Evolution, control and success of combination therapy with Ampicilin-sulbactam/Ceftazidime-Avibactam during a Carbapenem-Resistant Acinetobacter baumannii outbreak in burn Intensive Care Unit.

We present our findings on interpatient transmission, epidemic control measures, and the outcomes of a series of ten critically ill burn patients who were either colonized or infected with carbapenem-resistant Acinetobacter baumannii (CRAB). None of the five infected patients achieved clinical cure, and all experienced relapses. Microbiological failure was observed in 40% of the infected patients. The isolated CRAB strains were found to carry blaOXA-23 and armA resistance genes. Despite the lack of clinical cure, all five infected patients survived and were discharged from the Burn Intensive Care Unit.

Unmasking Bartonella henselae infection in the shadows of long COVID thanks to clinical metagenomics.

The diagnosis of long COVID often relies on symptoms post-COVID-19, occasionally lacking biological evidence. This case study illustrates how investigating long COVID uncovered an underlying bartonellosis through clinical metagenomics. Following mild COVID-19, a 26-year-old woman experienced persistent symptoms during 5 months, including axillary adenopathy. Pathological examination, 16 S rRNA PCR, and clinical metagenomic analysis were done on an adenopathy biopsy. The latter revealed Bartonella henselae DNA and RNA. Treatment with clarithromycin improved symptoms. This case underscores the relevance of clinical metagenomics in diagnosing hidden infections. Post-COVID symptoms warrant thorough investigation, and bartonellosis should be considered in polyadenopathy cases, regardless of a recent history of cat or flea exposures.

Detection of CTX-M-15 ESBL in XDR Haemophilus parainfluenzae from a urethral swab.

OBJECTIVES: Haemophilus parainfluenzae is an opportunistic pathogen causing respiratory tract infection and sexually transmitted diseases. The emergence of multidrug resistance in this species is particularly worrisome, especially since the recent description of CTX-M-15 ESBL-producing isolates in Spain. The aim of this study was to characterize a CTX-M-15-producing H. parainfluenzae clinical isolate, HP01, obtained from a urethral swab. METHODS: MICs were determined with gradient strips for this isolate. Hydrolysis assays were performed with the ß LACTA test. Genomic DNA from HP01 was subjected to Illumina and Oxford Nanopore sequencing to investigate the genetic environment of blaCTX-M-15. Phylogenetic analysis was performed with available H. parainfluenzae genomes from the NCBI database, including CTX-M-15 producers. RESULTS: HP01, an XDR isolate, was resistant to penicillin, third-generation cephalosporins, fluoroquinolones, macrolides, cyclines and co-trimoxazole and susceptible only to carbapenems and rifampicin. HP01 carried blaTEM-1, blaCTX-M-15, tet(M), catS and mef(E)/mel and harboured amino acid substitutions in PBP3, PBP5, GyrA, ParC and FolA implicated in resistance. Genomic analysis revealed that blaCTX-M-15 was carried by a Tn3-like transposon inserted into a novel integrative and conjugative element (ICE), ICEHpaSLS, present on the chromosome and belonging to the ICEHin1056 family described in Haemophilus influenzae. The tet(M)-MEGA element was also detected on the chromosome. No plasmid was found. The phylogenetic analysis showed that four H. parainfluenzae producing CTX-M-15 clustered in the same clade. CONCLUSIONS: Here we report the description of an XDR H. parainfluenzae producing blaCTX-M-15 isolated from a urethral swab. The blaCTX-M-15 gene was inserted into an ICE structure similar to those recently described in CTX-M-15 producers in Spain. The emergence of XDR H. parainfluenzae producing blaCTX-M-15 is a matter of great concern. Careful surveillance is required to prevent its spread.

Two cases of extensively drug-resistant (XDR) Neisseria gonorrhoeae infection combining ceftriaxone-resistance and high-level azithromycin resistance, France, November 2022 and May 2023.

We report two extensively drug-resistant (XDR) Neisseria gonorrhoeae (NG) isolates combining high-level resistance to azithromycin and resistance to ceftriaxone, obtained in France from two heterosexual patients, one of whom returned from Cambodia. Whole genome sequencing identified MLST ST16406, the mosaic penA-60.001 which caused ceftriaxone resistance in the internationally spreading FC428 clone, and the A2059G mutation in the 23S rRNA gene. The NG isolates F93 and F94 were related to XDR isolates detected in Austria and the United Kingdom in 2022.

Performance evaluation of a PCR panel (FilmArray® Pneumonia Plus) for detection of respiratory bacterial pathogens in respiratory specimens: A systematic review and meta-analysis.

BACKGROUND: Accuracy and timing of antibiotic therapy remain a challenge for lower respiratory tract infections. New molecular techniques using Multiplex Polymerase Chain Reaction, including the FilmArray® Pneumonia Plus Panel [FAPP], have been developed to address this. The aim of this study is to evaluate the FAPP diagnostic performance for the detection of the 15 typical bacteria of the panel from respiratory samples in a meta-analysis from a systematic review. METHODS: We searched PubMed and EMBASE from January 1, 2010, to December 31, 2022, and selected any study on the FAPP diagnostic performance on respiratory samples compared to the reference standard, bacterial culture. The main outcome was the overall diagnostic accuracy with sensitivity and specificity. We calculated the log Diagnostic Odds Ratio and analyzed performance for separate bacteria, antimicrobial resistance genes, and according to the sample type. We also reported the FAPP turnaround time and the out-of-panel bacteria number and species. This study is registered with PROSPERO (CRD42021226280). RESULTS: From 10 317 records, we identified 30 studies including 8 968 samples. Twenty-one were related to intensive care. The overall sensitivity and specificity were 94% [95% Confidence Interval (CI) 91-95] and 98% [95%CI 97-98], respectively. The log Diagnostic Odds Ratio was 6.35 [95%CI 6.05-6.65]. 9.3% [95%CI 9.2-9.5] of bacteria detected in culture were not included in the FAPP panel. CONCLUSION: This systematic review reporting the FAPP evaluation revealed a high accuracy. This test may represent an adjunct tool for pulmonary bacterial infection diagnostic and antimicrobial stewardship. Further evidence is needed to assess the impact on clinical outcome.

In vitro activity of apramycin against 16S-RMTase-producing Gram-negative isolates.

OBJECTIVES: Apramycin is an aminoglycoside (AG) with a unique structure that is little affected by plasmid-mediated mechanisms of AG resistance, including most AG-modifying enzymes and 16S rRNA methyltransferases (16S-RMTases). We evaluate the activity of apramycin against a collection of 16S-RMTase-producing isolates, including Enterobacterales, non-fermenting bacteria, and carbapenemase producers. METHODS: In total, 164 non-duplicate 16S-RMTase-producing isolates, including 84 Enterobacterales, 53 Acinetobacter baumannii and 27 Pseudomonas aeruginosa isolates, were included in the study. Whole-genome sequencing (WGS) was performed on all isolates with Illumina technology. The minimum inhibitory concentration (MIC) of apramycin was determined by broth microdilution with customized Sensititre plates (Thermo Fisher Scientific, Dardilly, France). RESULTS: We found that 95% (156/164) of the 16S-RMTase-producing isolates were susceptible to apramycin, with a MIC50 of 4 mg/L and a MIC90 of 16 mg/L, respectively. Resistance rates were higher in P. aeruginosa (11%) than in A. baumannii (4%) or Enterobacterales (4%) (P < 0.0001 for each comparison). Eight isolates were resistant to apramycin, including one isolate with an MIC >64 mg/L due to the acquisition of the aac(3)-IV gene. The genetic environment of the aac(3)-IV gene was similar to that in the pAH01-4 plasmid of an Escherichia coli isolate from chicken in China. CONCLUSION: Resistance to apramycin remains rare in 16S-RMTase-producing isolates. Apramycin may, therefore, be an interesting alternative treatment for infections caused by 16S-RMTase and carbapenemase producers.

Multicenter Evaluation of the FilmArray Blood Culture Identification 2 Panel for Pathogen Detection in Bloodstream Infections.

The FilmArray Blood Culture Identification 2 panel (BCID2; bioMérieux) is a fully automated PCR-based assay for identifying bacteria, fungi, and bacterial resistance markers in positive blood cultures (BC) in about 1 h. In this multicenter study, we evaluated the performance of the BCID2 panel for pathogen detection in positive BC. Conventional culture and BCID2 were performed in parallel at four tertiary-care hospitals. We included 152 positive BC-130 monomicrobial and 22 polymicrobial cultures-in this analysis. The BCID2 assay correctly identified 90% (88/98) of Gram-negative and 89% (70/79) of Gram-positive bacteria. Five bacterial isolates targeted by the BCID2 panel and recovered from five positive BC, including three polymicrobial cultures, were missed by the BCID2 assay. Fifteen isolates were off-panel organisms, accounting for 8% (15/182) of the isolates obtained from BC. The mean positive percent agreement between the BCID2 assay and standard culture was 97% (95% confidence interval, 95 to 99%), with agreement ranging from 67% for Candida albicans to 100% for 17 targets included in the BCID2 panel. BCID2 also identified the blaCTX-M gene in seven BC, including one for which no extended-spectrum ß-lactamase (ESBL)-producing isolate was obtained in culture. However, it failed to detect ESBL-encoding genes in three BC. Two of the 18 mecA/C genes detected by the BCID2 were not confirmed. No carbapenemase, mecA/C, or MREJ targets were detected. The median turnaround time was significantly shorter for BCID2 than for culture. The BCID2 panel may facilitate faster pathogen identification in bloodstream infections. IMPORTANCE Rapid molecular diagnosis combining the identification of pathogens and the detection of antibiotic resistance genes from positive blood cultures (BC) can improve the outcome for patients with bloodstream infections. The FilmArray BCID2 panel, an updated version of the original BCID, can detect 11 Gram-positive bacteria, 15 Gram-negative bacteria, 7 fungal pathogens, and 10 antimicrobial resistance genes directly from a positive BC. Here, we evaluated the real-life microbiological performance of the BCID2 assay in comparison to the results of standard methods used in routine practice at four tertiary care hospitals.

Metagenomic next-generation sequencing restores the diagnosis of a rare infectious complication of B cell depletion.

A 45-year-old female patient receiving rituximab for B cell non-Hodgkin follicular lymphoma presented unexplained recurrent fever, abdominal discomfort, and pollakiuria. We performed shotgun metagenomic sequencing from peri-kidney collection that identified a co-infection with Mycoplasma hominis and Ureaplasma urealyticum. The patient recovered with sequelae after appropriate antibiotic treatment was given.

Identification of Streptomyces spp. in a Clinical Sample: Always Contamination? Results of a French Retrospective Study.

Background: Streptomyces are environmental gram-positive bacilli that can cause ubiquitous mycetoma and, more rarely, invasive infections. We describe the clinical relevance of Streptomyces spp. identified in human samples and characteristics of patients with invasive Streptomyces infections. Methods: We conducted a retrospective (2006-2017) study of Streptomyces isolates identified in clinical samples in French microbiology laboratories. Streptomyces genus was confirmed by a specific 16S rRNA polymerase chain reaction, and antibiotic susceptibility testing was performed by disk diffusion and trimethoprim-sulfamethoxazole minimum inhibitory concentration (E-test) if resistance was suspected. Patient characteristics, treatments, and outcomes were collected. Invasive infection was defined as a positive culture from a sterile site with signs of infection but without cutaneous inoculation. Results: Of 137 Streptomyces isolates, all were susceptible to amikacin (113/113) and linezolid (112/112), and 92.9% to imipenem (105/113). Using disk diffusion, 50.9% (57/112) of isolates were susceptible to trimethoprim-sulfamethoxazole, but most of the apparently resistant isolates (25/36, 69.4%) tested by E-test were ultimately classified as susceptible. Clinical data were obtained for 63/137 (45.9%) isolates: 30 (47.6%) invasive infections, 8 (12.7%) primary cutaneous infections, 22 (34.9%) contaminations, 3 (4.7%) respiratory colonization. Patients with invasive infection were more frequently receiving corticosteroids than patients without invasive infection (11/30, 36.7%, vs 2/25, 8.0%; P = .03), and at 6-month follow-up, 14 of them were cured, 3 had relapsed, 4 were dead, and 9 were lost to follow-up. Conclusions: Half of the clinical samples that grew Streptomyces were from patients with invasive infection. In that case, antimicrobial therapy should include 1 or 2 antibiotics among linezolid, amikacin, or imipenem.

Clinical performance of four multiplex real-time PCR kits detecting urogenital and sexually transmitted pathogens.

OBJECTIVES: We evaluated the clinical performances of four multiplex real-time PCR commercial kits for the detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium and Trichomonas vaginalis: the STI PLUS ELITe MGB kit (ELITechGroup), N. gonorrhoeae/C. trachomatis/M. genitalium/T.vaginalis Real-TM kit (Sacace Biotechnologies), Allplex STI Essential kit (Seegene), and FTD Urethritis Plus kit (Fast-Track Diagnostics). METHODS: The kit performance for C. trachomatis, N. gonorrhoeae, M. genitalium and T. vaginalis detection was compared to that of the cobas CT/NG and TV/MG kits (Roche Diagnostics) using 425 samples, mainly urine and cervicovaginal, throat and rectal swabs. Detection of Ureaplasma parvum, U. urealyticum and Mycoplasma hominis were compared to that of in-house TaqMan PCRs. RESULTS: The four kits showed good performances for the detection of C. trachomatis. They all presented a low positive agreement for the detection of M. genitalium and T. vaginalis (ranges 63.3-74.1% and 51.2-68.4%, respectively) compared to the cobas MG/TV kit. The Seegene and Sacace kits showed additional low positive agreement for the detection of N. gonorrhoeae (71.2%, 95%CI 61.8-79.0 and 63.1%, 95%CI 53.5-71.8, respectively). We observed a slight but significant lower negative agreement for N. gonorrhoeae detection using the ELITechGroup kit (92.5%, 89.1-94.9) and for M. genitalium detection using the Fast-Track kit (93.2%, 89.6-95.7) compared to other kits. CONCLUSION: Multiplex real-time PCR kits are convenient methods for the detection of several pathogens associated with sexually transmitted infections (STIs) in a single step, but colonizing Ureaplasma spp. and M. hominis species should not be included in these kits. Users should be aware of the weak performance of some kits for the detection of M. genitalium and T. vaginalis.

Azithromycin Resistance in Shiga Toxin-Producing Escherichia coli in France between 2004 and 2020 and Detection of mef(C)-mph(G) Genes.

We described and characterized Shiga-toxin-producing Escherichia coli (STEC) strains with high levels of resistance to azithromycin isolated in France between 2004 and 2020. Nine of 1,715 (0.52%) STEC strains were resistant to azithromycin, with an increase since 2017. One isolate carried a plasmid-borne mef(C)-mph(G) gene combination, described here for the first time for E. coli. Azithromycin resistance, although rare, needs consideration, as this treatment may be useful in cases of STEC infection.

Ceftriaxone-resistant, multidrug-resistant Neisseria gonorrhoeae with a novel mosaic penA-237.001 gene, France, June 2022.

We report a ceftriaxone-resistant, multidrug-resistant urogenital gonorrhoea case in a heterosexual woman in France, June 2022. The woman was successfully treated with azithromycin 2 g. She had unprotected sex with her regular partner, who developed urethritis following travel to Vietnam and Switzerland. Whole genome sequencing of the gonococcal isolate (F92) identified MLST ST1901, NG-STAR CC-199, and the novel mosaic penA-237.001, which caused ceftriaxone resistance. penA-237.001 is 98.7% identical to penA-60.001, reported in various ceftriaxone-resistant strains, including the internationally spreading FC428 clone.

Impact of a 24/7 multiplex-PCR on the management of patients with confirmed viral meningitis.

Objectives: The relevance of syndromic multiplex-PCR for the etiological diagnosis of meningitis or meningoencephalitis is still a matter of debate. Here, we studied the impact of a 24/7 multiplex-PCR on the management of patients consulting in the emergency department for suspicion of community-acquired meningitis. Methods: We conducted a single-center retrospective study at the Emergency department of Lariboisière University Hospital (Paris, France) including all patients suspected of meningitis. During period 1 (April 2014-March 2017), the molecular assays used for the detection of infectious agents in the cerebrospinal fluid (CSF) were performed during the daytime. During period 2 (April 2017-March 2019), multiplex-PCR (BioFire® Filmarray® Meningitis/Encephalitis Panel [ME], bioMérieux) was performed 24/7. Results: During the periods 1 and 2, 4 100 and 3 574 patients were included and 284 (6.9%) and 308 (8.6%) meningitis were diagnosed, respectively. During the periods 1 and 2, the most common causes of meningitis were enterovirus (23.9% and 29.5%), varicella zoster virus (10.2% and 6.8%) and herpes simplex virus-2 (4.2% and 8.1%). For patients with confirmed viral meningitis, a significant decrease was found between period 1 and period 2, respectively for the rate of hospitalization (73.9% vs 42.0%; p < 0.05), the length of stay (3[2­5] vs 2[1­3] days; p < 0.05), the empirical antiviral (26.1% vs 14.5%) and antibacterial administrations (29.3% vs 14.5%; p < 0.05). Conclusions: Multiplex-PCR is an important tool in the diagnosis of infectious meningitis in the emergency department and is relevant in the management of meningitis by screening for patients who do not require hospitalization and antibacterial therapy.

Rapid identification of bacteria from respiratory samples of patients hospitalized in intensive care units, with FilmArray Pneumonia Panel Plus.

OBJECTIVES: This study aimed to evaluate the performance of FilmArray Pneumonia Panel Plus (FA-PP) for the detection of typical bacterial pathogens in respiratory samples from patients hospitalized in intensive care units (ICUs). METHODS: FA-PP was implemented for clinical use in the microbiology laboratory in March 2020. A retrospective analysis on a consecutive cohort of adult patients hospitalized in ICUs between March 2020 and May 2020 was undertaken. The respiratory samples included sputum, blind bronchoalveolar lavage (BBAL) and protected specimen brush (PSB). Conventional culture and FA-PP were performed in parallel. RESULTS: In total, 147 samples from 92 patients were analysed; 88% had coronavirus disease 2019 (COVID-19). At least one pathogen was detected in 46% (68/147) of samples by FA-PP and 39% (57/147) of samples by culture. The overall percentage agreement between FA-PP and culture results was 98% (93-100%). Bacteria with semi-quantitative FA-PP results ≥105 copies/mL for PSB samples, ≥106 copies/mL for BBAL samples and ≥107 copies/mL for sputum samples reached clinically significant thresholds for growth in 90%, 100% and 91% of cultures, respectively. FA-PP detected resistance markers, including mecA/C, blaCTX-M and blaVIM. The median turnaround time was significantly shorter for FA-PP than for culture. CONCLUSIONS: FA-PP may constitute a faster approach to the diagnosis of bacterial pneumonia in patients hospitalized in ICUs.