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).
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.
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.
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.
The dissemination of carbapenemase-producing
(CPE) is a major threat to public health. Rapid and accurate detection of CPE is essential for initiating appropriate antimicrobial treatment and ...establishing infection control measures. The carbapenem inactivation method (CIM), which has good sensitivity and specificity but a detection time of 20 h, was recently described. In this study, we evaluated the performances of a new version, the CIMplus test, which allows detection of carbapenemases in 8 h and characterization of carbapenemase classes, according to the Ambler classification, in 20 h. A panel of 110 carbapenem-resistant
strains, including 92 CPE strains (with NDM, VIM, IMP, KPC, GES, OXA-48, and OXA-48-like enzymes), was used to evaluate test performance. Carbapenemase activity was detected at 8 h and 20 h. Characterization of carbapenemase classes, using specific inhibitors, was possible in 20 h. The CIMplus test had sensitivities of 95.7% and 97.8% at 8 h and 20 h, respectively, and a specificity of 94.4%, independent of the culture duration. Using a decision algorithm, this test was successful in identifying the carbapenemase class for 98.9% of tested CPE isolates (87/88 isolates). In total, the characterization was correct for 100%, 96.9%, and 100% of Ambler class A, B, and D isolates, respectively. Therefore, this test allows detection of carbapenemase activity in 8 h and characterization of carbapenemase classes, according to the Ambler classification, in 20 h. The CIMplus test represents a simple, affordable, easy-to-read, and accurate tool that can be used without any specific equipment.
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.
MICs were determined with gradient strips for this isolate. Hydrolysis assays were performed with the β 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.
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.
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.
•A retrospective single-centre study was undertaken including 147 samples from 92 patients.•The overall percentage agreement was 98% for detection of typical bacteria.•Significant thresholds in ...culture were compared with nucleic acid copy number.•Median turnaround time was significantly shorter for the FilmArray Pneumonia Panel Plus than for culture.
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).
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.
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.
FA-PP may constitute a faster approach to the diagnosis of bacterial pneumonia in patients hospitalized in ICUs.
The FilmArray® Pneumonia Plus (FA-PP) panel can provide rapid identifications and semiquantitative results for many pathogens. We performed a prospective single-center study in 43 critically ill ...patients with coronavirus disease 2019 (COVID-19) in which we performed 96 FA-PP tests and cultures of blind bronchoalveolar lavage (BBAL). FA-PP detected 1 or more pathogens in 32% (31/96 of samples), whereas culture methods detected at least 1 pathogen in 35% (34/96 of samples). The most prevalent bacteria detected were Pseudomonas aeruginosa (n = 14) and Staphylococcus aureus (n = 11) on both FA-PP and culture. The FA-PP results from BBAL in critically ill patients with COVID-19 were consistent with bacterial culture findings for bacteria present in the FA-PP panel, showing sensitivity, specificity, and positive and negative predictive value of 95%, 99%, 82%, and 100%, respectively. Median turnaround time for FA-PP was 5.5 h, which was significantly shorter than for standard culture (26 h) and antimicrobial susceptibility testing results (57 h).
•Activity of apramycin against a collection (n = 164) of 16S-RMTase producers.•Most of the 16S-RMTase-producing isolates (95%) were susceptible to apramycin.•Resistance rates were higher in P. ...aeruginosa than in A. baumannii or Enterobacterales.•One ST156 E. coli had a minimum inhibitory concentration (MIC) >64 mg/L due to acquisition of the aac(3)-IV gene.
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.
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).
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.
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.
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
gene in seven BC, including one for which no extended-spectrum β-lactamase (ESBL)-producing isolate was obtained in culture. However, it failed to detect ESBL-encoding genes in three BC. Two of the 18
genes detected by the BCID2 were not confirmed. No carbapenemase,
, 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.
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.
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
, which caused ceftriaxone resistance.
is 98.7% identical to
, reported in various ceftriaxone-resistant strains, including the internationally spreading FC428 clone.
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