Clinical Evaluation of Nontuberculous Mycobacteria (NTM) Elite Agar, a New Medium for the Isolation of NTM: a Multicenter Study.

Nontuberculous mycobacteria (NTM) are gaining interest with the increased number of infected patients. NTM Elite agar is designed specifically for the isolation of NTM without the decontamination step. We assessed the clinical performance of this medium combined with Vitek mass spectrometry (MS) matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) technology for the isolation and identification of NTM in a prospective multicenter study, including 15 laboratories (24 hospitals). A total of 2,567 samples from patients with suspected NTM infection were analyzed (1,782 sputa, 434 bronchial aspirates, 200 bronchoalveolar lavage samples, 34 bronchial lavage samples, and 117 other samples). A total of 220 samples (8.6%) were positive with existing laboratory methods against 330 with NTM Elite agar (12.8%). Using the combination of both methods, 437 isolates of NTM were detected in 400 positive samples (15.6% of samples). In total, 140 samples of the standard procedures (SP) and 98 of the NTM Elite agar were contaminated. NTM Elite agar showed a higher performance for rapidly growing mycobacteria (RGM) species than SP (7% versus 3%, P < 0.001). A trend has been noted for the Mycobacterium avium complex (4% with SP versus 3% with NTM Elite agar, P = 0.06). The time to positivity was similar (P = 0.13) between groups. However, the time to positivity was significantly shorter for the RGM in subgroup analysis (7 days with NTM and 6 days with SP, P = 0.01). NTM Elite agar has been shown to be useful for the recovery of NTM species, especially for the RGM. Using NTM Elite agar + Vitek MS system in combination with SP increases the number of NTM isolated from clinical samples.

The geographic diversity of nontuberculous mycobacteria isolated from pulmonary samples: an NTM-NET collaborative study.

A significant knowledge gap exists concerning the geographical distribution of nontuberculous mycobacteria (NTM) isolation worldwide. To provide a snapshot of NTM species distribution, global partners in the NTM-Network European Trials Group (NET) framework (www.ntm-net.org), a branch of the Tuberculosis Network European Trials Group (TB-NET), provided identification results of the total number of patients in 2008 in whom NTM were isolated from pulmonary samples. From these data, we visualised the relative distribution of the different NTM found per continent and per country. We received species identification data for 20 182 patients, from 62 laboratories in 30 countries across six continents. 91 different NTM species were isolated. Mycobacterium avium complex (MAC) bacteria predominated in most countries, followed by M. gordonae and M. xenopi. Important differences in geographical distribution of MAC species as well as M. xenopi, M. kansasii and rapid-growing mycobacteria were observed. This snapshot demonstrates that the species distribution among NTM isolates from pulmonary specimens in the year 2008 differed by continent and differed by country within these continents. These differences in species distribution may partly determine the frequency and manifestations of pulmonary NTM disease in each geographical location.

Subspecies Distribution and Antimicrobial Susceptibility Testing of Mycobacterium abscessus Clinical Isolates in Madrid, Spain: a Retrospective Multicenter Study.

Mycobacterium abscessus (MABS) is the most pathogenic and drug-resistant rapidly growing mycobacteria. However, studies on MABS epidemiology, especially those focusing on subspecies level, are scarce. We aimed to determine MABS subspecies distribution and its correlation with phenotypic and genotypic antibiotic profiles. A retrospective multicenter study of 96 clinical MABS isolates in Madrid between 2016 to 2021 was conducted. Identification at the subspecies level and resistance to macrolides and aminoglycosides were performed by the GenoType NTM-DR assay. The MICs of 11 antimicrobials tested against MABS isolates were determined using the broth microdilution method (RAPMYCOI Sensititer titration plates). Clinical isolates included 50 (52.1%) MABS subsp. abscessus; 33 (34.4%) MABS subsp. massiliense; and 13 (13.5%) MABS subsp. bolletii. The lowest resistance rates corresponded to amikacin (2.1%), linezolid (6.3%), cefoxitin (7.3%), and imipenem (14.6%), and the highest to doxycycline (100.0%), ciprofloxacin (89.6%), moxifloxacin (82.3%), cotrimoxazole (82.3%), tobramycin (81.3%), and clarithromycin (50.0% at day 14 of incubation). Regarding tigecycline, although there are no susceptibility breakpoints, all strains but one showed MICs ≤ 1 µg/mL. Four isolates harbored mutations at positions 2058/9 of the rrl gene, one strain harbored a mutation at position 1408 of the rrl gene, and 18/50 harbored the T28C substitution at erm(41) gene. Agreement of the GenoType results with clarithromycin and amikacin susceptibility testing was 99.0% (95/96). The rate of MABS isolates showed an upward trend during the study period, being M. abscessus subsp. abscessus the most frequently isolated subspecies. Amikacin, cefoxitin, linezolid, and imipenem showed great in vitro activity. The GenoType NTM-DR assay provides a reliable and complementary tool to broth microdilution for drug resistance detection. IMPORTANCE Infections caused by Mycobacterium abscessus (MABS) are increasingly being reported worldwide. Identifying MABS subspecies and assessing their phenotypic resistance profiles are crucial for optimal management and better patient outcomes. M. abscessus subspecies differ in erm(41) gene functionality, which is a critical determinant of macrolide resistance. Additionally, resistance profiles of MABS and the subspecies distribution can vary geographically, highlighting the importance of understanding local epidemiology and resistance patterns. This study provides valuable insights into the epidemiology and resistance patterns of MABS and its subspecies in Madrid. Elevated resistance rates were observed for several recommended antimicrobials, emphasizing the need for cautious drug use. Furthermore, we assessed the GenoType NTM-DR assay, which examines principal mutations in macrolides and aminoglycosides resistance-related genes. We observed a high level of agreement between the GenoType NTM-DR assay and the microdilution method, indicating its usefulness as an initial tool for early initiation of appropriate therapy.

[Microbiological diagnosis of urinary tract infections]. / Diagnóstico microbiológico de las infecciones del tracto urinario.

For the diagnosis of urinary tract infection (UTI), besides the quantification of bacteria in the urine, cellular elements contained in the urine, the collection method used and the clinical syndrome should also be considered. Therefore, the microbiological diagnosis of UTI should be performed by an experienced person who takes into account the diversity of situations that may influence the result of each of the cultures. The processing of urine samples depends on the number of samples received daily. In laboratories with a high number, it is impossible to culture each of them, so negative urines have to be ruled out by using automated systems and cultivate only those that are positive. This review includes an analysis of the methods currently available for this screening. It also includes procedures to be performed in special situations such as prostatitis, UTI caused by fastidious microorganisms and other kind of infections that may be diagnosed in a urine test.

Prediction of infection caused by extended-spectrum beta-lactamase-producing Enterobacteriaceae: development of a clinical decision-making nomogram.

OBJECTIVE: This study aimed to assess the population at risk of infection by extended-spectrum beta-lactamase (ESBL)-producing organisms, using clinical criteria. MATERIALS AND METHODS: All urine cultures positive for Enterobacteriaceae in a Spanish hospital department from January 2010 to 2014 were reviewed. All isolates with ESBL-positive strains were collected, and isolates received during the first week of each month with ESBL-negative strains from symptomatic patients hospitalized or admitted to the emergency room. Multivariate analysis of the factors involved was undertaken and a nomogram developed to predict the probability of infection by ESBL-producing microorganisms. RESULTS: The study included 1524 patients with urinary tract infection (UTI): 416 ESBL-positive and 1108 ESBL-negative. In univariate analysis, risk factors were: male gender (p = 0.036), age (p < 0.0001), nursing home (p < 0.0001), previous antimicrobial therapy (p < 0.0001) or hospitalization (p < 0.0001), diabetes (p < 0.0001), chronic renal insufficiency (p < 0.0001), severe underlying disease (p < 0.0001), neoplasia (p = 0.0005), urological (p < 0.0001) and non-urological invasive procedure (p = 0.0003), recurrent UTI (p < 0.0001), urological (p < 0.0001) or abdominal surgery (p < 0.0001) and permanent urethral catheter (p < 0.0001). In multivariate analysis, the data set was split into a development cohort of 1067 patients and a validation cohort of 457 cases. A nomogram was developed to predict the probability of infection by ESBL-producing bacteria, which included seven variables: age (p < 0.0001), gender (p = 0.004), nursing home (p < 0.0001), previous antimicrobial therapy (p = 0.04) or hospitalization (p < 0.0001), recurrent UTI (p < 0.0001) and non-urological invasive procedure (p = 0.005). The discriminative accuracy was 0.79 (95% confidence interval 0.77-0.83). CONCLUSIONS: A nomogram was developed that predicts the risk of infection by ESBL-producing Enterobacteriaceae with reasonable accuracy. It could improve clinical decision making and enable more efficient empirical treatment.

[Microbiological diagnosis of bacterial lower respiratory tract infections]. / Diagnóstico microbiológico de las infecciones bacterianas del tracto respiratorio inferior.

Microbiological diagnosis of bacterial lower respiratory tract infections has relevant limitations and related controversy, depending on the clinical setting and diagnostic methods used, and its value is contingent on an accurate clinical diagnosis and previous antimicrobial therapy. The limitations reside in a low diagnostic yield of the causative agent and the difficulty of determining the clinical significance of the agents recovered. This report examines the current microbiological diagnostic yield of the main clinical entities and etiological agents, indications for invasive or non-invasive specimen collection procedures, and proper specimen processing and culture in the appropriate media. Criteria regarding specimen suitability and indications for quantitative cultures are established. Criteria for evaluating the results are provided, and the current fast diagnostic techniques are described.