Phylogenetic Structure and Comparative Genomics of Multi-National Invasive Haemophilus influenzae Serotype a Isolates.

Recent reports have indicated a rise of invasive disease caused by Haemophilus influenzae serotype a (Hia) in North America and some European countries. The whole-genome sequences for a total of 410 invasive Hia isolates were obtained from 12 countries spanning the years of 1998 to 2019 and underwent phylogenetic and comparative genomic analysis in order to characterize the major strains causing disease and the genetic variation present among factors contributing to virulence and antimicrobial resistance. Among 410 isolate sequences received, 408 passed our quality control and underwent genomic analysis. Phylogenetic analysis revealed that the Hia isolates formed four genetically distinct clades: clade 1 (n = 336), clade 2 (n = 13), clade 3 (n = 3) and clade 4 (n = 56). A low diversity subclade 1.1 was found in clade 1 and contained almost exclusively North American isolates. The predominant sequence types in the Hia collection were ST-56 (n = 125), ST-23 (n = 98) and ST-576 (n = 51), which belonged to clade 1, and ST-62 (n = 54), which belonged to clade 4. Clades 1 and 4 contained predominantly North American isolates, and clades 2 and 3 predominantly contained European isolates. Evidence of the presence of capsule duplication was detected in clade 1 and 2 isolates. Seven of the virulence genes involved in endotoxin biosynthesis were absent from all Hia isolates. In general, the presence of known factors contributing to ß-lactam antibiotic resistance was low among Hia isolates. Further tests for virulence and antibiotic susceptibility would be required to determine the impact of these variations among the isolates.

Carbapenemase-producing Enterobacteriaceae in an inpatient post-acute care facility: Impact on time to functional recovery.

BACKGROUND: The carriage of carbapenemase-producing Enterobacteriaceae (CPE) might lengthen the time to functional recovery (TTFR) for inpatients in post-acute care (PAC) units. OBJECTIVE: We aimed to assess the impact of CPE carriage on TTFR in a PAC facility. METHODS: This 2-year retrospective cohort study included 20 CPE-positive patients and 54 CPE-negative patients admitted to 3 PAC units (general, orthopaedic and neurological rehabilitation units) in a teaching hospital from January 2017 to December 2019. Potential risk factors and demographic data were collected from patients' medical records, the French national hospital discharge database, and the hospital's CPE surveillance database. Functional recovery was defined as the median difference in functional independence measure (FIM) between admission and discharge from each unit. Survival analysis and multiple Cox regression models were used to predict the TTFR and identify factors associated with functional recovery. RESULTS: The overall median [interquartile range] TTFR was 50 days [36-66]. Longer median TTFR was associated with CPE carriage (63 vs 47 days in the CPE-negative group; adjusted hazard ratio (aHR) 0.35, 95% CI 0.13-0.97) and presence of a peripheral venous catheter (aHR 3.51, 1.45-8.46); shorter TTFR was associated with admission to an orthopaedic versus general rehabilitation unit (aHR 3.11, 1.24-7.82). CONCLUSIONS: CPE carriage in inpatient PAC facilities was associated with long TTFR. Further studies are needed to explore the mechanisms involved in these adverse events and to identify possible preventive measures.

SARS-CoV-2 infection long time after full vaccination is related to a lack of neutralizing antibodies.

SARS-CoV-2 infections after COVID-19 vaccination are not unexpected, but those occurring more than 14 days after second vaccine dose need to be investigated. We describe a well-characterized infection which occurred almost 2 months after full vaccination, and provide the evidence of a link with a lack of anti-SARS-CoV-2 neutralizing antibodies.

How to improve donor skin availability: Pragmatic procedures to minimize the discard rate of cryopreserved allografts in skin banking.

BACKGROUND: Microbial contamination of human skin allografts is a frequent cause of allograft discard. Our purpose was to evaluate the discard rate of skin bank contaminated allografts and specific procedures used to reduce allograft contamination without affecting safety. METHODS: We conducted at the Lille Tissue Bank a retrospective study of all deceased donors (n = 104) harvested from January 2018 to December 2018. Skin procurement was split into 3 zones: the back of the body and the two legs that were processed separately. It represented 433 cryopreserved skin allograft pouches of approximatively 500 cm² each. Donors were almost equally split between brain-dead (53%, 55/104) and cadaveric (47%, 49/104) donors. RESULTS: Out of all donors, 42 (40.5%) had at least one sampling zone with a positive microbiological test resulting in 106 (24%) contaminated skin pouches. The contamination rate did not vary according to the harvested zone or type of donor. Traumatic deaths showed significantly less contamination rates than other death types (p < 0.05). Contamination rate decreased with time spent in the antibiotic solution. The risk of having contaminated allografts was five-fold higher when the skin spent less than 96 h in the antibiotic cocktail (p < 0.05). According to our validation protocol, most donors (32/42, 76%) had skin allografts contaminated with bacteria (mainly Staphylococcus spp) compatible with clinical use. No recipient infection was recorded as a result of skin graft contaminated with saprophytic or non-pathogenic germs. By harvesting 3 separate zones per donor, the total surface area for clinical use increased by 53% for contaminated donors. Overall, the proportion of contamination-related discarded allografts was 3.2% (14/433 of pouches). CONCLUSION: Few simple pragmatic measures (including skin incubation in the antibiotic bath for at least 96 h at 4 °C, splitting the skin harvesting areas to minimize the risk of cross-infection and clinical use of allografts contaminated with saprophytic and non-pathogenic germs) can reduce the discard rate of contaminated allografts without affecting clinical safety.

Prospective evaluation of the Amplidiag® CarbaR+VRE assay for direct screening of carbapenemase producing gram-negative bacilli from rectal swabs.

This prospective study evaluated the ability of the qPCR Amplidiag® CarbaR+VRE assay to detect Carbapenemase-producing Gram-negative bacilli (CP-GNB) directly on 1830 rectal swabs extracted using the fully automated platform Amplidiag® Easy instrument. The Amplidiag® CarbaR+VRE assay gave a positive signal for 94 rectal swabs, whereas only 70 grew with CP-GNB on chromogenic media including 4 VIM-producing P. aeruginosa, 8 OXA-23-producing A. baumannii and 58 carbapenemase-producing Enterobacteriaceae. All the CP-GNB culture positive were detected by the Amplidiag® CarbaR+VRE assay. Twenty-four qPCR-positive and culture-negative samples were further investigated using targeted PCRs and subsequent DNA sequencing. Seventeen and 7 of these were positive and negative with PCR/DNA sequencing, respectively. Taken together, the Amplidiag® CarbaR+VRE could detect carbapenemases directly from rectal swabs in 3h 30 using a fully automated platform and showed high biological performances (sensitivity, specificity, and negative and positive predictive values were 100%, 98.6%, 100%, and 74.5%, respectively).

Case Report: Ocular Microsporidiosis: Case in a Patient Returning from India and Review of the Literature.

Microsporidia are protists close to the kingdom of fungi that may cause eye infections. Most cases are reported in Asia and affect both immunocompromised and immunocompetent patients. Here, we report a rare case of microsporidial keratoconjunctivitis in an immunocompetent French patient 3 weeks after returning from India. In our patient, Weber trichrome staining of conjunctival scrapings revealed rounded elements approximately 1-3 µm in size. Conventional polymerase chain reaction analysis by ribosomal RNA subunit sequencing showed 100% identity with Vittaforma corneae. Treatment by corneal debridement combined with fluoroquinolone eye drops allowed complete resolution of the lesions. Although rare, ocular microsporidiosis should be investigated in a patient who is native to Asia or has returned from an endemic area and presents with keratoconjunctivitis of undetermined etiology.

Is a chlorine dioxide wiping procedure suitable for the high-level disinfection of nasendoscopes?

BACKGROUND: Nasendoscopes are widely used in the outpatient ENT setting. Their reprocessing requires high-level disinfection (HLD). Recently, a wiping procedure using chlorine dioxide (ClO2) has been proposed as an alternative to HLD traditional procedures. OBJECTIVE: To assess the effectiveness of the HLD wiping procedure versus soaking procedure on a contaminated nasendoscope. METHOD: A nasendoscope was contaminated with four strains of bacteria and Bacillus subtilis spores. After HLD either with the wiping procedure or with the soaking procedure (PA), the reduction of the initial contamination was determined. FINDINGS: The wiping procedure with ClO2 displayed more than 5 log reduction for vegetative bacteria after 30 s contact time (CT) and 4 log reduction on B. subtilis spores after 2 min CT. The soaking procedure with PA displayed similar results on planktonic bacteria after 10 min CT but the log reduction of B. subtilis remained below 4. CONCLUSION: The ClO2 wiping procedure showed bactericidal and sporicidal efficacy on a contaminated nasendoscope in a shorter time compared to the PA soaking procedure. Thus, ClO2 wiping procedure might be considered as an alternative to the traditional HLD procedure for nasendoscopes.

Identification of microorganisms grown on chromogenic media by MALDI-TOF MS.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and chromogenic media are widely used in clinical microbiology laboratories to facilitate the rapid selection and identification of pathogens. The aim of this study was to evaluate whether usage of chromogenic media limits the diagnostic performance of MALDI-TOF MS for microbial identification. A total of 386 microorganisms collected and analyzed at five laboratories were included. Isolates were cultured on relevant chromogenic media and non-selective agar plates in parallel and identified using the Bruker MALDI-TOF MS. Among the tested isolates, no misidentification was recorded and there was no medium-related difference in the identification level. However, score values were overall slightly but significantly lower for isolates grown on chromogenic media. In conclusion, the use of chromogenic culture media tested here had no relevant impact on MALDI-TOF MS performance for diagnostic purposes.

Molecular Characterization of Carbapenem-Nonsusceptible Enterobacterial Isolates Collected during a Prospective Interregional Survey in France and Susceptibility to the Novel Ceftazidime-Avibactam and Aztreonam-Avibactam Combinations.

An interregional surveillance program was conducted in the northwestern part of France to determine the prevalence of carbapenem-nonsusceptible Enterobacteriaceae (CNSE) isolates and their susceptibility to ceftazidime-avibactam and aztreonam-avibactam combinations. Nonduplicate CNSE clinical isolates were prospectively collected from six hospitals between June 2012 and November 2013. MICs of ceftazidime and aztreonam, alone or combined with a fixed concentration of avibactam (4 µg/ml), and those of carbapenems (comparator agents) were determined. MICs of ertapenem in combination with phenylalanine arginine-naphthylamide dihydrochloride (PAßN) were also determined to assess active efflux. Genes encoding carbapenemases, plasmid-mediated AmpC enzymes, extended-spectrum ß-lactamases (ESBLs), and major outer membrane proteins (OMPs) were amplified and sequenced. OMPs were also extracted for SDS-PAGE analysis. Among the 139 CNSE isolates, mainly Enterobacter spp. and Klebsiella pneumoniae, 123 (88.4%) were ertapenem nonsusceptible, 12 (8.6%) exhibited reduced susceptibility to all carbapenems, and 4 Proteeae isolates (2.9%) were resistant to imipenem. Carbapenemase production was detected in only two isolates (producing OXA-48 and IMI-3). In contrast, OMP deficiency, in association with AmpCs and/or ESBLs (mainly CTX-M-9, SHV-12, and CTX-M-15), was largely identified among CNSE isolates. The ceftazidime-avibactam and aztreonam-avibactam combinations exhibited potent activity against CNSE isolates (MIC50/MIC90, 1/1 µg/ml and 0.5/0.5 µg/ml, respectively) compared to that of ceftazidime and aztreonam alone (MIC50/MIC90, 512/512 µg/ml and 128/512 µg/ml, respectively). This study reveals the in vitro activity of ceftazidime-avibactam and aztreonam-avibactam combinations against a large collection of porin-deficient enterobacterial isolates that are representative of the CNSE recovered in the northern part of France.

Proposed reclassification of Pasteurella lymphangitidis Sneath & Stevens 1990 as Yersinia pseudotuberculosis.

The 16S rRNA gene sequences of Pasteurella lymphangitidis, Yersinia pseudotuberculosis and Yersinia pestis were found to be identical and multilocus sequence analysis could not discriminate between the three species. The susceptibility to a Y. pseudotuberculosis phage and the presence of the Y. pseudotuberculosis-specific invasin gene in P. lymphangitidis indicate that the latter should be reclassified as Y. pseudotuberculosis.

Septic arthritis caused by noncapsulated Haemophilus influenzae.

Since the introduction of type b Haemophilus influenzae vaccination, noncapsulated H. influenzae has become responsible for most cases of invasive H. influenzae diseases. In our two cases of septic arthritis, we isolated strains with ß-lactamase-positive amoxicillin-clavulanate resistance (BLPACR). Thus, the increasing prevalence of BLPACR should be taken into account when empirical therapy is chosen for septic arthritis.

CHROMagar Yersinia, a new chromogenic agar for screening of potentially pathogenic Yersinia enterocolitica isolates in stools.

CHROMagar Yersinia (CAY) is a new chromogenic medium for the presumptive detection of virulent Yersinia enterocolitica in stools. Based on a comparative analysis of 1,494 consecutive stools from hospitalized patients, CAY was found to be just as sensitive as the reference medium (cefsulodin-irgasan-novobiocin agar) but was significantly more specific and had a very low false-positive rate. CAY reduces the workload (and thus costs) for stool analysis and can therefore be recommended for routine laboratory use.

NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer.

Instability in the composition of gut bacterial communities (dysbiosis) has been linked to common human intestinal disorders, such as Crohn's disease and colorectal cancer. Here, we show that dysbiosis caused by Nod2 deficiency gives rise to a reversible, communicable risk of colitis and colitis-associated carcinogenesis in mice. Loss of either Nod2 or RIP2 resulted in a proinflammatory microenvironment that enhanced epithelial dysplasia following chemically induced injury. The condition could be improved by treatment with antibiotics or an anti-interleukin-6 receptor-neutralizing antibody. Genotype-dependent disease risk was communicable via maternally transmitted microbiota in both Nod2-deficient and WT hosts. Furthermore, reciprocal microbiota transplantation reduced disease risk in Nod2-deficient mice and led to long-term changes in intestinal microbial communities. Conversely, disease risk was enhanced in WT hosts that were recolonized with dysbiotic fecal microbiota from Nod2-deficient mice. Thus, we demonstrated that licensing of dysbiotic microbiota is a critical component of disease risk. Our results demonstrate that NOD2 has an unexpected role in shaping a protective assembly of gut bacterial communities and suggest that manipulation of dysbiosis is a potential therapeutic approach in the treatment of human intestinal disorders.

A Staphylococcus aureus small RNA is required for bacterial virulence and regulates the expression of an immune-evasion molecule.

Staphylococcus aureus, a pathogen responsible for hospital and community-acquired infections, expresses many virulence factors under the control of numerous regulatory systems. Here we show that one of the small pathogenicity island RNAs, named SprD, contributes significantly to causing disease in an animal model of infection. We have identified one of the targets of SprD and our in vivo data demonstrate that SprD negatively regulates the expression of the Sbi immune-evasion molecule, impairing both the adaptive and innate host immune responses. SprD interacts with the 5' part of the sbi mRNA and structural mapping of SprD, its mRNA target, and the 'SprD-mRNA' duplex, in combination with mutational analysis, reveals the molecular details of the regulation. It demonstrates that the accessible SprD central region interacts with the sbi mRNA translational start site. We show by toeprint experiments that SprD prevents translation initiation of sbi mRNA by an antisense mechanism. SprD is a small regulatory RNA required for S. aureus pathogenicity with an identified function, although the mechanism of virulence control by the RNA is yet to be elucidated.

Remote control of intestinal tumorigenesis by innate immunity.

Chronic intestinal inflammation has been linked to the development of colorectal cancer. Recent studies suggest that during chronic inflammation, the innate immune system may facilitate colon tumorigenesis in genetically predisposed individuals in response to certain indigenous microorganisms and/or cell remnants. In these individuals, therapeutic approaches that reroute the innate immune system's inflammatory and antimicrobial activities might help prevent colon tumorigenesis and metastasis.

[Comparison of antimicrobial susceptibility of 1,217 Escherichia coli isolates from women with hospital and community-acquired urinary tract infections]. / Comparaison de la sensibilité aux antibiotiques de 1,217 isolats consécutifs de Escherichia coli responsables d'infections urinaires féminines en ville et à l'hôpital.

INTRODUCTION: The treatment of urinary tract infection (UTI) in women is based mainly on empirical antibiotic therapy. It requires up-to-date knowledge of the susceptibility patterns of the bacteria most commonly identified in that setting. The aim of this prospective study was to measure the antibiotic susceptibility of Escherichia coli isolates responsible for UTIs in women from a single area and to compare it in hospital and community settings. MATERIALS AND METHODS: From May 2003 through April 2004, UTI was diagnosed in 1838 women around Rennes (France), 893 of them inpatients admitted to the teaching hospital and 945 outpatients in the community. We determined the susceptibility to 7 antibiotics of the resulting 1217 E. coli isolates. RESULTS: E. coli resistance rates in hospitalized and community patients were respectively 47.9% and 39.2% for aminopenicillins, 47.3% and 25.4% for coamoxiclav, 19.2% and 14.1% for cotrimoxazole, 14.3% and 5.7% for first-generation quinolones, and 8.9% and 3.7% for fluoroquinolones. All these rates were significantly higher among hospitalized patients (p<0.05). Conversely, resistance to injectable third-generation cephalosporins and fosfomycin was similar and infrequent in both groups. CONCLUSION: Comparisons with previous data show that activity of third-generation cephalosporins and fosfomycin on E. coli appears unchanged, in contrast to the increased resistance rates to other antibiotics usually prescribed for UTI.