High Blood Eosinophil Count at Stable State is Not Associated with Airway Microbiota Distinct Profile in COPD

Purpose

The heterogeneity of clinical features in COPD at stable state has been associated with airway microbiota. Blood eosinophil count (BEC) represents a biomarker for a pejorative evolution of COPD, including exacerbations and accelerated FEV1 decline. We aimed to analyse the associations between BEC and airway microbiota in COPD at stable state.

Patients and Methods

Adult COPD patients at stable state (RINNOPARI cohort) were included and characterised for clinical, functional, biological and morphological features. BEC at inclusion defined 2 groups of patients with low BEC <300/mm3 and high BEC ≥300/mm3. Sputa were collected and an extended microbiological culture was performed for the identification of viable airway microbiota.

Results

Fifty-nine subjects were included. When compared with the low BEC (n=40, 67.8%), the high BEC group (n=19, 32.2%) had more frequent exacerbations (p<0.001) and more pronounced cough and sputum (p<0.05). The global composition, the number of bacteria per sample and the α-diversity of the microbiota did not differ between groups, as well as the predominant phyla (Firmicutes), or the gender repartition.

Conclusion

In our study, high BEC in COPD at stable state was associated with a clinical phenotype including frequent exacerbation, but no distinct profile of viable airway microbiota compared with low BEC.

Bronchiectasis in renal transplant patients: a cross-sectional study

BACKGROUND

Bronchiectasis is a chronic airway disease characterized by permanent and irreversible abnormal dilatation of bronchi. Several studies have reported the development of bronchiectasis after renal transplantation (RT), but no prospective study specifically assessed bronchiectasis in this population. This study aimed to compare features of patients with bronchiectasis associated with RT to those with idiopathic bronchiectasis.

METHODS

Nineteen patients with bronchiectasis associated with RT (RT-B group) and 23 patients with idiopathic bronchiectasis (IB group) were prospectively included in this monocentric cross-sectional study. All patients underwent clinical, functional, laboratory, and CT scan assessments. Sputum was collected from 25 patients (n = 11 with RT-B and n = 14 with IB) and airway microbiota was analyzed using an extended microbiological culture.

RESULTS

Dyspnea (≥ 2 on mMRC scale), number of exacerbations, pulmonary function tests, total bronchiectasis score, severity and prognosis scores (FACED and E-FACED), and quality of life scores (SGRQ and MOS SF-36) were similar in the RT-B and IB groups. By contrast, chronic cough was less frequent in the RT-B group than in the IB group (68% vs. 96%, p = 0.03). The prevalence and diversity of the airway microbiota in sputum were similar in the two groups.

CONCLUSION

Clinical, functional, thoracic CT scan, and microbiological characteristics of bronchiectasis are overall similar in patients with IB and RT-B. These results highlight that in RT patients, chronic respiratory symptoms and/or airway infections should lead to consider the diagnosis of bronchiectasis. Further studies are required to better characterize the pathophysiology of RT-B including airway microbiota, its incidence, and impact on therapeutic management.

Current cough and sputum assessed by the cough and sputum assessment-questionnaire (CASA-Q) is associated with quality of life impairment in cystic fibrosis

BACKGROUND

Cough and sputum are major symptoms in cystic fibrosis (CF) that contribute to the impairment of quality of life.

METHODS

This prospective single centre cross-sectional pilot study aimed to evaluate the results of a self-administered questionnaire assessing cough and sputum symptoms (2 domains), and their impact (2 domains) on daily activities in the previous week, named the Cough and Sputum Assessment Questionnaire (CASA-Q) in CF adult patients at stable state, and to analyse associations with clinical, functional, microbiological, radiological data, and two quality of life scales: the Cystic Fibrosis Questionnaire Revised (CFQ-R) and the Saint George Respiratory Questionnaire (SGRQ).

RESULTS

Forty-eight patients were included in this analysis (69% men; median age of 27.8 ± 8.1 years; median body mass index of 21.8 + 3.3 kg/m²; mean FEV1 of 64 ± 30% of the predicted value). The mean values of the CASA-Q domains were 58 ± 23 for cough symptoms, 77 ± 24 for cough impact, 62 ± 25 for sputum symptoms and 84 ± 21 for sputum impact. Impairment in CASA-Q cough and sputum domains was associated with dyspnea mMRC scale (p < 0.005 for all 4 domains of CASA-Q) and exacerbations in the previous year (p < 0.05 for CASA-Q symptoms domains). We also found correlations between all domains of the CASA-Q and quality of life questionnaires including SGRQ (p < 0.001) and to a lesser extend CFQ-R. We identified a clinical phenotype (female gender, ΔF508 heterozygous mutation, dyspnea mMRC scale) associated with an impairment of CASA-Q score and quality of life using a 2-step cluster analysis.

CONCLUSIONS

CASA-Q allows the assessment of cough and sputum in CF adult patients and is associated with quality of life impairment. This simple easy-to-use tool could be used in routine clinical practice and in clinical studies to assess cough and sputum in CF patients.

TRIAL REGISTRATION

The study was registered on ClinicalTrials.gov (NCT02924818, first posted on 5th October 2016).

Development of an antibody fused with an antimicrobial peptide targeting Pseudomonas aeruginosa: A new approach to prevent and treat bacterial infections

The increase in emerging drug resistant Gram-negative bacterial infections is a global concern. In addition, there is growing recognition that compromising the microbiota through the use of broad-spectrum antibiotics can impact long term patient outcomes. Therefore, there is the need to develop new bactericidal strategies to combat Gram-negative infections that would address these specific issues. In this study, we report and characterize one such approach, an antibody-drug conjugate (ADC) that combines (i) targeting the surface of a specific pathogenic organism through a monoclonal antibody with (ii) the high killing activity of an antimicrobial peptide. We focused on a major pathogenic Gram-negative bacterium associated with antibacterial resistance: Pseudomonas aeruginosa. To target this organism, we designed an ADC by fusing an antimicrobial peptide to the C-terminal end of the VH and/or VL-chain of a monoclonal antibody, VSX, that targets the core of P. aeruginosa lipopolysaccharide. This ADC demonstrates appropriately minimal levels of toxicity against mammalian cells, rapidly kills P. aeruginosa strains, and protects mice from P. aeruginosa lung infection when administered therapeutically. Furthermore, we found that the ADC was synergistic with several classes of antibiotics. This approach described in this study might result in a broadly useful strategy for targeting specific pathogenic microorganisms without further augmenting antibiotic resistance.

[Systematic investigation of surgical site infections (SSI) in plastic reconstructive and aesthetic surgery (ERCS): Feedback]

Surgical site infection (SSI) in plastic, reconstructive and aesthetic surgery (ERCP) is quite uncommon compared to other surgical specialities but remains one of the main complications. The aim of our study was to provide feedback on the systematic investigation of SSI in ERCP. This is a monocentric retrospective study, including all paediatric and adult patients who have undergone ERCP surgery between 01/01/2014 and 31/12/2021. During this period, the department systematically investigated all SSI cases. Eight thousand eight hundred and seventy-eight surgical procedures were performed. The SSI rate was 0.34%. Thirty SSIs (19W,11M), with a mean age of 56 years (none paediatric), were investigated. Twenty-seven patients suffered from comorbidities. The surgical indications included 17 cases of skin cancer, 7 cases of weight loss, 4 cases of breast reconstruction, 1 lipoma, 1 pectus excavatum. Eleven surgeries consisted in lymphnode procedures (8 sentinel lymphnodes, 3 curage). The average operating time was 116minutes. Nineteen patients received antibiotic prophylaxis. The average time to onset of SSI after surgery was 10 days. The most prevalent bacteria were commensals of the skin flora and the digestive tract. Apart from surgical management, 100% of patients were treated with antibiotics. High age, multiple comorbidities, long, combined procedures, placement of equipment, lymph node surgery, post-operative punctures on implanted equipment, are all risks factors for SSI. The implementation of a systematic monitoring of SSI within our department has provided us with the opportunity to analyse our data in real time and allow us to adjust our practices if necessary. This process can be used in other plastic reconstructive and aesthetic surgery departments. The collection and analysis of SSIs is both easily done and the procedure is well standardized. The assistance of the operational hygiene team is a key asset for the success of this project. The development of this type of procedure on a national level could be an asset to improve the management of SSI by taking advantage of the experience of a larger number of centres.

[Involvement of inorganic phosphate starvation in Pseudomonas aeruginosa bacterial virulence]

Pseudomonas aeruginosa is a bacterium causing a wide spectrum of nosocomial and opportunistic respiratory infections. As an element essential for bacterial metabolism , phosphorus is incorporated as an inorganic phosphate and regulated by a two-component PhoB-PhoR system. Recently, it has been shown that as a result of overexpression of virulence factors, including the PhoB transcription factor, P. aeruginosa exhibited increased virulence in phosphate-deficient conditions. Exploration of the relationship between phosphate homeostasis and P. aeruginosa virulence could effectively contribute to the development of new, simple and innovative therapeutic strategies.

Evaluation of ceftolozane-tazobactam susceptibility on a French nationwide collection of Enterobacterales

OBJECTIVES

Ceftolozane-tazobactam (C/T) proved its efficacy for the treatment of infections caused by non-carbapenemase producing Pseudomonas aeruginosa and Enterobacterales. Here, we aimed to provide susceptibility data on a large series of Enterobacterales since the revision of EUCAST categorization breakpoints in 2020.

METHODS

First, C/T susceptibility was determined on characterized Enterobacterales resistant to third generation cephalosporins (3GCs) (extended spectrum β-lactamase [ESBL] production or different levels of AmpC overexpression) (n = 213) and carbapenem-resistant Enterobacterales (CRE) (n = 259), including 170 carbapenemase producers (CPE). Then, 1632 consecutive clinical Enterobacterales responsible for infection were prospectively collected in 23 French hospitals. C/T susceptibility was determined by E-test® (biomérieux) and broth microdilution (BMD) (Sensititre™, Thermo Scientific) to perform method comparison.

RESULTS

Within the collection isolates, 88% of 3GC resistant strains were susceptible to C/T, with important variation depending on the resistance mechanism: 93% vs. 13% susceptibility for CTX-M and SHV-ESBL producers, respectively. Only 20% of the CRE were susceptible to C/T. Among CPE, 80% of OXA-48-like producers were susceptible to C/T, whereas all metallo-β-lactamase producers were resistant. The prospective study revealed that 95.6% of clinical isolates were susceptible to C/T. Method comparison performed on these 1632 clinical isolates demonstrated 99% of categorization agreement between MIC to C/T determined by E-test® in comparison with the BMD (reference) and only 74% of essential agreement.

CONCLUSION

Overall, C/T showed good activity against wild-type Enterobacterales, AmpC producers, and ESBL-producing Escherichia coli but is less active against ESBL-producing Klebsiella pneumoniae, and CRE. E-test® led to an underestimation of the MICs in comparison to the BMD reference.

Current concepts on Pseudomonas aeruginosa interaction with human airway epithelium

Pseudomonas aeruginosa is a major, but opportunistic, respiratory pathogen, which rarely infects healthy individuals, mainly due to the barrier effect of the human airway epithelium (HAE). This review explores the interaction of P. aeruginosa with HAE and the progression of the infection. The basolateral part of the epithelium, which includes the basolateral membrane of the epithelial cells and the basement membrane, is inaccessible in normal tight epithelia with intact junctions. We highlight how P. aeruginosa exploits weaknesses in the HAE barrier to gain access to the basolateral part of the epithelium. This access is crucial to initiate respiratory infection and is mainly observed in the injured epithelium, in repairing or chronically remodeled epithelium, and during extrusion of senescent cells or cell multiplication during normal epithelium renewal. The subsequent adhesion of the bacteria and cytotoxic action of virulence factors, including the toxins delivered by the type 3 secretion system (T3SS), lead to retractions and cell death. Eventually, P. aeruginosa progressively reaches the basement membrane and propagates radially through the basal part of the epithelium to disseminate using twitching and flagellar motility.

An upgraded version of carbapenem inactivation method to detect Bacteroides fragilis carbapenemase

An increase of carbapenemase-producing Bacteroides fragilis infections is observed. To detect such a resistance in B. fragilis, several tests exist that are expensive or show poor sensitivity and specificity. Therefore, we upgraded the Anaerobic Carbapenem Inactivation Method (Ana-CIM) to easily screen for carbapenemase-producing B. fragilis. The presence of carbapenemase cfiA gene was identified in 50 B. fragilis isolates by PCR. We modified the Ana-CIM by (1) increasing the bacterial inoculum, and (2) measuring the differences in diameter between the negative control and the testing disc. We correctly classified the cfiA-negative and positive isolates and could define a cut-off of positivity at 2 mm. Our modified Ana-CIM allowed to correctly discriminate the 31 cfiA-positive with meropenem MICs ranging from 1 to > 32 µg/mL. We anticipate that our modified Ana-CIM could be used in most clinical laboratories to easily screen for carbapenemase-producing B. fragilis, even at low levels.

A high-throughput sequencing approach identifies immunotherapeutic targets for bacterial meningitis in neonates

BACKGROUND

Worldwide, Escherichia coli is the leading cause of neonatal Gram-negative bacterial meningitis, but full understanding of the pathogenesis of this disease is not yet achieved. Moreover, to date, no vaccine is available against bacterial neonatal meningitis.

METHODS

Here, we used Transposon Sequencing of saturated banks of mutants (TnSeq) to evaluate E. coli K1 genetic fitness in murine neonatal meningitis. We identified E. coli K1 genes encoding for factors important for systemic dissemination and brain infection, and focused on products with a likely outer-membrane or extra-cellular localization, as these are potential vaccine candidates. We used in vitro and in vivo models to study the efficacy of active and passive immunization.

RESULTS

We selected for further study the conserved surface polysaccharide Poly-β-(1-6)-N-Acetyl Glucosamine (PNAG), as a strong candidate for vaccine development. We found that PNAG was a virulence factor in our animal model. We showed that both passive and active immunization successfully prevented and/or treated meningitis caused by E. coli K1 in neonatal mice. We found an excellent opsonophagocytic killing activity of the antibodies to PNAG and in vitro these antibodies were also able to decrease binding, invasion and crossing of E. coli K1 through two blood brain barrier cell lines. Finally, to reinforce the potential of PNAG as a vaccine candidate in bacterial neonatal meningitis, we demonstrated that Group B Streptococcus, the main cause of neonatal meningitis in developed countries, also produced PNAG and that antibodies to PNAG could protect in vitro and in vivo against this major neonatal pathogen.

INTERPRETATION

Altogether, these results indicate the utility of a high-throughput DNA sequencing method to identify potential immunotherapy targets for a pathogen, including in this study a potential broad-spectrum target for prevention of neonatal bacterial infections.

FUNDINGS

ANR Seq-N-Vaq, Charles Hood Foundation, Hearst Foundation, and Groupe Pasteur Mutualité.

In vitro susceptibility of nonfermenting Gram-negative rods to meropenem-vaborbactam and delafloxacin

Aim: Meropenem-vaborbactam and delafloxacin activities were not assessed against Achromobacter spp. (Achr), Burkholderia cepacia complex (Bcc) and Stenotrophomonas maltophilia (Smal). Methodology: A total of 106 Achr, 57 Bcc and 100 Smal were tested with gradient diffusion test of meropenem-vaborbactam, delafloxacin and comparators. Results: Meropenem-vaborbactam MIC₅₀ were 4 μg/ml for Achr, 1 μg/ml for B. cepacia, 2 μg/ml for B. cenocepacia and B. multivorans, and 32 μg/ml for Smal. Delafloxacin MIC₅₀ were 4 μg/ml for Achr, 0.25 μg/ml for B. cepacia and B. multivorans, 2 μg/ml for B. cenocepacia, and 0.5 μg/m for Smal. meropenem-vaborbactam MICs were fourfold lower than meropenem for 28.3% Achr, 77.2% B. cepacia, 53.8% B. cenocepacia and 77.2% B. multivorans. Conclusion: Meropenem-vaborbactam and delafloxacin are in vitro active against Bcc and Achr.

The Nicotinic Receptor Polymorphism rs16969968 Is Associated with Airway Remodeling and Inflammatory Dysregulation in COPD Patients

Genome-wide association studies unveiled the associations between the single nucleotide polymorphism rs16969968 of CHRNA5, encoding the nicotinic acetylcholine receptor alpha5 subunit (α5SNP), and nicotine addiction, cancer, and COPD independently. Here, we investigated α5SNP-induced epithelial remodeling and inflammatory response in human COPD airways. We included 26 α5SNP COPD patients and 18 wild-type α5 COPD patients in a multi-modal study. A comparative histologic analysis was performed on formalin-fixed paraffin-embedded lung tissues. Isolated airway epithelial cells from bronchial brushings were cultivated in the air-liquid interface. Broncho-alveolar fluids were collected to detect inflammatory mediators. Ciliogenesis was altered in α5SNP COPD bronchial and bronchiolar epithelia. Goblet cell hyperplasia was exacerbated in α5SNP small airways. The broncho-alveolar fluids of α5SNP COPD patients exhibited an increase in inflammatory mediators. The involvement of the rs16969968 polymorphism in airway epithelial remodeling and related inflammatory response in COPD prompts the development of innovative personalized diagnostic and therapeutic strategies.

Discrimination of Escherichia coli, Shigella flexneri, and Shigella sonnei using lipid profiling by MALDI-TOF mass spectrometry paired with machine learning

Matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry (MALDI‐TOF MS) has become a staple in clinical microbiology laboratories. Protein‐profiling of bacteria using this technique has accelerated the identification of pathogens in diagnostic workflows. Recently, lipid profiling has emerged as a way to complement bacterial identification where protein‐based methods fail to provide accurate results. This study aimed to address the challenge of rapid discrimination between Escherichia coli and Shigella spp. using MALDI‐TOF MS in the negative ion mode for lipid profiling coupled with machine learning. Both E. coli and Shigella species are closely related; they share high sequence homology, reported for 16S rRNA gene sequence similarities between E. coli and Shigella spp. exceeding 99%, and a similar protein expression pattern but are epidemiologically distinct. A bacterial collection of 45 E. coli, 48 Shigella flexneri, and 62 Shigella sonnei clinical isolates were submitted to lipid profiling in negative ion mode using the MALDI Biotyper Sirius® system after treatment with mild‐acid hydrolysis (acetic acid 1% v/v for 15 min at 98°C). Spectra were then analyzed using our in‐house machine learning algorithm and top‐ranked features used for the discrimination of the bacterial species. Here, as a proof‐of‐concept, we showed that lipid profiling might have the potential to differentiate E. coli from Shigella species using the analysis of the top five ranked features obtained by MALDI‐TOF MS in the negative ion mode of the MALDI Biotyper Sirius® system. Based on this new approach, MALDI‐TOF MS analysis of lipids might help pave the way toward these goals.

A qnrD-Plasmid Promotes Biofilm Formation and Class 1 Integron Gene Cassette Rearrangements in Escherichia coli

Bacteria within biofilms may be exposed to sub-minimum inhibitory concentrations (sub-MICs) of antibiotics. Cell-to-cell contact within biofilms facilitates horizontal gene transfers and favors induction of the SOS response. Altogether, it participates in the emergence of antibiotic resistance. Aminoglycosides at sub-MICs can induce the SOS response through NO accumulation in E. coli carrying the small plasmid with the quinolone resistance qnrD gene (pDIJ09-518a). In this study, we show that in E. coli pDIJ09-518a, the SOS response triggered by sub-MICs of aminoglycosides has important consequences, promoting genetic rearrangement in class 1 integrons and biofilm formation. We found that the integrase expression was increased in E. coli carrying pDIJ09-518a in the presence of tobramycin, which was not observed for the WT isogenic strain that did not carry the qnrD-plasmid. Moreover, we showed that biofilm production was significantly increased in E. coli WT/pDIJ09-518a compared to the WT strain. However, such a higher production was decreased when the Hmp-NO detoxification pathway was fully functional by overexpressing Hmp. Our results showing that a qnrD-plasmid can promote biofilm formation in E. coli and potentiate the acquisition and spread of resistance determinants for other antibiotics complicate the attempts to counteract antibiotic resistance and prevention of biofilm development even further. We anticipate that our findings emphasize the complex challenges that will impact the decisions about antibiotic stewardship, and other decisions related to retaining antibiotics as effective drugs and the development of new drugs.

First use of a new rapid multiplex PCR system for the microbiological diagnosis and the clinical management of severe infectious keratitis: A case report

Purpose

Observations

Conclusions and importance

Contribution of the anaerobic blood culture vial for the recovery of Candida glabrata: a retrospective multicentric study

Although Candida spp are aerobic microorganisms, some Candida strains, mainly Candida glabrata, can be recovered from anaerobic blood culture vials. We assessed the contribution of the anaerobic vials for the diagnosis of candidemia, especially for C. glabrata. We conducted a multicenter retrospective study including eight University or regional hospitals. A single episode of monomicrobial candidemia per patient was included from September 1st, 2016, to August 31st, 2019. The characteristics of all aerobic and anaerobic blood culture vials sampled within 2 hours before and after the first positive blood culture vials were recorded (type of vials, result, and for positive vials time-to-positivity and Candida species). Overall, 509 episodes of candidemia were included. The main species were C. albicans (55.6%) followed by C. glabrata (17.1%), C. parapsilosis (4.9%), and C. tropicalis (4.5%). An anaerobic vial was positive in 76 (14.9%) of all episodes of which 56 (73.8%) were due to C. glabrata. The number of C. glabrata infections only positive in anaerobic vials was 1 (2.6%), 1 (11.1%), and 15 (37.5%) with the BACT/ALERT 3D the BACT/ALERT VIRTUO and the BACTEC FX instrument respectively (P &lt; 0.01). The initial positivity of an anaerobic vial was highly predictive of the isolation of C. glabrata with the BACTEC FX (sensitivity of 96.8%). C. glabrata time-to-positivity was shorter in anaerobic vial than aerobic vial with all instruments. Anaerobic blood culture vials improve the recovery of Candida spp mainly C. glabrata. This study could be completed by further analyzes including mycological and pediatric vials.

Antimicrobial Resistance in Enterobacterales Recovered from Urinary Tract Infections in France

In the context of increasing antimicrobial resistance in Enterobacterales, the management of these UTIs has become challenging. We retrospectively assess the prevalence of antimicrobial resistance in Enterobacterales isolates recovered from urinary tract samples in France, between 1 September 2017, to 31 August 2018. Twenty-six French clinical laboratories provided the susceptibility of 134,162 Enterobacterales isolates to 17 antimicrobials. The most frequent species were E. coli (72.0%), Klebsiella pneumoniae (9.7%), Proteus mirabilis (5.8%), and Enterobacter cloacae complex (2.9%). The overall rate of ESBL-producing Enterobacterales was 6.7%, and ranged from 1.0% in P. mirabilis to 19.5% in K. pneumoniae, and from 3.1% in outpatients to 13.6% in long-term care facilities. Overall, 4.1%, 9.3% and 10.5% of the isolates were resistant to cefoxitin, temocillin and pivmecillinam. Cotrimoxazole was the less active compound with 23.4% resistance. Conversely, 4.4%, 12.9%, and 14.3% of the strains were resistant to fosfomycin, nitrofurantoin, and ciprofloxacin. However, less than 1% of E. coli was resistant to fosfomycin and nitrofurantoin. We identified several trends in antibiotics resistances among Enterobacterales isolates recovered from the urinary tract samples in France. Carbapenem-sparing drugs, such as temocillin, mecillinam, fosfomycin, cefoxitin, and nitrofurantoin, remained highly active, including towards ESBL-E.

A qnr-plasmid allows aminoglycosides to induce SOS in Escherichia coli

The plasmid-mediated quinolone resistance (PMQR) genes have been shown to promote high-level bacterial resistance to fluoroquinolone antibiotics, potentially leading to clinical treatment failures. In Escherichia coli, sub-minimum inhibitory concentrations (sub-MICs) of the widely used fluoroquinolones are known to induce the SOS response. Interestingly, the expression of several PMQR qnr genes is controlled by the SOS master regulator, LexA. During the characterization of a small qnrD-plasmid carried in E. coli, we observed that the aminoglycosides become able to induce the SOS response in this species, thus leading to the elevated transcription of qnrD. Our findings show that the induction of the SOS response is due to nitric oxide (NO) accumulation in the presence of sub-MIC of aminoglycosides. We demonstrated that the NO accumulation is driven by two plasmid genes, ORF3 and ORF4, whose products act at two levels. ORF3 encodes a putative flavin adenine dinucleotide (FAD)-binding oxidoreductase which helps NO synthesis, while ORF4 codes for a putative fumarate and nitrate reductase (FNR)-type transcription factor, related to an O₂-responsive regulator of hmp expression, able to repress the Hmp-mediated NO detoxification pathway of E. coli. Thus, this discovery, that other major classes of antibiotics may induce the SOS response could have worthwhile implications for antibiotic stewardship efforts in preventing the emergence of resistance.

Extended Bacteria Culture-Based Clustering Identifies a Phenotype Associating Increased Cough and Enterobacterales in Stable Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease characterized by airflow limitation. This chronic respiratory disease represents the third leading cause of death worldwide. Alteration of the airway microbiota has been reported to be associated with exacerbation frequency in COPD, but its role on the symptoms in patients at stable state is still incompletely described. This study aimed to determine whether bacteria isolated in sputum can be associated with the clinical features of COPD patients within stable state. Our study highlights, for the first time, that altered microbiota with Enterobacterales is associated with pejorative clinical symptoms in stable COPD patients. The airway microbiota of 38 patients was analyzed using an extended culture approach and mass spectrometry identification. Cluster analysis by principal coordinate analysis of the bacterial communities showed that the patients could be classified into three distinct clusters in our cohort. The clusters showed no differences in proportions of the phylum, but one of them was associated with a high prevalence of Enterobacterales (71.4% in cluster 1 vs. 0% in cluster 3), loss of microbiota diversity, and higher bacterial load (10⁷ vs. 10⁵ CFU/ml, respectively) and characterized by predominant cough and impact on mental health. These novel findings, supported by further studies, could lead to modifying the processing of COPD sputum in the everyday practice of clinical microbiology laboratories.

Retrospective multicentric study on Campylobacter spp. bacteremia in France: the Campylobacteremia study

BACKGROUND

Campylobacter spp. bacteremia is a severe infection. A nationwide 5-year retrospective study was conducted to characterize its clinical features and prognostic factors.

METHODS

Patients diagnosed with Campylobacter spp. bacteremia in 37 French hospitals participating in the surveillance network of the National Reference Center for Campylobacter and Helicobacter were included from January 1, 2015, to December 31, 2019. The goal was to analyze the effects of a delay of appropriate antibiotic therapy and other risk factors on 30-day mortality, antibiotic resistance, patient characteristics and prognosis according to the Campylobacter species.

FINDINGS

Among the 592 patients, Campylobacter jejuni and Campylobacter fetus were the most commonly identified species (42.9 and 42.6%, respectively). The patients were elderly (median age 68 years), and most had underlying conditions, mainly immunodepression (43.4%), hematologic malignancies (25.9%), solid neoplasms (23%) and diabetes (22.3%). C. jejuni and Campylobacter coli were associated with gastrointestinal signs, and C. fetus was associated with secondary localizations. Among the 80 patients (13.5%) with secondary localizations, 12 had endocarditis, 38 vascular, 24 osteo-articular and 9 ascitic fluid infections. The thirty-day mortality rate was 11.7%, and an appropriate antibiotic treatment was independently associated with 30-day survival (odds ratio [OR]=0.47, 95% CI [0.24-0.93], p=0.03). The median efficient therapy initiation delay was quite short (2 days, IQR [0-4]) but it had no significant impact on 30-day mortality (p=0.78).

INTERPRETATION

Campylobacter spp. bacteremia mainly occurred in elderly immunocompromised individuals with variable clinical presentations according to the species involved. Appropriate antimicrobial therapy was associated with improved 30-day survival.

In Vitro Antimicrobial Susceptibility Profiles of Gram-Positive Anaerobic Cocci Responsible for Human Invasive Infections

The aim of this multicentre study was to determine the in vitro susceptibility to anti-anaerobic antibiotics of Gram-positive anaerobic cocci (GPAC) isolates responsible for invasive infections in humans. A total of 133 GPAC isolates were collected in nine French hospitals from 2016 to 2020. All strains were identified to the species level (MALDI-TOF mass spectrometry, 16S rRNA sequencing). Minimum inhibitory concentrations (MICs) of amoxicillin, piperacillin, cefotaxime, imipenem, clindamycin, vancomycin, linezolid, moxifloxacin, rifampicin, and metronidazole were determined by the reference agar dilution method. Main erm-like genes were detected by PCR. The 133 GPAC isolates were identified as follows: 10 Anaerococcus spp., 49 Finegoldia magna, 33 Parvimonas micra, 30 Peptoniphilus spp., and 11 Peptostreptococcus anaerobius. All isolates were susceptible to imipenem, vancomycin (except 3 P. micra), linezolid and metronidazole. All isolates were susceptible to amoxicillin and piperacillin, except for P. anaerobius (54% and 45% susceptibility only, respectively). MICs of cefotaxime widely varied while activity of rifampicin, and moxifloxacin was also variable. Concerning clindamycin, 31 were categorized as resistant (22 erm(A) subclass erm(TR), 7 erm(B), 1 both genes and 1 negative for tested erm genes) with MICs from 8 to >32 mg/L. Although GPACs are usually susceptible to drugs commonly used for the treatment of anaerobic infections, antimicrobial susceptibility should be evaluated in vitro.

Algorithm for rational use of Film Array Pneumonia Panel in bacterial coinfections of critically ill ventilated COVID-19 patients

The FilmArray Pneumonia Panel has proven to be an effective tool for rapid detection of main respiratory pathogens. However, its rational use needs appropriate knowledge and formation regarding its indication and interpretation. Herein, we provide some advices to help with success of its daily routine use, particularly in critically ill ventilated COVID-19 patients.

Clinical Trial registration number: NCT04453540.

Epidemiology and clinical characteristics of Klebsiella spp. meningitis in France

OBJECTIVES

To describe the epidemiology of Klebsiella spp. meningitis in France with respect to clinical and bacteriological data.

METHODS

We performed a four-year multicenter, retrospective, observational study. The primary objective was to provide a clinical description of patients with Klebsiella spp. meningitis. Secondary objectives were to compare community-acquired meningitis and healthcare-associated meningitis and to analyze factors associated with mortality.

RESULTS

We enrolled 131 patients with Klebsiella spp. meningitis. Eighty-two (62.6%) infections were reported following neurosurgery. Twenty-eight strains (21.4%) were resistant to third-generation cephalosporins (3GC). The median [IQR] cellularity was 980/mm³ [116-5,550], the median protein level was 5.67 [1.62-9] g/L and the median CSF glucose level was 2.5 [0-3.4] mmol/L. The in-hospital mortality rate was 23.6%. Community-acquired meningitis isolates were more frequently susceptible to 3GC than isolates from healthcare-associated meningitis (89.2% versus 72%; p=0.04). Comorbidities reported for patients with community-acquired meningitis were mainly diabetes mellitus and liver cirrhosis. In multivariate analysis, focal neurological disorder at the time of diagnosis was the only factor associated with in-hospital mortality (p=0.01).

CONCLUSIONS

Purulent meningitis caused by Klebsiella spp. needs to be considered in patients with community-acquired meningitis and pre-existing conditions, as well as in case of meningitis following neurosurgical procedures.

Insomnia in adults with cystic fibrosis: strong association with anxiety/depression and impaired quality of life

BACKGROUND

While sleep disruption is a common complaint among children with cystic fibrosis (CF), only a few studies have investigated insomnia in adults. The aim of this study was to identify factors associated with insomnia in clinically stable adult CF patients.

METHODS

Twenty-eight CF patients (18M/10F), with a median age of 27 (22-34) (median (interquartile range) years and a median of forced expiratory volume in one second of 72 (39-93) % predicted completed questionnaires on insomnia (Insomnia Severity Index, ISI), sleep quality (PSQI), daytime sleepiness (Epworth), restless legs syndrome (IRLS), pain (NRS), anxiety/depression (HAD) and quality of life (CFQ-R 14+). Respiratory assessment data, including symptoms, sputum analysis, arterial blood gases, 6-min walking test, pulmonary function tests and polysomnographic variables, were also analyzed.

RESULTS

Forty-three percent of patients were insomniac (ISI > 7). Compared with non-insomniac patients (ISI ≤ 7), insomniac patients had more severely impaired quality of life and a higher HAD score: median anxiety score of 9 (8-11) vs 4 (3-6) (p < 0.0001), median depression score of 7 (5-10) vs 1 (1-4) (p < 0.001), with a positive correlation between ISI and HAD anxiety/depression scores (r = 0.702/r = 0.701, respectively, p < 0.0001). Insomnia was also associated with mMRC dyspnea scale ≥ 2, restless legs syndrome, pain and lower SpO₂ during sleep.

CONCLUSIONS

The strong association between insomnia, impaired quality of life and increased HAD score should prompt physicians to be particularly attentive to the management of anxiety and depression in adult CF patients with insomnia.

TRIAL REGISTRATION

On clinicaltrials.gov (NCT02924818, date of registration: October 5, 2016).

Phenotypic and genotypic quinolone resistance in Escherichia coli underlining GyrA83/87 mutations as a target to detect ciprofloxacin resistance

Background

Quinolone resistance (QR) is one component of the MDR emerging in Escherichia coli and is of particular concern given the widespread use of fluoroquinolones.

Objectives

To characterize the QR phenotypes and genotypes in E. coli responsible for bloodstream infections and to propose molecular determinants that could be targeted to predict ciprofloxacin resistance.

Methods

E. coli isolates from blood cultures in three French hospitals were studied for quinolone MICs and characterization of genotypic QR determinants (QRg).

Results

Among 507 isolates tested for MICs, 148 (29.2%) were resistant to quinolones based on EUCAST breakpoints and 143 (28.2%) harboured at least one QRg. QRg were mainly mutations in the QRDR (138 isolates, 27.2%), with 55.8% of these isolates carrying at least three QRDR mutations. gyrA mutations predominated (92.8%) followed by parC (61.6%), parE (32.6%) and gyrB (1.4%) mutations. Only 4.7% of the isolates harboured a plasmid-mediated quinolone resistance (PMQR) gene: aac(6′)-Ib-cr (60.0%) or qnr (qnrS, qnrB) (32.0%). For the first time in France, we reported the qepA4 allele of the plasmid-encoded efflux pump QepA. Only five isolates carried PMQR without a QRDR mutation. The positive predictive value (PPV) for ciprofloxacin resistance was 100% for any QRg and 99.2% for gyrA mutations specifically.

Conclusions

QR observed in E. coli isolates involved in bloodstream infections is still mainly due to QRDR mutations, especially at codons GyrA83/87, which could be used as a molecular target to rapidly detect resistance.

First description of IncX3 NDM-5-producing plasmid within Escherichia coli ST448 in Mali

Carbapenem resistance in Enterobacteriaceae has become an increasingly worrying threat. So far, no epidemiological data regarding NDM-producing enterobacterial isolates has been available on these strains in West Africa. The aim of this study was to seek for carbapenemase-producing Enterobacteriaceae clinical strains isolated in Bamako Teaching Hospital in Mali. Of 50 strains isolated between May 2016 and September 2016, we found a ST448 E. coli harbouring an IncX3 plasmid with bla _NDM-5 embedded in the ΔISAba125-ble _MBL structure. This study reports the first description of NDM-5 in Mali isolated in an undescribed ST E. coli in West Africa.

2134. Differential Changes in Breath Volatile Metabolites to Identify Carbapenem-Resistant Enterobacteriaceae (CRE) in a Murine Pneumonia Model

Background

CRE infections cause significant mortality, in large part because rapid identification of these infections is challenging. We tested the hypothesis that CRE and their isogenic carbapenem-susceptible counterparts have differential metabolic responses to carbapenem therapy.

Methods

We generated isogenic pairs of E. coli, E. cloacae, and K. pneumoniae by inserting a bla_NDM-1-containing plasmid into carbapenem-susceptible E. coli, E. cloacae, and K. pneumoniae. We confirmed phenotypic meropenem (MPM) resistance per CLSI breakpoints for Enterobacteriaceae (MIC ≥4) in the NDM-1⁺ member and susceptibility (MIC≤1) in the NDM-1^- member of each pair. We administered 2 × 10⁸ CFU of each isolate intranasally to 23–28 g male C57BL/6J mice, infecting 6 mice with the NDM-1⁺ member and 6 with the NDM-1⁻ member of each species pair (12 mice per bacterial species). 24 hours after infection, we treated 3 mice in each NDM-1⁺ and NDM-1⁻ bacterial species cohort with MPM over 4 hours, and the other 3 mice in each cohort with saline over 4 hours as controls, confirming adequate infection (a target of 10⁶ CFU/g of lung tissue) in quantitative lung homogenate cultures. We then collected breath samples from each mouse via tracheostomy using a murine ventilator, identifying all volatile metabolites in each sample using thermal desorption-gas chromatography/tandem mass spectrometry. We used Wilcoxon tests to examine differences in metabolite abundance between MPM and saline-treated control mice in the NDM-1⁺ and NDM-1⁻ a member of each species pair, with a two-sided P-value threshold of < 0.1.

Results

Several breath volatile metabolites changed differentially within each NDM-1⁺/NDM-1^- pair, outlined in Table 1 (E. coli), Table 2 (E. cloacae), and Table 3 (K. pneumoniae). Each listed metabolite that changed with MPM did not change with MPM in mice infected with each isogenic counterpart

Conclusion

There are differential in vivo metabolic responses with effective vs. ineffective treatment of mice with pneumonia caused by E. coli, E. cloacae, and K. pneumoniae pairs that are genetically identical other than bla_NDM-1; this differential treatment response can potentially be used to identify these infections.

Disclosures

All authors: No reported disclosures.

Occurrence of Carbapenemase-Producing Klebsiella pneumoniae in Bat Guano

The aim of this study was to screen for the presence of carbapenemase-producing Enterobacteriaceae (CPE) isolates from bat guano in Bejaia, Algeria. Guano samples (n = 110) were collected in Aokas's cave, Bejaia, Algeria, between March and May 2016. Samples were plated on MacConkey agar supplemented with ertapenem (0.5 mg/L) and vancomycin (32 mg/L). The isolates were identified and antimicrobial susceptibility was determined using disk diffusion method. Carbapenemase, extended spectrum β-lactamases, plasmid-mediated AmpC, and plasmid-mediated quinolone resistance genes were studied using PCR and sequencing. Clonal relatedness was studied using multilocus sequence typing (MLST). Two CPE isolates were identified as Klebsiella pneumoniae. PCR and sequencing identified the blaOXA-48 in one K. pneumoniae strain (CS34) and blaKPC-3 in the other strain (CS63). K. pneumoniae CS63 was found to carry bla_TEM-1 and aac(6')-Ib genes. The MLST showed that K. pneumoniae CS63 was assigned to ST512, whereas K. pneumoniae CS34 belonged to ST1878. This is the first description of CPE from bats' guano.

Detection of different classes of carbapenemases: Adaptation and assessment of a phenotypic method applied to Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii, and proposal of a new algorithm

A new phenotypic method for detecting carbapenemases has been adapted (assembling of two MAST® kits, including one that contains faropenem to which a temocillin disk has been added) then assessed using 101 bacterial strains (Enterobacteriaceae with assays on Pseudomonas aeruginosa and Acinetobacter baumannii) including 62 which produce genetically identified carbapenemases. Concerning Carbapenemase-Producing Enterobacteriaceae (CPE), there is 100% sensitivity for Klebsiella pneumoniae carbapenemase (KPC, Ambler class A) and OXA-48 (Ambler class D), and 91% for metallo-beta-lactamase (MBL, Ambler class B), with a 97% sensitivity for all carbapenemases, with a specificity of 100%. The test is also efficient for detecting Pseudomonas aeruginosa carbapenemases (sensitivity between 82 and 100% and 100% specificity). The major innovation is the combined use of faropenem and temocillin for reliable detection (excellent performance with 100% sensitivity and specificity) of OXA-48. This study has led to the development of a new algorithm to detect the different classes of carbapenemases, for first-line diagnosis, by combining this modified MAST® test with immunochromatographic methods and molecular biology techniques.

Amoxicillin-tolerant Pasteurella multocida strain isolated from chronic dermohypodermitis after suboptimal exposure to amoxicillin is not associated with reduced growth rate

Pasteurella multocida is rarely observed in human chronic infections. A Pasteurella multocida strain was isolated from a skin biopsy of chronic dermohypodermitis in a 21-year-old woman without an immunocompromised state. As this strain was viable one month after a cat scratch despite treatment by amoxicillin-clavulanic acid, we compared this strain's growth rate, amoxicillin Minimal Inhibitory and Bactericidal Concentrations (MIC and MBC), resistance to serum and ability to activate neutrophil granulocytes with those of control strains isolated during acute infections in humans without previous antibiotics exposure. This particular strain was not more resistant to serum and did not induce a lower phagocytic activity than control strains. It did not grow more slowly than control strains even after suboptimal exposure to amoxicillin. This particular strain was tolerant to amoxicillin but tolerance did not appear sufficient alone for the induction of a chronic infection in a host without an immunocompromised state.

Carriage of ESBL-producing Enterobacteriaceae in French hospitals: the PORTABLSE study

BACKGROUND

Currently, contact precautions are recommended for patients colonized or infected with extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE). Recent studies have challenged this strategy. This study aimed to assess the rate of ESBL-PE faecal carriage among hospitalized patients according to type of hospital ward, and to identify risk factors associated with carriage.

METHODS

A point prevalence study was conducted in five different types of hospital ward [medical, surgical, intensive care unit (ICU), after care and rehabilitation, and geriatric] in eight French hospitals. All patients included in the study provided a fresh stool sample.

RESULTS

In total, 554 patients were included in the study, with a median age of 73 years (range 60-82 years). The overall faecal carriage rate of ESBL-PE was 17.7%. The most frequently encountered species among ESBL-PE was Escherichia coli (71.4%), followed by Klebsiella pneumoniae (14.3%). Risk factors associated with ESBL-PE faecal carriage on univariate analysis were: living in the Paris region (P<0.01) and hospitalization on a geriatric ward (P<0.01). Interestingly, the cumulative duration of hospital stay before screening was not associated with a significantly higher prevalence of ESBL-PE carriage, regardless of ward type. The ESBL-PE colonization rate was much higher for patients hospitalized on geriatric wards (28.1%) and ICUs (21.7%) compared with those for patients hospitalized on surgical wards (14.8%), medical wards (12.8%) or aftercare and rehabilitation (11.2%).

CONCLUSION

The overall prevalence of ESBL-PE faecal carriage was 17.7%, with only 21% of patients identified previously as carriers. The delay between admission and screening was not associated with an increase in ESBL-PE faecal carriage.

New in vivo model to analyse the expression of angiogenic genes in the borders of a cleft lip

Defects in the fusion of facial buds can result from an anomaly in tissue development or apoptosis, or both. Our working hypothesis was that anomalies in the development of tissues could be caused by a genetic angiogenic defect. Our main objective was to design a reproducible experimental model to study the expression of angiogenic genes in the borders of cleft lips with or without cleft palate. We therefore prospectively studied seven non-syndromic patients, three with a cleft lip (2 right, 1 left), and four with a cleft lip and palate (1 bilateral, 2 right, 1 left), with no CGH (comparative genomic hybridisation) array, who had primary operations to repair their clefts. We also used four controls (cultured fibroblasts from healthy skin samples). The mean (range) age at operation was 44 (13-77) days. We studied the lateral and medial borders histologically and did qPCR (quantitative real-time polymerase chain reaction) analysis for gene expression with 22 genes of interest (and two housekeeping genes) involved in cleft lip and angiogenesis. The qPCR analysis found significant (p<0.05) overexpression of eight genes in the medial border and seven in the lateral border, and underexpression of nine genes in the medial, and ten in the lateral border. The difference in expression between the two borders was not significant. This preliminary study has enabled us to develop a new method to analyse the expression of angiogenic genes in the borders of cleft lips.

[Surgical management of animal bites in children]

Children represent a population at risk, because of their short size, their naivety and their attraction to animals. The face and hands are the most specific locations in young children. Wounds are often multiple. In more than half the cases, the child knows the animal, which are dogs and cats by frequency argument. The bite episode occurs mostly when the child is alone with the pet without direct supervision, while playing or stroking the animal. As in all bites, pediatric lesions are infectious, functional and aesthetic emergencies, but the goal of this work was primarily to make a point on principles of surgical management of animal bites in children, highlighting pediatric specificities. Animal bites require psychological, anesthetic and surgical treatment, adapted to the child, in a specialized structure. Hospitalization and general anesthesia are more frequent in children. Any suspicion of mistreatment (and/or abuse) should lead to the child's hospitalization, even if wounds do not justify monitoring in a surgical environment. Emergency surgery is essential to limit functional and aesthetic consequences. The healing capacities of the child and the frequent lack of co-morbidity allow a conservative surgical treatment with suture, repositioning skin flaps and controlled healing in the first place. Immobilization, drainage, and antibiotics will complete the surgery. The healing process, however, leads to a specific management during scar remodeling phase and growth. Psychological care of the child and parents should not be forgotten, and has to start at the same time as surgical treatment at in acute phase.

Antibiotic resistance and virulence: Understanding the link and its consequences for prophylaxis and therapy

"Antibiotic resistance is usually associated with a fitness cost" is frequently accepted as common knowledge in the field of infectious diseases. However, with the advances in high-throughput DNA sequencing that allows for a comprehensive analysis of bacterial pathogenesis at the genome scale, including antibiotic resistance genes, it appears that this paradigm might not be as solid as previously thought. Recent studies indicate that antibiotic resistance is able to enhance bacterial fitness in vivo with a concomitant increase in virulence during infections. As a consequence, strategies to minimize antibiotic resistance turn out to be not as simple as initially believed. Indeed, decreased antibiotic use may not be sufficient to let susceptible strains outcompete the resistant ones. Here, we put in perspective these findings and review alternative approaches, such as preventive and therapeutic anti-bacterial immunotherapies that have the potential to by-pass the classic antibiotics.