whooping cough, has remained endemic and there is a resurgence in some countries despite vaccination. Bordetella pertussis produces a wide range of virulence factors which are assumed to play an important role in infection and transmission, including tracheal colonization factor (TcfA). Here we show that clinical isolates belonging to distinct lineages may lose their ability to produce TcfA. Irreversible and reversible loss occurred, respectively, by recombination between repeats leading to deletion of the tcfA gene and by mutations in a polymorphic G-track. These phenomena may reflect adaptation to distinct niches.