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Objectives: This study measured the impact of the first wave of COVID-19 pandemic (COVID-19) (March–April 2020) on the incidence of bloodstream infections (BSIs) at Assistance Publique – Hôpitaux de Paris (APHP), the largest multisite public healthcare institution in France. Methods: The number of patient admission blood cultures (BCs) collected, number of positive BCs, and antibiotic resistance and consumption were analysed retrospectively for the first quarter of 2020, and also for the first quarter of 2019 for comparison, in 25 APHP hospitals (ca. 14 000 beds). Results: Up to a fourth of patients admitted in March–April 2020 in these hospitals had COVID-19. The BSI rate per 100 admissions increased overall by 24% in March 2020 and 115% in April 2020, and separately for the major pathogens (Escherichia coli, Klebsiella pneumoniae, enterococci, Staphylococcus aureus, Pseudomonas aeruginosa, yeasts). A sharp increase in the rate of BSIs caused by microorganisms resistant to third-generation cephalosporins (3GC) was also observed in March–April 2020, particularly in K. pneumoniae, enterobacterial species naturally producing inducible AmpC (Enterobacter cloacae...), and P. aeruginosa. A concomitant increase in 3GC consumption occurred. Conclusions: The COVID-19 pandemic had a strong impact on hospital management and also unfavourable effects on severe infections, antimicrobial resistance, and laboratory work diagnostics.

Objectives Isoniazid-monoresistant tuberculosis (HR-TB) is the most prevalent form of drug-resistant TB worldwide and in France and is associated with poorer treatment outcomes compared with drug-susceptible TB (DS-TB). The objective of this study was to determine the characteristics of HR-TB patients in France and to compare outcomes and safety of treatment for HR-TB and DS-TB. Methods We performed a case-control multicenter study to identify risk factors associated with HR-TB and compare treatment outcomes and safety between HR-TB patients and DS-TB patients. Results Characteristics of 99 HR-TB patients diagnosed and treated in the university hospitals of Paris, Lille, Caen and Strasbourg were compared with 99 DS-TB patients. Female sex (OR = 2.2; 1.0–4.7), birth in the West-Pacific World Health Organization region (OR = 4.6; 1.1–18.7) and resistance to streptomycin (OR = 77.5; 10.1–594.4) were found to be independently associated with HR-TB. Rates of treatment success did not differ significantly between HR-TB and DS-TB. Conclusions Factors associated with HR-TB are not significant enough to efficiently screen TB patients at risk of HR-TB. The systematic implementation of rapid molecular testing on clinical samples remains the only effective way to make the early diagnosis of HR-TB and adapt treatment.

Whole genome sequencing of Mycobacterium tuberculosis complex (MTBC) strains is a new and rapidly growing tool to obtain results regarding resistance, virulence factors and phylogeny of the strains. Bioinformatics tools presented as user-friendly and easy to use are available online. The objective of this work was to evaluate the performances of two bioinformatics tools, easily accessible on the internet, for the analysis of sequencing data of MTBC strains.Two hundred and twenty-seven MTBC strains isolated at the laboratory of the Avicenne Hospital between 2015 and 2021 were sequenced using Illumina®(USA) MiSeq technology. An analysis of the sequencing data was performed using the two tools Mykrobe and PhyResSE. Sequencing quality, resistance or susceptibility status and phylogeny were investigated for each strain. Genotypic resistance results were compared to the results obtained by phenotypic drug susceptibility testing performed in the hospital’s routine laboratory.Using the PhyResSE tool we found an average coverage of 98% against the reference strain H37Rv and an average depth of 119X. No information on sequencing quality was obtained with the Mykrobe tool. The concordance of each tool with the phenotypic method for determining susceptibility to first-line anti-tuberculosis drugs was 95%. Mykrobe and PhyResSE tools identified resistance to second-line anti-tuberculosis drugs in 5.3% and 5.7% of cases respectively. The sensitivity and specificity of each tool compared to the phenotypic method was respectively 70% and 98% for Mykrobe and 76% and 97% for PhyResSE. Finally, the two tools showed 99.5% agreement in lineage determination.The Mykrobe and PhyResSE bioinformatics tools were easy to use, fast and efficient. The Mykrobe tool had the advantage of being offline and its interface was more user-friendly. The use of these platforms depends on their accessibility and updating. However, their use is accessible to people not trained in bioinformatics and would allow a complementary approach to phenotypic methods for the study of MTBC strains.

Background Mycetoma is a chronic granulomatous subcutaneous infection caused by anaerobic pseudofilamentous bacteria or fungi. It is commonly prevalent in tropical and subtropical countries. Men are more susceptible to the disease due to greater participation in agricultural works. Mycetoma commonly involves lower extremities, wherein untreated cases lead to aggressive therapeutic choices, such as amputation of the affected body organs and consequently lifelong disability. Case presentation In this report, we present the rare case of a 58-year-old man, originally from Algeria with a left foot chronic tumefaction of 5 years. In the initial clinical examination, mycetoma was diagnosed based on tumefaction and the presence of multiple sinuses with the emission of white grains. The latter was observed via direct examination. The histopathological analysis demonstrated an actinomycetoma caused by bacteria, as the etiological agent. Imaging showed a bone involvement with osteolysis at the levels of 2nd to 4th metatarsal diaphysis. The mycological and bacterial cultures were both negative. For an accurate diagnosis, the obtained grains were subjected to molecular analysis, targeting the 16S-rDNA gene. Molecular identification yielded Actinomadura madurae as the causal agent, and 800/160 mg of trimethoprim/sulfamethoxazole was prescribed twice a day for 1 year, as a treatment. Conclusion Considering low information about this disease, especially in non-endemic areas, it is of high importance to enhance the knowledge and awareness of clinicians and healthcare providers, in particular in the countries with immigration issues.

Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) are a major public health concern worldwide. Little is known about the prevalence of ESBL-PE colonization in rehabilitation wards in France. Our aim was to determine the prevalence of ESBL-PE colonization in rehabilitation wards in the Parisian area and to identify potential risk factors for ESBL-PE carriage.This one-day prospective study was performed in three rehabilitation wards in Paris, France, between September 1, 2016, and June 26, 2017. Rectal samples were collected for microbial analysis from patients who were present at 8am and all isolates recovered were identified by mass spectrometry. The presence of ESBL-PE was confirmed using a double-disk synergy test according to EUCAST recommendations. Risk factors for colonization were determined by univariate and multivariate analyses.A total of 136 patients were analyzed (50.7% of female patients; median age 71 years). Twenty-eight patients (20.6%) were colonized with ESBL-PE on the day of sampling. Escherichia coli was identified in 15 (50%) cases and Klebsiella pneumoniae in six (20%). None of the variables studied was significantly associated with a higher risk of ESBL-PE colonization. However, there was a tendency for a higher risk of ESBL-PE colonization with dementia (OR = 6.116 [95%CI: 0.92-40.57]; p = 0.06) and diabetes with complications (OR = 2.853 [95%CI: 1-8.16]; p = 0.05).Patients in rehabilitation wards showed a high rate of ESBL-PE colonization (21%). Continuous monitoring of antibiotic resistance among potentially pathogenic bacteria, including ESBL-PE, is crucial as colonized patients represent an important reservoir for transmission after discharge outside the hospital setting.

SUMMARY Background Little is known about patient risk factors associated with environmental contamination. Aim To evaluate the rate of environmental contamination and to investigate individual risk factors. Methods A prospective cohort study was conducted. Each day, five rooms occupied by patients were selected. Five critical surfaces were systematically swabbed twice a day before and after cleaning. Clinical characteristics of all patients were collected. Logisitic regression was performed to evaluate the association between environmental contamination and patients' characteristics. Findings A total of 107 consecutive patients were included and 1052 environmental samples were performed. Nineteen (18%) patients were known previously colonized/infected with a multidrug-resistant organism (MDRO). Respectively, 723 (69%) and 112 (11%) samples grew with ≥1 and >2.5 cfu/cm2 bacteria, resulting in 62 (58%) contaminated rooms. Considering positive samples with at least one pathogenic bacterium, 16 (15%) rooms were contaminated. By univariate and multivariate analysis, no variables analysed were associated with the environmental contamination. Considering contaminated rooms with >2.5 cfu/cm2, three factors were protective for environmental contamination: known MDRO carriers/infected patients (odds ratio: 0.25; 95% confidence interval: 0.09–0.72; P = 0.01), patients with urinary catheter (0.19; 0.04–0.89; P = 0.03) and hospitalization in single room (0.3; 0.15–0.6; P Conclusion This study was conducted in a non-outbreak situation and showed a low rate of environmental contamination with pathogenic bacteria. Only 11% of environmental samples grew with >2.5 cfu/cm2, and they were related to non-pathogenic bacteria. No risk factors associated with environmental contamination were identified.

International audience; OBJECTIVES: Isoniazid-monoresistant tuberculosis (HR-TB) requires early diagnosis and adapted treatment to achieve optimal outcomes. The primary aim of the study was to assess the impact of the implementation of rapid diagnostic tests on HR-TB treatment in France. METHODS: We designed a retrospective multicentre study including consecutive HR-TB patients diagnosed in 2016 and 2017. Implementation of a molecular assay detecting isoniazid resistance directly on a clinical sample was recorded. The association between early implementation of such assays and adequate treatment was assessed by a multivariable Cox proportional hazards model. RESULTS: Overall, 99 HR-TB patients were included from 20 University Hospitals. Among all smear-positive HR-TB patients, only 26% beneficiated from early molecular HR detection. This detection was independently associated with shorter time to adequate treatment (HR~=~2.0 [1.1-3.8], p~=~0.03). CONCLUSION: In our study, molecular detection of HR on an initial sample was independently associated with earlier treatment adaptation.

International audience; Temocillin is used for several years in some European countries but, only since 2015 in France. We assessed the susceptibility of Enterobacterales strains isolated from blood culture 1 year before (2014) and 2 years after (2017) its use in France. 1,387 strains were included by 17 clinical laboratories located throughout France: 363 in 2014 and 1,024 in 2017. The rate of resistance to temocillin was 4.6% and 26.7% in 3rd generation cephalosporin (3GC) susceptible and resistant strains respectively. Cephalosporinase-overproducer (COPE) strains were significantly more resistant to temocillin (37.7%) than ESBL-producer (ESBL-PE) (23.5%) (P < 0.01). The rate of temocillin resistance was correlated to the number of inactive beta-lactams. The rate of resistance to temocillin trend to increase from 13.9% in 2014 to 23.9% in 2017 (P < 0.01). Temocillin remains highly active against Enterobacterales but the trend in resistance should be assessed over time.

Background Legionella pneumophila (L. pneumophila) is a gram-negative intracellular bacillus composed of sixteen different serogroups. It is mostly known to cause pneumonia in individuals with known risk factors as immunocompromised status, tobacco use, chronic organ failure or age older than 50 years. Although parapneumonic pleural effusion is frequent in legionellosis, pleural empyema is very uncommon. In this study, we report a case of fatal pleural empyema caused by L. pneumophila serogroup 1 in an 81-year-old man with multiple risk factors. Case summary An 81-year-old man presented to the emergency with a 3 wk dyspnea, fever and left chest pain. His previous medical conditions were chronic lymphocytic leukemia, diabetes mellitus, chronic kidney failure, hypertension and hyperlipidemia, without tobacco use. Chest X-ray and comouted tomography-scan confirmed a large left pleural effusion, which puncture showed a citrine exudate with negative standard bacterial cultures. Despite intravenous cefotaxime antibiotherapy, patient's worsening condition after 10 d led to thoracocentesis and evacuation of 2 liters of pus. The patient progressively developed severe hypoxemia and multiorgan failure occurred. The patient was treated by antibiotherapy with cefepime and amikacin and with adequate symptomatic shock treatment, but died of uncontrolled sepsis. The next day, cultures of the surgical pleural liquid samples yielded L. pneumophila serogroup 1, consistent with the diagnosis of pleural legionellosis. Conclusion L. pneumophila should be considered in patients with multiple risk factors and undiagnosed pleural empyema unresponsive to conventional antibiotherapy.

International audience; In a prospective, nationwide study in France of Escherichia coli responsible for pneumonia in patients receiving mechanical ventilation, we determined E. coli antimicrobial susceptibility, phylotype, O-type, and virulence factor gene content. We compared 260 isolates with those of 2 published collections containing commensal and bacteremia isolates. The preponderant phylogenetic group was B2 (59.6%), and the predominant sequence type complex (STc) was STc73. STc127 and STc141 were overrepresented and STc95 underrepresented in pneumonia isolates compared with bacteremia isolates. Pneumonia isolates carried higher proportions of virulence genes sfa/foc, papGIII, hlyC, cnf1, and iroN compared with bacteremia isolates. Virulence factor gene content and antimicrobial drug resistance were higher in pneumonia than in commensal isolates. Genomic and phylogenetic characteristics of E. coli pneumonia isolates from critically ill patients indicate that they belong to the extraintestinal pathogenic E. coli pathovar but have distinguishable lung-specific traits.

We report the case of a lung abscess due to Prevotella baroniae with a co-infection by Abiotrophia defective, which is a ‘nutritionally variant streptococci’ (NVS), in a 48-year-old patient. The delayed diagnosis of this co-infection led to multiple failures of medical treatment and need for surgery. Pathogenicity of these bacteria is well known, particularly in endocarditis, but not in lung infection. In pulmonary abscesses, co-infection with NVS is difficult to detect. It may explain some medical treatment failures. This case highlights the importance to systematically search for and consider NVS in such clinical contexts.

To identify tools that will result in faster diagnosis, making the current pulmonary tuberculosis strategy more efficient.A 4-year (2015-2018) retrospective study. The gold standard for diagnosis was a positive culture from a respiratory specimen. All sputum, fibroscopy and post-fibroscopy specimens (for smear negative patients) were collected. Each specimen was analyzed through smear examination and culture. All nucleic acid amplification testing results were included. Analyses looked at the incremental yield of positive cases of each successive specimen collection, and time to diagnosis.A total of 354 patients had at least one positive culture. Sputum allowed a diagnosis in 92% of cases (including a gain in sensitivity of around 7% for the third sputum specimen), with 160 smear-positive patients (45%). Among smear-negative patients, 109 underwent a fibroscopy procedure (culture sensitivity of 75%), and 59 had a post-fibroscopy specimen collected, which together identified the rest of the patients (8%). Molecular testing was used in 237 specimens. Median time to diagnosis was 11 days, which was significantly reduced among smear-negative patients when molecular testing was used (P0.001). Shortening the delay between sputum specimen collections did not alter procedure sensitivity.We identified several aspects of the French tuberculosis diagnosis algorithm that could be improved, and posed the basis for a prospective study. Centers in higher incidence areas could benefit from a dedicated, predefined procedure exploring suspicions of tuberculosis. A high suspicion score of tuberculosis could drive the reasoned use of molecular testing in such settings.

We undertook a comprehensive comparative analysis of a collection of 30 small (

Whole-genome sequencing plays now a leading role in epidemiologic studies of tuberculosis. DNA extraction of Mycobacterium tuberculosis complex (MTBC) requires complete inactivation of the strains, to be handled for further molecular procedures. In this study we compared two chloroform-based denaturation methods (one with a step of heat killing, one without) to a traditional heat inactivation method. Our results showed that 40% of the strains of MTBC treated by the traditional protocol resulted in a positive culture whereas no culture was observed with the two chloroform-based protocols. The DNA extracts obtained with chloroform-based protocols preparation were successfully used for whole-genome sequencing. We recommend inactivation with our rapid and efficient denaturation method using chloroform without heat killing which met our expectations and biosecurity requirements.

We previously identified an operon involved in an arginine deiminase (ADI) pathway (arc operon) on a CTX-M-producing plasmid from an O102-ST405 strain of Escherichia coli. As the ADI pathway was shown to be involved in the virulence of various Gram-positive bacteria, we tested whether the ADI pathway could be involved in the epidemiological success of extended-spectrum-␤-lactamase (ESBL)-producing E. coli strains. We studied two collections of human E. coli isolated in France (n ϭ 493) and England (n ϭ 1,509) and show that the prevalence of the arc operon (i) is higher in ESBL-producing strains (12.1%) than in nonproducers (2.5%), (ii) is higher in CTX-M-producing strains (16%) than in other ESBL producers (3.5%), and (iii) increased over time in ESBL-producing strains from 0% before 2000 to 43.3% in 2011 to 2012. The arc operon, found in strains from various phylogenetic backgrounds, is carried by IncF plasmids (85%) or chromosomes (15%) in regions framed by numerous insertion sequences, indicating multiple arrivals. Competition experiments showed that the arc operon enhances fitness of the strain in vitro in ly-sogeny broth with arginine. In vivo competition experiments showed that the arc operon is advantageous for the strain in a mouse model of urinary tract infection (UTI), whereas it is a burden in a mouse model of intestinal colonization. In summary , we have identified a trait linked to CTX-M-producing strains that is responsible for a trade-off between two main E. coli lifestyles, UTI and gut commensalism. This trait alone cannot explain the wide spread of ESBLs in E. coli but merits epidemiological surveillance.

Editor’s Perspective What We Already Know about This Topic What This Article Tells Us That Is New Background Oropharyngeal care with chlorhexidine to prevent ventilator-associated pneumonia is currently questioned, and exhaustive microbiologic data assessing its efficacy are lacking. The authors therefore aimed to study the effect of chlorhexidine mouthwash on oropharyngeal bacterial growth, to determine chlorhexidine susceptibility of these bacteria, and to measure chlorhexidine salivary concentration after an oropharyngeal care. Methods This observational, prospective, single-center study enrolled 30 critically ill patients under mechanical ventilation for over 48 h. Oropharyngeal contamination was assessed by swabbing the gingivobuccal sulcus immediately before applying 0.12% chlorhexidine with soaked swabs, and subsequently at 15, 60, 120, 240, and 360 min after. Bacterial growth and identification were performed, and chlorhexidine minimal inhibitory concentration of recovered pathogens was determined. Saliva was collected in 10 patients, at every timepoint, with an additional timepoint after 30 min, to measure chlorhexidine concentration. Results Two hundred fifty bacterial samples were analyzed and identified 48 pathogens including Streptococci (27.1%) and Enterobacteriaceae (20.8%). Oropharyngeal contamination before chlorhexidine mouthwash ranged from 103 to 107 colony-forming units (CFU)/ml in the 30 patients (median contamination level: 2.5·106 CFU/ml), and remained between 8·105 (lowest) and 3·106 CFU/ml (highest count) after chlorhexidine exposure. These bacterial counts did not decrease overtime after chlorhexidine mouthwash (each minute increase in time resulted in a multiplication of bacterial count by a coefficient of 1.001, P = 0.83). Viridans group streptococci isolates had the lowest chlorhexidine minimal inhibitory concentration (4 [4 to 8] mg/l); Enterobacteriaceae isolates had the highest ones (32 [16 to 32] mg/l). Chlorhexidine salivary concentration rapidly decreased, reaching 7.6 [1.8 to 31] mg/l as early as 60 min after mouthwash. Conclusions Chlorhexidine oropharyngeal care does not seem to reduce bacterial oropharyngeal colonization in critically ill ventilated patients. Variable chlorhexidine minimal inhibitory concentrations along with low chlorhexidine salivary concentrations after mouthwash could explain this ineffectiveness, and thus question the use of chlorhexidine for ventilator-associated pneumonia prevention.

Purpose. Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a leading cause of severe community-acquired pneumonia, liver abscess and disseminated infection in the Far East. Data regarding the incidence, clinical features and microbiological characteristics related to hvKp infections in the Western world are scarce. Methodology. The incidence, clinical features and microbiological characteristics of hvKp infections were investigated through a 5-year survey conducted in a single French intensive care unit. K. pneumoniae strains were screened for hypermucoviscosity based on a string test. Multilocus sequence typing and multiplex PCR analysis targeting virulence genes were performed on string test-positive strains. Results. Over a 53-month period, a total of 59 infections due to K. pneumoniae were identified including 26 community-onset infections. Twelve hvKp infections were documented, accounting for 46.1 % of community-acquired K. pneumoniae. Community-acquired pneumonia (n=6), aspiration pneumonia (n=4) and liver abscess (n=2) represented initial sites and mode of infection. Compared to non-hvKp infections, patients with hvKp infections displayed higher rates of multi-organ failure (83.3 % vs 35.7 %; P=0.04), but mortality rates were not different (50 % vs 35 %; P=0.71). Strains K1/ST23 (n=5) and K2/ST86 (n=5) predominated. All hvKp strains displayed wild-type susceptibility. Conclusion. hvKp represent a potentially underestimated cause of fatal infections in the Western world.

Background Extensively-drug-resistant bacteria (XDRB) have emerged as a major source of resistance. Hospitalization abroad seems to be the major risk factor associated with carriage, and numerous reports have warned about the risk of in-hospital transmission. However, little is known regarding possible community transmission. Methods A retrospective matched case–control study was conducted in a Parisian teaching hospital, which included patients admitted to hospital with a history of travel abroad over the preceding 12 months. Each XDRB carrier at admission (case) was matched with two non-carriers (controls) hospitalized in the same ward and admitted during the same month. Aim To describe and identify risk factors associated with XDRB carriage at admission. Findings Forty-six cases and 92 controls were enrolled. The results of univariate and multi-variate analyses showed that health repatriation was the only factor associated with a higher risk of carrying XDRB (odds ratio 3.22, 95% confidence interval 1.23–7.84; P=0.01). Surprisingly, one-third of the study population had not been hospitalized abroad within the preceding 12 months. The most frequently identified XDRB species were Escherichia coli (36%), Enterococcus spp. (17%) and Klebsiella pneumoniae (9%), and the most frequently identified enzyme was OXA-48 (36%). Conclusion In this retrospective study, health repatriation was the only risk factor for XDRB carriage identified at admission. Furthermore, the data suggest community-onset transmission. Therefore, there is an urgent need to conduct studies in high-risk countries to identify the risk factors associated with community carriage.

P1 bacteriophages lysogenize bacteria as independent plasmid-like elements. We describe here a P1-like bacteriophage, RCS47, carrying a bla SHV-2 gene, isolated from a clinical strain of Escherichia coli from phylogroup B1, and we report the prevalence of P1-like prophages in natural E. coli isolates. We found that 70% of the sequence of RCS47, a 115-kb circular molecule, was common to the reference P1 bacteriophage under GenBank accession no. AF234172.1 , with the shared sequences being 99% identical. RCS47 had acquired two main foreign DNA fragments: a 9,636-bp fragment mobilized by two IS 26 elements containing a bla SHV-2 gene, and an 8,544-bp fragment mobilized by two IS 5 elements containing an operon encoding a dimethyl sulfoxide reductase. The reference P1 prophage plasmid replication gene belonged to the IncY incompatibility group, whereas that of RCS47 was from an unknown group. The lytic capacity of RCS47 and bla SHV-2 gene transduction, through the lysogenization of RCS47 in the recipient E. coli strains, were not demonstrated. The prevalence of P1-like prophages in various animal and human E. coli strain collections, as determined by the PCR detection of repL , the lytic replication gene, was 12.6%. No differences in the prevalences of these prophages were found between extended-spectrum β-lactamase (ESBL)-producing and non-ESBL-producing strains ( P = 0.69), but this prevalence was lower in phylogroup B2 than in the other phylogroups ( P = 0.008), suggesting epistatic interactions between P1 family phages and the genetic background of E. coli strains. P1-like phages are part of the mobile elements that carry antibiotic resistance. The high prevalence of P1-like prophages suggests their role may be underestimated.

BACKGROUND Transfusion-transmitted bacterial infection (TTBI) is still one of the most feared complications of blood transfusion. CASE REPORT We report a fatal case involving an 8-year-old child with congenital dyskeratosis complicated by severe aplastic anemia who was regularly transfused with platelet (PLT) concentrates for 5 years. The patient received an apheresis PLT concentrate (APC) on Day 0 due to thrombocytopenia complicated by mucocutaneous hemorrhage. Thirty minutes after the start of the transfusion, bradycardia and dyspnea appeared, quickly followed by chills, nausea, vomiting, headache, and hyperthermia. TTBI was suspected and the patient was immediately treated with intravascular antibiotherapy. On Day 3, the patient developed severe acute respiratory distress syndrome leading to death on Day 7. Patient blood cultures and APC cultures were both positive for Citrobacter koseri. RESULTS The donor was a 19-year-old woman. She had previously given blood. No infectious symptom was reported during the medical interviews before and after the donation and no postdonation information was received. On the day of the donation (Day −2), her white blood cell count was 5.83 × 109/L. She came back on Day 8 to undergo additional tests. The cultures from blood, stool, urine, the skin of the inside of the elbow at the point of needle insertion, and ear samples were all negative for C. koseri. However, a nasal sample was positive for C. koseri. CONCLUSION The isolates from the donor's blood cultures, the APC bag, the attached tube, and the donor's nasal sample all gave identical profiles; they were thus identified as the same strain and the TTBI was confirmed.

Cutaneous diphtheria is uncommon in Europe. In this study, we report a case of imported cutaneous infection due to a non-toxigenic but tox gene-bearing (NTTB) strain of Corynebacterium diphtheriae. The NTTB strains are recognized as emerging pathogens across Europe, and physicians and bacteriologists should be aware of the circulation of these strains.

Introduction La PCR en temps reel est un outil tres interessant pour le diagnostic de la tuberculose qui reste une maladie infectieuse grave et de diagnostic parfois long. Les formes extrapulmonaires qui representent 27 % des cas de tuberculoses sont difficiles a diagnostiquer. Nous avons evalue les performances du test GeneXpert MTB/RIF (Cepheid) pour le diagnostic des formes extrapulmonaires afin d’implanter le test en routine. Materiels et methodes Analyse retrospective des resultats des echantillons d’origine extrapulmonaire pour lesquels une recherche de mycobacterie a ete realisee a la fois par culture et par un test PCR en temps reel GeneXpert MTB/RIF dans notre laboratoire L3 du 1er janvier 2015 au 31 aout 2017. Les performances de la PCR ont ete comparees a la culture (gold standard) et analysees en fonction de la nature de l’echantillon recu au laboratoire. Resultats Au total, 139 patients ont ete inclus dans le cadre d’une suspicion de tuberculose extrapulmonaire. Au total, 144 echantillons d’origine extrapulmonaire ont ete etudies. Pour 96 echantillons, PCR et cultures etaient negatives et pour 27 echantillons les deux techniques etaient positives et ont permis d’etablir le diagnostic de tuberculose extrapulmonaire. De facon interessante, pour 9 echantillons, la PCR etait positive alors que la culture etait restee negative. Sur ces 9 echantillons, 7 venaient de patients sous traitement antituberculeux, ce qui explique les resultats de la culture negative. Enfin pour 11 echantillons, la PCR etait negative alors que la culture etait positive. Ainsi, dans notre etude, en comparaison a la culture, les performances du test GeneXpert MTB/RIF sont les suivantes : Se 71 %, Sp 91 %, VPP 75 % et VPN 90 %. D’apres l’analyse des donnees en fonction du type de prelevement, les performances de la PCR par rapport a la culture sont les suivantes : Se 90 %, Sp 87 %, VPP 82 % et VPN 93 % pour les tuberculoses ganglionnaires ; Se 25 %, Sp 97 %, VPP 50 % et VPN 92 % pour les meningites tuberculeuses ; Se 100 %, Sp 92 %, VPP 80 % et VPN 100 % pour les prelevements osteo-articulaires ; Sp 85 % et VPN 78 % pour les liquides de sereuses. Conclusion La PCR en temps reel GeneXpert MTB/RIF presente, d’apres les donnees de notre etude pour les tuberculoses extrapulmonaires, une sensibilite superieure a celle de l’examen microscopique (71 % versus 20 % dans notre etude). Les performances de ce test sont interessantes dans le diagnostic des formes ganglionnaires et osseuses par rapport a la culture. La culture reste malgre tout un element important pour le diagnostic. La qualite et le volume des echantillons sont des criteres de qualite indispensables a evaluer pour rendre le diagnostic bacteriologique plus performant.

Introduction L’objectif de cette etude etait d’evaluer les pratiques concernant le diagnostic microbiologique de la tuberculose (TB) en Europe. Materiels et methodes Une enquete a ete menee en novembre 2018 aupres des membres du groupe ESGMYC (European Study Group for Mycobacterial Infections) a l’aide d’un questionnaire en ligne de 30 items. Resultats Parmi les membres de l’ESGMYC (135 personnes), 58 ont repondu au questionnaire, representant 15 pays europeens et 2 pays extra europeens (Singapour et Australie). La majorite des participants travaillaient dans un service de maladies infectieuses (62 %) ou de microbiologie clinique (29 %). Les sources d’informations medicales utilisees pour leur pratique etaient des recommandations nationales seules pour 7 % d’entre eux et internationales pour 87.5 %. Concernant le diagnostic de la TB pulmonaire (TBp), 96 % des participants faisaient au moins 1 BK crachat le matin a jeun avec 2 (20,7 %) ou 3 prelevements (79,3 %) realises au total sur une duree soit de 3 (58,6 %), 2 (32,8 %) ou 1 jours (13,8 %). En l’absence d’expectorations, les alternatives etaient le crachat induit (67,2 %), la fibroscopie bronchique (FB) (58,6 %) et le tubage gastrique (25,9 %). Un test de biologie moleculaire (BM) etait realise systematiquement pour 36 (62,1 %) repondants, sur 1 (48 %) ou plusieurs prelevements respiratoires (52 %). En cas de forte suspicion de TBp avec examen microscopique (EM) des crachats negatif, 4 (6,9 %) cliniciens debutaient le traitement, 10 (17,2 %) attendaient le resultat de la culture et 44 (78,6 %) realisaient d’autres examens (BM 66 %, FB 61,3 %). En cas d’EM + 47 (84 %) participants recherchaient une mutation de resistance (MR) a la rifampicine, 15 (27 %) une MR a l’INH, 4 (7 %) d’autres MR et 9 (16 %) aucune MR. La BM et la mesure de l’ADA (adenosine desaminase) etaient utilisees pour le diagnostic des TB extra pulmonaires dans 83,6 % et 40,4 % des cas respectivement, l’ADA etant demandee principalement pour les pleuresies (95,7 %), le LCS (34,8 %) et le liquide peritoneal (21,7 %). Le controle des BK crachats etait realise systematiquement a M2 et M5-M6 pour respectivement 47 (82,5 %) et 34 (59,6 %) des participants. Pour le diagnostic de la TB maladie, 32,8 % des repondants utilisaient les tests IGRAs et 24,1 % l’IDR. Conclusion Les recommandations internationales sur la prise en charge de la TB concernent surtout les pays de forte incidence. Cette etude montre des pratiques de diagnostic heterogenes au sein de l’Europe, region de faible incidence et de ressources elevees meme si la biologie moleculaire a pris une place importante dans la plupart des centres. Des recommandations europeennes, sous l’egide de l’ECCMID, seraient probablement necessaires pour homogeneiser les pratiques diagnostiques et guider les differents acteurs regionaux en charge de la tuberculose.

Introduction Le diagnostic microbiologique des tuberculoses pulmonaires (TBp), repose toujours, en 2019, sur un algorithme fastidieux laissant peu de place aux outils de biologie moleculaire (BM). L’objectif de cette etude est d’evaluer la performance des principaux tests microbiologiques utilises dans un centre tertiaire a forte incidence de TB et d’etablir un etat des lieux permettant de definir une strategie diagnostique optimale. Materiels et methodes Analyse retrospective mono-centrique des resultats microbiologiques provenant de prelevements bronchopulmonaires des patients avec culture positive a M. tuberculosis complex sur une periode de 3 ans (1er janvier 2015 au 31 decembre 2017) : evaluation des performances diagnostiques du 3e tubage gastrique ou BK-crachat (BKc), de la fibroscopie bronchique (FB), du BKc post-FB, ainsi que de la BM (geneXpert MTB/RIF). Resultats Un total de 307 patients ont eu au moins une culture positive a M. tuberculosis complex a partir de prelevements broncho-pulmonaires, dont 11 diagnostics fortuits au cours d’une FB realisee pour une autre indication. Apres leur exclusion, 296 patients ont ete inclus dans l’etude dont 139 etaient bacilliferes (47 %). Le 3e BKc a permis un diagnostic supplementaire pour 4 % des TB bacilliformes et 11 % des non bacilliformes. Les performances de l’examen direct (ED) n’etaient pas affectees par une strategie realisant le 2e BKc le meme jour que le 1er BKc (fin de matinee) ou le lendemain (au reveil, p = 0,9). De meme, les performances des cultures pour les patients non bacilliferes n’etaient pas significativement differentes selon la strategie (p = 0,3). La mediane de positivite des cultures en milieu liquide etait plus precoce chez les patients bacilliferes (6j [4 ; 8]) que chez les non-bacilliferes (16j [12 ; 20] p Conclusion Notre serie a permis de mettre en evidence : – un raccourcissement possible du delai entre les prelevements sans impact negatif ; – un prelevement profond (FB) permet une rentabilite diagnostique supplementaire non negligeable pour les patients non bacilliferes (3,4 %) ; – la contribution interessante de la BM sur differents types de prelevements, en ciblant bien les fortes suspicions de TBp pour un meilleur rapport cout-efficacite.

Introduction La forme ganglionnaire est la principale localisation des tuberculoses extra-pulmonaires. Malgre l’existence de recommandations sur le traitement, le clinicien est parfois confronte a des difficultes diagnostiques et de traitement. L’objectif de cette etude est d’etudier les caracteristiques et l’evolution clinique des patients presentant une tuberculose ganglionnaire. Materiels et methodes Etude descriptive des cas de tuberculose ganglionnaire a Mycobacterium tuberculosis complex diagnostiquees par PCR (test Cepheid MTB/RIF) et/ou par culture a l’hopital Avicenne du 1er janvier 2015 au 31 janvier 2019. La presentation clinique et l’evolution ont ete comparees selon le continent de naissance. Resultats Soixante-douze patients, soit 19 % des 382 tuberculoses diagnostiquees sur la periode, avaient une forme ganglionnaire. La majorite etaient de sexe masculin (n = 58, 81 %). L’âge median etait de 32 ans (IQR 26–44). Quinze pourcent (n = 11) des patients etaient nes en Inde, 11 % (n = 8) au Pakistan, 10 % (n = 7) au Bangladesh et 8 % (n = 6) au Sri Lanka. Les personnes originaires du continent asiatique representaient donc 46 % des cas de tuberculose ganglionnaire contre 22 % (68/310) des tuberculoses non ganglionnaires. Les patients nes en Afrique Sub-Saharienne representaient 38 % (n = 27) des patients. L’atteinte ganglionnaire touchait principalement la region cervicale (54 %, n = 39) puis sus-claviculaire (36 %, n = 26). Une atteinte pulmonaire etait associee chez 31 % (n = 22) des patients, 7 % (n = 5) des patients etaient infectes par le VIH et aucun n’etaient diabetique. L’examen direct n’etait positif que dans 14 % (n = 10) des cas alors que la PCR, lorsqu’elle etait pratiquee sur l’echantillon, etait positive dans 89 % des cas (n = 25/28). La majorite des souches etaient multisensibles aux anti-tuberculeux de premiere ligne : seuls 8 % (n = 6) des patients avaient une souche resistante a l’isoniazide, toutes etaient sensibles a la rifampicine. La duree mediane de traitement etait de 6 mois et 22 % (n = 16) etaient traites 9 mois ou plus. Un traitement par corticoides etait associe dans 18 % des cas (n = 13) pour une duree de 1 a 3 mois. L’adenopathie etait notee persistante a l’examen clinique du 12° mois chez 13 % (n = 6) des 47 patients renseignes. En raison d’une mauvaise evolution, une exerese chirurgicale a ete realisee chez 3 patients. La presentation clinique et l’evolution etaient identiques entre les differents continents de naissance, excepte pour les personnes nees en Asie qui avaient plus de localisation ganglionnaire exclusive (82 % versus 58 %, p = 0,03). Conclusion Dans notre etude, les tuberculoses ganglionnaires representent pres d’1/5e des cas de tuberculose et touchent en particulier les patients nes en Asie. Il est necessaire de determiner les facteurs de risques ou les facteurs genetiques pouvant expliquer la plus grande susceptibilite de cette population. L’usage des corticoides et de la chirurgie devrait etre mieux precises.

Cutaneous diphtheria is uncommon in Europe. In this study, we report a case of imported cutaneous infection due to a non-toxigenic but tox gene-bearing (NTTB) strain of Corynebacterium diphtheriae. The NTTB strains are recognized as emerging pathogens across Europe, and physicians and bacteriologists should be aware of the circulation of these strains.

Introduction Les tests de diagnostic bacteriologique de la tuberculose pulmonaire (TBp) sont peu sensibles et contraignants. Nous avons voulu evaluer l’interet du 3e BK crachat (BKc), de la fibroscopie bronchique (FB) et de la biologie moleculaire (BM) comme investigations augmentant la sensibilite du diagnostic. Materiels et methodes Analyse retrospective des resultats de toutes les cultures (C) positives a Mycobacterium tuberculosis sur prelevements bronchopulmonaires dans notre groupe hospitalier du 1er janvier 2015 au 31 decembre 2017 : evaluation des rendements diagnostiques respectifs du 3e BKc, de la fibroscopie bronchique, du BKc post-FB et de la BM (Xpert MTB/RIF). Resultats Au total, 263 patients ont eu au moins une culture positive (C+) a M. tuberculosis a partir de prelevements bronchopulmonaires. Le delai median de positivation de la culture en milieu liquide etait tres court pour les TBp bacilliferes : 6 jours [2–21] versus 15 [2–38] pour les TBp non bacilliferes. Les TBp MDR representaient 1,9 % (5) des patients. Parmi les TBp, 121 (46 %) etaient bacilliferes (examen microscopique EM+). Pour les 263 TBp, le 3e BKC a permis un rendement supplementaire diagnostique de 2,4 % quand les 2 1ers BKc etaient negatifs (4 EM+ supplementaires pour les 121 patients bacilliferes et 2 C+ en plus pour les 142 patients non bacilliferes). Parmi les 142 TBp non bacilliferes, 51 (36 %) fibroscopies bronchiques et BKC post-FB ont permis de faire un diagnostic chez 9 patients (2 EM+,7 C+) non diagnostiques sur les 3 premiers BKc (EM−, C−) soit un rendement supplementaire de 17,6 %. Pour les TBp bacilliferes, 35 patients ont eu les 2 premiers BKc le 1er jour des prelevements (j1) et le 3e BKc a j2. Les taux de positivite du 2e BKc a j1 et du 3e BKc a j2 etaient proches (28 vs 25, respectivement) confirmant la possibilite de raccourcir les delais de prelevements. La sensibilite du Genexpert MTB/RIF etait de 100 % pour les TBp bacilliferes. Le resultat de la recherche de mutation de resistance rpob a la rifampicine concordait dans tous les cas avec les resultats phenotypiques. Pour les TBp non bacilliferes (TBpEM-C+), le test Xpert a ete realise a la discretion du clinicien dans 24 cas permettant un diagnostic precoce pour 14 d’entre eux, soit une Se de 58,3 %. Conclusion Il ressort dans notre serie que : – l’apport du 3e BK crachat est faible mais non negligeable ; – prelever les deux premiers BKc a j1 et le 3e a j2 permet un gain de temps sans perte de sensibilite diagnostique ; – le diagnostic de la TBp non bacillifere reste toujours dependant d’un delai de culture prolonge. L’utilisation elargie du test Xpert et de la FB bronchique en cas de forte suspicion de TB permettent d’ameliorer la sensibilite diagnostique globale. Les scores de prediction clinique existant pourraient aider le clinicien a cibler les fortes suspicions de TBp.

The epidemiology of multidrug-resistant bacteria (MDRB) has changed significantly in European healthcare settings, with a decrease in frequency of meticillin-resistant Staphylococcus aureus and an increase in extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae. Little is known about the effects of these changes on ventilator-associated pneumonia (VAP). A retrospective 5-year trend analysis of ICU antibiotic consumption and resistance in bacteria causing VAP was undertaken. Poisson regression analysis between complete microbiological data and antibiotic consumption was performed. In total, 252 episodes of VAP in 184 patients were identified between 2007 and 2011, from which 364 causal bacteria were isolated. Enterobacteriaceae isolation rates increased significantly over this period [from 6.64 to 10.52 isolates/1000 patient-days; P=0.006], mostly due to an increase in AmpC-producing Enterobacteriaceae (APE) (2.85-4.51 isolates/1000 patient-days; P=0.013), whereas the number of episodes due to S. aureus and Pseudomonas aeruginosa remained stable. A positive association was found between the increase in APE infections and an increase in past-year antibiotic consumption: amoxicillin/clavulanic acid (P=0.003), ceftazidime and cefepime (P=0.007), carbapenems (P=0.002), fluoroquinolones (P=0.012), macrolides (P=0.002) and imidazoles (P=0.004). No such association was found for the emergence of resistance in P. aeruginosa. These results indicate a change in the epidemiology of VAP, with Enterobacteriaceae exceeding P. aeruginosa and S. aureus. Moreover, a positive correlation was observed between antibiotic consumption and the incidence of potentially MDRB such as APE. No such correlation was found for ESBL-producing Escherichia coli and antibiotic-resistant P. aeruginosa.

Introduction Evaluer l’efficience du laboratoire pour le diagnostic bacteriologique de la tuberculose en croisant les cas cliniquement repertories a ceux bacteriologiquement documentes au cours de l’annee 2015. Materiels et methodes Interrogation des donnees patients a partir du logiciel d’aide a la prescription, du logiciel de production de resultats de laboratoire et du logiciel de gestion du dossier patient. Inclusion des patients repertories en 2015. Cent soixante-cinq cas repartis en 4 groupes selon la presence d’une prescription d’isoniazide (INH+ ou −) et les resultats d’investigations microbiologiques (BAC+ ou BAC−) : groupe A (INH+, BAC− [ n = 10]) ; groupe B (INH+, BAC+ et culture positive a Mycobacterium tuberculosis complex [Mtb cx] [C+] [ n = 71]) ; groupe C (INH+, BAC+ mais culture negative a Mtb cx [C−] [ n = 54]) et groupe D (INH−, BAC+, C+ [ n = 30]). Pour l’objectif poursuivi, seuls les groupes B, C et D ayant fait l’objet d’investigations bacteriologiques, ont ete retenus ( n = 155). Pour chaque patient, les donnees cliniques ont ete analysees. Resultats L’analyse des donnees cliniques a permis d’obtenir les resultats suivants. Pour les 71 patients du groupe B (45 %), il existait une parfaite coherence clinique, biologique et therapeutique avec 40 tuberculoses pulmonaires (TP) 13 tuberculoses mixtes (TM) et 18 tuberculoses extrapulmonaires (TXP). Pour les 54 patients du groupe C (35 %), 4 cas etaient inexploitables car sans information clinique. Sur les 50 cas restants, nous avons repertorie 10 infections tuberculeuses latentes (ITL), 6 mycobacterioses, 11 traitements d’epreuves, 8 TP, TM ou TXP deja sous traitement lors des investigations bacteriologiques pouvant expliquer les resultats de culture negatifs. En revanche, pour 15 cas (2 TP, 4 TM et 9 TXP) une C+ n’a pas ete obtenue. Pour les 30 patients du groupe D (19 %), nous avons repertorie 19 TP, 2 TM et 9 TXP. L’efficience globale de laboratoire etait de 96 % pour les TP, meilleure que pour les TM (79 %) et TEX (75 %). Une analyse du nombre des investigations pratiquees pour les C− indique qu’un nombre insuffisant d’investigations est a mettre en avant. Conclusion A partir de l’ensemble des cas de TB repertories, le laboratoire a apporte un diagnostic positif pour 96 % des cas de TP. Il apparait que l’efficience du laboratoire est satisfaisante pour le diagnostic des TP et la principale cause de deficit de diagnostic bacteriologique repose sur un defaut d’investigations. Pour les TXP, l’analyse est plus complexe ; neanmoins le laboratoire a apporte sa contribution au diagnostic dans 3 cas sur 4.

Introduction Identifier rapidement les cas de tuberculose en milieu hospitalier est un objectif prioritaire pour prevenir les cas secondaires chez les patients et les soignants. Multiplier les sources d’informations permettant une alerte rapide est primordiale. Nous avons evalue sur une periode d’un an la place du logiciel d’aide a la prescription medicamenteuse dans la detection des patients suivis pour tuberculose pulmonaire au sein d’un groupe hospitalier universitaire confronte a une des incidences de tuberculose pulmonaire les plus elevees de France. Materiels et methodes Tous les cas de tuberculose ont ete repertories du 01/01/2015 au 31/12/2015 en utilisant le logiciel d’aide a la prescription medicamenteuse et le logiciel de gestion de resultats de laboratoire. Toutes les prescriptions incluant de l’isoniazide (INH) en complement des donnees du laboratoire de microbiologie ont ete prises en compte. Resultats Pendant la periode d’etude, 165 cas ont ete identifies. Parmi ceux-ci, 30 (18 %) patients l’etaient uniquement par culture positive (absence de prescription informatisee d’INH). Cent trente-cinq patients (82 %) avaient une prescription d’INH dont 71 (52 %) avec une culture positive a Mycobacterium tuberculosis complex , 10 (8 %) sans aucune investigation bacteriologique (8 diagnostics faits l’annee precedente et 2 infections tuberculeuses latentes [ITL]) et 54 (40 %) sans aucun prelevement positif malgre des investigations bacteriologiques. Il s’agissait pour ce groupe de 10 ITL, 6 mycobacterioses (MA) et 38 cas cliniquement suspects de tuberculose maladie. En excluant les ITL, les MA et les cas diagnostiques l’annee precedente, 38 (28 %) des 135 cas retenus l’etaient grâce au logiciel d’aide a la prescription des medicaments. Conclusion En pratique le logiciel d’aide a la prescription a permis dans notre travail d’identifier 38 cas supplementaires de tuberculose maladie soit 23 % des cas de l’annee etudiee. L’alerte a partir du logiciel d’aide a la prescription nous parait etre un complement a ne pas negliger en complement de l’alerte microbiologique afin d’elargir la population des cas autour desquels une enquete doit etre menee dont la recherche de cas secondaires eventuels afin de maitriser au mieux le risque de diffusion intra-hospitalier.

The purpose of this study is to investigate whether exposure to nonsteroidal antiinflammatory drugs (NSAIDs) at the early stage of severe pneumococcal community-acquired pneumonia (CAP) requiring intensive care unit (ICU) admission may affect its presentation and outcome.Medical records of ICU adult patients (12-year period) with a pneumococcal CAP diagnosis were retrospectively analyzed according to previous NSAID exposure.One hundred six confirmed pneumococcal CAP were identified, 20 received NSAIDs within 4 (2-6) days before admission. Nonsteroidal antiinflammatory drug-exposed patients were younger (43.3 vs 62.2 years; P.0001), had less frequently at least one chronic comorbid condition (40% vs 75%; P = .003), had more often complicated pleural effusions (20% vs 2.3%; P = .01), and more frequent pleuropulmonary complications (odds ratio: 5.75 [1.97-16.76]). Nonsteroidal antiinflammatory drug patients required more often noninvasive ventilatory support (25% vs 4.6%; P = .003). Intensive care unit length of stay and mortality were similar.We report as severe pneumococcal pneumonia in young and healthy patients exposed to NSAIDs as in older, more comorbid, and nonexposed ones. Nonsteroidal antiinflammatory drug use may mask initial symptoms and delay antimicrobial therapy, thus predisposing to worse outcomes.

The sequence of pTN48, a plasmid of the FII-FIB replicon type that encodes a CTX-M-14 enzyme in an Escherichia coli strain of the phylogenetic group D2 O102-ST405 clone, was determined. pTN48 is, for the most part, a mosaic of virulence, antibiotic resistance, and addiction system modules found in various other plasmids. The presence of multiple addiction systems indicates that the plasmid should be stably maintained in the E. coli clone, favoring dissemination of the CTX-M-14 enzyme. The epidemiology of extended-spectrum beta-lactamases (ESBLs) has drastically changed in recent years. An explosive spread of CTX-M-type enzymes, with Escherichia coli as the main host, has occurred in both hospital and community settings worldwide (4, 23). Two phenomena may explain such an epidemic profile: the spread of plasmids bearing antibiotic resistance genes between bacterial strains and the spread of bacterial clones bearing resistance-encoding plasmids. Recently, the application of multilocus sequence typing revealed that a few E. coli clones with the ability to capture a large panel of ESBLs have disseminated internationally (5, 7, 14, 16, 18, 19). Furthermore, it has been shown that two of these clones, the O25b sequence type 131 (ST131) clone of the B2 phylogenetic group and the O102-ST405 clone of the D2 phylogenetic group, were highly virulent in a mouse model of septicemia (6, 16). The dissemination of such resistant and virulent clones constitutes a major public health concern and prompted us to examine ESBL-encoding plasmids associated with these clones. We therefore sequenced pTN48, a nonconjugative plasmid of the FII-FIB replicon type carrying a CTX-M-14

Early detection of Pseudomonas aeruginosa and early aggressive treatment are recommended to delay chronic infection in cystic fibrosis (CF) patients. The aim of this study was to assess a quantitative PCR (q-PCR) assay for the diagnosis of early P. aeruginosa colonization in 23 young CF patients (group A, age range 7–18 years) and to survey the eradication of P. aeruginosa in 10 young CF patients (group B, age range 5–18 years) after an initial antibiotic treatment. q-PCR results for consecutive sputum samples from each patient during a period of 18 months were compared with bacterial cultures during the same period plus an additional period of 12 months, and with concomitant clinical signs of pulmonary exacerbation. The q-PCR and bacterial cultures were negative for 17 of the 23 patients in group A and six of the 10 patients in group B during the study period. However, consecutive positive q-PCR results were observed for one patient in group A and three patients in group B, while the bacterial cultures for the same sputum sample remained negative. They preceded positive P. aeruginosa bacterial cultures at 7 and 8 months for two patients in group B. These positive results were associated with a worsening of the clinical status of patients, but pulmonary exacerbation appeared non-specific for the diagnosis of early P. aeruginosa colonization since pulmonary exacerbations were observed in patients in whom q-PCR or bacterial culture remained negative. In conclusion, q-PCR may be a useful additional tool to provide information on the P. aeruginosa status of CF patients.