Chlorhexidine decontamination of sputum for culturing Mycobacterium tuberculosis

Comparison of Power Ultrasound and NALC-NaOH Decontamination Methods for Stool Mycobacterial Culture: A Prospective Study

Stool samples have been reported to be useful for the diagnosis of pulmonary tuberculosis (PTB), especially in patients who are unable to produce sputum. However, contamination limits the usefulness of stool specimens in mycobacterial culture. In this study, a novel decontamination method of power ultrasound (PU) was evaluated for mycobacterial isolation from suspected PTB cases. Stool samples (n = 650) were collected, and each sample was divided into approximately three equal groups. In addition to an AFB smear (Auramine O method), the stool samples were treated using different decontamination methods (NaOH-NALC vs. PU methods). The sensitivity (calculated against CRS) and contamination rates between the two methods were compared using McNemar's test. Of the 650 samples, 32 (4.92%) stool samples treated with the NaOH-NALC method were culture-positive, including Mycobacterium tuberculosis (M.TB; n = 21, 3.23%) and nontuberculous mycobacteria (NTM; n = 11, 1.69%). Sixty-one (9.38%) stool samples treated with the PU method were culture-positive, including M.TB (n = 37, 5.69%) and NTM (n = 24, 3.69%). Statistical analysis showed that a significant difference was found in the isolation rate of M.TB and NTM between the two methods (p < 0.05). Additionally, compared with the NALC-NaOH method (19.07%), stool samples treated with the PU method (13.23%) had a significantly lower contamination rate (p < 0.05). In conclusion, our findings suggest that the utilization of the PU method as a novel decontamination technique could significantly enhance the isolation rates of both NTM and M.TB when stool specimens are employed for culture. Compared to the NaOH-NALC method, this approach proves to be more effective in facilitating stool mycobacterial culture.

Evolution of Laboratory Diagnosis of Tuberculosis

Tuberculosis (TB) is an infectious disease of global public health importance caused by the Mycobacterium tuberculosis complex. Despite advances in diagnosis and treatment, this disease has worsened with the emergence of multidrug-resistant strains of tuberculosis. We aim to present and review the history, progress, and future directions in the diagnosis of tuberculosis by evaluating the current methods of laboratory diagnosis of tuberculosis, with a special emphasis on microscopic examination and cultivation on solid and liquid media, as well as an approach to molecular assays. The microscopic method, although widely used, has its limitations, and the use and evaluation of other techniques are essential for a complete and accurate diagnosis. Bacterial cultures, both in solid and liquid media, are essential methods in the diagnosis of TB. Culture on a solid medium provides specificity and accuracy, while culture on a liquid medium brings rapidity and increased sensitivity. Molecular tests such as LPA and Xpert MTB/RIF have been found to offer significant benefits in the rapid and accurate diagnosis of TB, including drug-resistant forms. These tests allow the identification of resistance mutations and provide essential information for choosing the right treatment. We conclude that combined diagnostic methods, using several techniques and approaches, provide the best result in the laboratory diagnosis of TB. Improving the quality and accessibility of tests, as well as the implementation of advanced technologies, is essential to help improve the sensitivity, efficiency, and accuracy of TB diagnosis.

Assessment and validation of enrichment and target capture approaches to improve Mycobacterium tuberculosis WGS from direct patient samples

Within-host Mycobacterium tuberculosis (Mtb) diversity may detect antibiotic resistance or predict tuberculosis treatment failure and is best captured through sequencing directly from sputum. Here, we compared three sample pre-processing steps for DNA decontamination and studied the yield of a new target enrichment protocol for optimal whole-genome sequencing (WGS) from direct patient samples. Mtb-positive NALC-NaOH-treated patient sputum sediments were pooled, and heat inactivated, split in replicates, and treated by either a wash, DNase I, or benzonase digestion. Levels of contaminating host DNA and target Mtb DNA were assessed by quantitative PCR (qPCR), followed by WGS with and without custom dsDNA target enrichment. The pre-treatment sample has a high host-to-target ratio of DNA (6,168 ± 1,638 host copies/ng to 212.3 ± 59.4 Mtb copies/ng) that significantly decreased with all three treatments. Benzonase treatment resulted in the highest enrichment of Mtb DNA at 100-fold compared with control (3,422 ± 2,162 host copies/ng to 11,721 ± 7,096 Mtb copies/ng). The custom dsDNA probe panel successfully enriched libraries from as little as 0.45 pg of Mtb DNA (100 genome copies). Applied to direct sputum the dsDNA target enrichment panel increased the percent of sequencing reads mapping to the Mtb target for all three pre-processing methods. Comparing the results of the benzonase sample sequenced both with and without enrichment, the percent of sequencing reads mapping to the Mtb increased to 90.95% from 1.18%. We demonstrate a low limit of detection for a new custom dsDNA Mtb target enrichment panel that has a favorable cost profile. The results also demonstrate that pre-processing to remove contaminating extracellular DNA prior to cell lysis and DNA extraction improves the host-to-Mtb DNA ratio but is not adequate to support average coverage WGS without target capture.

Rapid electrochemical detection of Mycobacterium tuberculosis in sputum by measuring Ag85 activity with disposable carbon sensors

An electrochemical assay for the detection of the enzymatic activity of the antigen 85 (Ag85) tuberculosis (TB) biomarker was developed and evaluated for the qualitative detection of Mycobacterium tuberculosis in decontaminated sputum. For this purpose, the electroactive properties of both synthetic p-aminophenyl-6-O-octanoyl-3-d-glucopyranoside (p-APOG) substrate and p-aminophenyl-6-3-d-glucopyranoside (p-APG) product released after the removal of the octanoyl fatty acid by the Ag85 were investigated with disposable carbon screen-printed electrodes by cyclic voltammetry. Since specific anodic responses were obtained for the p-APOG substrate and the p-APG product, the intensity of the oxidation peak of the p-APG (E = + 0.35 V vs. Ag/AgCl) was selected as the analytical response for the detection of the Ag85 acyltransferase activity. Once the proof of concept of the Ag85 electrochemical assay was validated with a commercially-available Ag85B protein, its specificity was further assessed by analyzing pure cultures of various bacteria including tuberculous and non-tuberculous mycobacteria as well as different species found in patients' sputum. Finally, with a specificity of 78% and a sensitivity of 89%, the method was successfully compared to microscopy and culture routine tests for TB testing in 36 frozen fluidized and decontaminated sputum. This suggests that owing to its convenience, rapidity, low-cost and portability, the reported Ag85 electrochemical assay is a promising tool to screen patients for TB.

A New Culture Method for the Detection of Non-Tuberculous Mycobacteria in Water Samples from Heater-Cooler Units and Extracorporeal Membrane Oxygenation Machines

The isolation of non-tuberculous mycobacteria (NTM) from cultures is particularly laborious due to the potential overgrowth of coexisting non-acid fast bacilli. To reduce the overgrowth of these non-mycobacterial organisms, a decontamination step with NaOH or cetylpyridinium chloride is highly recommended before plating the samples on the culture medium. However, due to their toxicity, decontamination solutions tend to decrease NTM recovery from clinical and environmental samples. Here, we tested an alternative method for NTM recovery based on the use of NTM Elite agar, a selective medium that does not require a decontamination step. Using NTM Elite agar, we were able to detect non-tuberculous mycobacteria in 27.7% (30/108) of water samples analyzed. The average time to NTM detection was 18 days, but some strains required longer to grow, perhaps due to the stressful environmental conditions (periodical disinfection of devices). NTM Elite agar's effectiveness in inhibiting background flora was proven by the isolation of NTM from samples with and without background flora, showing no statistically significant differences in detection rates for different total viable counts of background flora (p = 0.4989). In conclusion, our findings indicate that effective NTM recovery from HCU- and ECMO-derived water samples can be achieved via filtration and direct culture of the filters on NTM Elite agar. This simple procedure can speed up laboratory work and provide an improved method, successfully resulting in low contamination and high detection rate, in addition to being less time-consuming. Its sensitivity and lack of a decontamination step make this protocol particularly useful for monitoring the effectiveness of device disinfection in hospital settings, even in the presence of low NTM loads. Reading timeframes should probably be extended to 7 weeks (i.e., well beyond the standard 4 weeks advised by the manufacturer), in order to isolate even the slow-growing mycobacteria. However, an extended incubation period is not necessary for exclusion of M. chimaera contamination of the devices, as M. chimaera isolation times do not generally exceed 3 weeks.

Comparison of Sputum Treated with Power Ultrasound and Routine NALC-NaOH Methods for Mycobacterial Culture: A Prospective Study

Mycobacterial culture remains the gold standard for the diagnosis of active tuberculosis. However, an appropriate digestion and decontamination method is essential for the effective recovery of tubercle bacilli in culture. The study was designed to compare the efficacy of sputum treated with power ultrasound (PU) and routine NALC-NaOH methods for mycobacterial culture from clinically suspected cases of pulmonary tuberculosis. To evaluate the PU and routine NALC-NaOH methods, sputum specimens (n = 597) were studied (culturing on MGIT 960), and the performances were compared. Of the 597 samples, 89 (14.91%) sputum samples treated with the NaOH-NALC method were mycobacterial culture positive, including Mycobacterium tuberculosis (M.TB; n = 77, 12.90%) and nontuberculous mycobacteria (NTM; n = 12, 2.01%). One hundred and ten (18.43%) sputum samples treated with the PU method were culture positive, including M.TB (n = 87, 14.57%) and NTM (n = 23, 3.85%). The PU method detected 10 additional cases of M.TB and 11 additional cases of NTM when compared to the NALC-NaOH method. Statistical analysis showed that a significant difference was found in the culture-positive ratio of M.TB and NTM between the two method groups (p < 0.05). Compared with that of the NALC-NaOH method (8.04%), sputum treated with PU method (4.86%) had a significantly lower contamination rate (p < 0.05). In conclusion, our data indicate that, compared with the NALC-NaOH method, the PU method is a rapid and effective approach for mycobacterial culture when detecting active TB. However, its accurate mechanism has not been well addressed, and further investigation is still required.

From Marine Metabolites to the Drugs of the Future: Squalamine, Trodusquemine, Their Steroid and Triterpene Analogues

This review comprehensively describes the recent advances in the synthesis and pharmacological evaluation of steroid polyamines squalamine, trodusquemine, ceragenins, claramine, and their diverse analogs and derivatives, with a special focus on their complete synthesis from cholic acids, as well as an antibacterial and antiviral, neuroprotective, antiangiogenic, antitumor, antiobesity and weight-loss activity, antiatherogenic, regenerative, and anxiolytic properties. Trodusquemine is the most-studied small-molecule allosteric PTP1B inhibitor. The discovery of squalamine as the first representative of a previously unknown class of natural antibiotics of animal origin stimulated extensive research of terpenoids (especially triterpenoids) comprising polyamine fragments. During the last decade, this new class of biologically active semisynthetic natural product derivatives demonstrated the possibility to form supramolecular networks, which opens up many possibilities for the use of such structures for drug delivery systems in serum or other body fluids.

Chemical susceptibility testing of non-tuberculous mycobacterium strains and other aquatic bacteria: Results of a study for the development of a more sensitive and simple method for the detection of NTM in environmental samples

The methods employed to detect non-tuberculous mycobacteria on environmental samples are essentially those classically used in clinical microbiology, which envisage a decontamination step to reduce the overgrowth of non-mycobacterial organisms before plating them on the culture medium. The aim of this study was to propose alternative culture techniques to improve non-tuberculous mycobacteria detection in environmental samples. We used artificially contaminated samples to compare the membrane filter washing procedure against direct plating of membrane filters on culture media in relation to M.chimaera and M.chelonae recovery efficiency. Moreover, we compared the efficacy of NTM Elite agar in inhibiting the growth of aquatic bacteria with that of cetylpyridinium chloride and N-acetyl-L-cysteine sodium hydroxide decontamination treatments. The washing procedure yielded a low release of both mycobacterium strains (6.6% for Mycobacterium chimaera and 7.5% for Mycobacterium chelonae) from the membrane filters; on the contrary, direct plating of membrane filters led to a 100% cell recovery. Water sample pretreatment with N-acetyl-L-cysteine sodium hydroxide (1%), despite achieving complete suppression of non-acid fast bacilli, caused a reduction in mycobacteria growth. Decontamination with cetylpyridinium chloride (0.005%) was found to be ineffective against Methylobacterium spp. and Burkholderia multivorans. NTM Elite agar was ineffective against B. multivorans, but it inhibited the growth of all other aquatic bacteria. Our results indicate that NTM Elite agar provides a valid alternative method of recovering non-tuberculous mycobacteria from environmental samples. It does not involve a decontamination step and provides greater recovery efficiency by skipping the washing step and directly plating the filters on the media.

Molecular detection of Mycobacterium tuberculosis sensu stricto in the soil of Niger

Mycobacterium tuberculosis (MTB) complex is comprising of pathogenic mycobacteria responsible for human and animal tuberculosis, a major public health problem in Niger. Although infected individuals are paramount sources of contamination, nevertheless alternative, neglected sources may play some role in minority forms of the infection. Accordingly, we investigated the presence of Mycobacterium tuberculosis complex in soil samples in Niger. A total of 103 soil samples were collected in six different areas in Niger in October and November 2018 and April and May 2020 from residential areas of tuberculosis patients. Screening PCR targeting M. tuberculosis complex CRISPR-Csm4 and Xpert MTB/RIF Ultra assay were applied to detect the M. tuberculosis complex. M. tuberculosis DNA was positively detected in five of 103 (5/103; 4.8%) soil samples (Dosso: one sample, Zinder: one sample and Niamey: three samples) using the CRISPR-Csm4 system. CRISPR-Csm4 gene sequence identified four M. tuberculosis sensu stricto (may be lineages 1, 3 or 4) and one M. tuberculosis L2 lineage (Beijing). Moreover, the five positive samples were confirmed by Xpert MTB/RIF Ultra assay as rifampicin-susceptible M. tuberculosis complex strains. However, culture remained negative after 42 days. In this study, we announced for the first time the presence of M. tuberculosis sensu stricto in the soil of Niger. Moreover, these detected lineages were identical to the dominant M. tuberculosis lineages in patients. The presence of common lineages of M. tuberculosis between the soil and human highlight the risk of transmission from the soil to human.

Improved detection of Mycobacterium tuberculosis and M. bovis in African wildlife samples using cationic peptide decontamination and mycobacterial culture supplementation

In South Africa, mycobacterial culture is regarded as the gold standard for the detection of Mycobacterium tuberculosis complex (MTBC) infection in wildlife even though it is regarded as “imperfect.” We compared a novel decontamination and mycobacterial culture technique (TiKa) to the conventional mycobacterium growth indicator tube (MGIT) system using known amounts of bacilli and clinical samples from MTBC-infected African buffaloes (Syncerus caffer), white rhinoceros (Ceratotherium simum), and African elephants (Loxodonta africana). Use of the TiKa-KiC decontamination agent on samples spiked with 10,000 to 10 colony forming units (cfu) of M. bovis (SB0121) and M. tuberculosis (H37Rv) had no effect on isolate recovery in culture. In contrast, decontamination with MGIT MycoPrep resulted in no growth of M. bovis samples at concentrations < 1,000 cfu and M. tuberculosis samples < 100 cfu. Subsequently, we used the TiKa system with stored clinical samples (various lymphatic tissues) collected from wildlife and paucibacillary bronchoalveolar lavage fluid, trunk washes, and endotracheal tube washes from 3 species with known MTBC infections. Overall, MTBC recovery by culture was improved significantly (p < 0.01) by using TiKa compared to conventional MGIT, with 54 of 57 positive specimens versus 25 of 57 positive specimens, respectively. The TiKa mycobacterial growth system appears to significantly enhance the recovery of MTBC members from tissue and paucibacillary respiratory samples collected from African buffaloes, African elephants, and white rhinoceros. Moreover, the TiKa system may improve success of MTBC culture from various sample types previously deemed unculturable from other species.

Real-time next-generation sequencing on shell-vial culture to contribute to diagnosis of lymphatic tuberculosis: a case report

Lymph node tuberculosis is a of limited clinical suspicion form of Mycobacterium tuberculosis infection. After 15 days incubation in a cellular culture and directly from the supernatant, 11 minutes of Oxford Nanopore MinION sequencing provided a preliminary result of an antibiotic-susceptible M. tuberculosis Indo-Oceanic lineage strain. Oxford Nanopore MinION sequencing is a promising tool for optimising the laboratory diagnosis of lymph node tuberculosis.

Whole Genome Sequence Analysis of Mycobacterium bovis Cattle Isolates, Algeria

Mycobacterium bovis (M. bovis), a Mycobacterium tuberculosis complex species responsible for tuberculosis in cattle and zoonotic tuberculosis in humans, is present in Algeria. In Algeria however, the M. bovis population structure is unknown, limiting understanding of the sources and transmission of bovine tuberculosis. In this study, we identified the whole genome sequence (WGS) of 13 M. bovis strains isolated from animals exhibiting lesions compatible with tuberculosis, which were slaughtered and inspected in five slaughterhouses in Algeria. We found that six isolates were grouped together with reference clinical strains of M. bovis genotype-Unknown2. One isolate was related to M. bovis genotype-Unknown7, one isolate was related to M. bovis genotype-Unknown4, three isolates belonged to M. bovis genotype-Europe 2 and there was one new clone for two M. bovis isolates. Two isolates from Blida exhibited no pairwise differences in single nucleotide polymorphisms. None of these 13 isolates were closely related to four zoonotic M. bovis isolates previously characterized in Algeria. In Algeria, the epidemiology of bovine tuberculosis in cattle is partly driven by cross border movements of animals and animal products.

Synthesis and Biological Activities of Naturally Functionalized Polyamines: An Overview

Recently, extensive researches have emphasized the fact that polyamine conjugates are becoming important in all biological and medicinal fields. In this review, we will focus our attention on natural polyamines and highlight recent progress in both fundamental mechanism studies and interests in the development and application for the therapeutic use of polyamine derivatives.

Culturomics Discloses Anti-Tubercular Enterococci Exclusive of Pulmonary Tuberculosis: A Preliminary Report

Mycobacterium tuberculosis causes pulmonary tuberculosis, a deadly infection of which the clinical expression and prognosis are not fully understood at the individual level, apart from genetic susceptibility traits. We investigated whether individual gut microbiota may correlate with pulmonary tuberculosis status. Culturomics investigations of gut microbiota in two pulmonary tuberculosis patients and two controls in Burkina Faso found 60 different bacterial species in patients and 97 in controls, including 45 in common. Further analysis of the results at the individual level indicated seven bacteria, including Enterococcus mundtii and Enterococcus casseliflavus, which were exclusively cultured in controls. Blind quantitative PCR-based exploration of faeces samples in two cohorts in Burkina Faso and in France confirmed a nonsignificant association of E. mundtii and E. casseliflavus with controls. Further in vitro explorations found four E. mundtii and E. casseliflavus strains inhibiting the growth of M. tuberculosis strains representative of four different lineages as well as Mycobacterium africanum, Mycobacterium canettii, and Mycobacterium bovis, in an inoculum-dependent manner. Heat-killed E. mundtii or E. casseliflavus were ineffective. These unprecedented observations of direct interactions between gut E. mundtii and E. casseliflavus with M. tuberculosis complex mycobacteria suggest that gut microbiota may modulate the expression of pulmonary tuberculosis.

Screening anti-infectious molecules against Mycobacterium ulcerans: A step towards decontaminating environmental specimens

Mycobacterium ulcerans, a non-tuberculous mycobacterium responsible for Buruli ulcer, resides in poorly defined environmental niches in the vicinity of stagnant water. Very few isolates have been confirmed. With a view to culturing M. ulcerans from such contaminated environmental specimens, we tested the in vitro susceptibility of the M. ulcerans CU001 strain co-cultivated with XTC cells to anti-infectious molecules registered in the French pharmacopoeia. We used a standardised concentration to identify molecules that were inactive against M. ulcerans and which could be incorporated into a decontaminating solution. Of 116 tested molecules, 64 (55.1%) molecules were ineffective against M. ulcerans CU001. These included 34 (29.3%) antibiotics, 14 (12%) antivirals, eight (6.8%) antiparasitics, and eight (6.8%) antifungals. This left 52 molecules which were active against M. ulcerans CU001. Three of the inactive antimicrobial molecules (oxytetracycline, polymyxin E and voriconazole) were then selected to prepare a decontamination solution which was shown to respect M. ulcerans CU001 viability. These three antimicrobials could be incorporated into a decontamination solution to potentially isolate and culture M. ulcerans from environmental samples.

Direct Determination of Pyrazinamide (PZA) Susceptibility by Sputum Microscopic Observation Drug Susceptibility (MODS) Culture at Neutral pH: the MODS-PZA Assay

Pyrazinamide (PZA) is considered the pivot drug in all tuberculosis treatment regimens due to its particular action on the persistent forms of Mycobacterium tuberculosis. However, no drug susceptibility test (DST) is considered sufficiently reliable for routine application. Although molecular tests are endorsed, their application is limited to known PZA resistance associated mutations. Microbiological DSTs for PZA have been restricted by technical limitations, especially the necessity for an acidic pH.

Pyrazinamide (PZA) is considered the pivot drug in all tuberculosis treatment regimens due to its particular action on the persistent forms of Mycobacterium tuberculosis. However, no drug susceptibility test (DST) is considered sufficiently reliable for routine application. Although molecular tests are endorsed, their application is limited to known PZA resistance associated mutations. Microbiological DSTs for PZA have been restricted by technical limitations, especially the necessity for an acidic pH. Here, for the first time, MODS culture at neutral pH was evaluated using high PZA concentrations (400 and 800 μg/ml) to determine PZA susceptibility directly from sputum samples. Sputum samples were cultured with PZA for up to 21 days at 37°C. Plate reading was performed at two time points: R1 (mean, 10 days) and R2 (mean, 13 days) for each PZA concentration. A consensus reference test, composed of MGIT-PZA, pncA sequencing, and the classic Wayne test, was used. A total of 182 samples were evaluated. The sensitivity and specificity for 400 μg/ml ranged from 76.9 to 89.7 and from 93.0 to 97.9%, respectively, and for 800 μg/ml ranged from 71.8 to 82.1 and from 95.8 to 98.6%, respectively. Compared to MGIT-PZA, our test showed a similar turnaround time (medians of 10 and 12 days for PZA-sensitive and -resistant isolates, respectively). In conclusion, MODS-PZA is presented as a fast, simple, and low-cost DST that could complement the MODS assay to evaluate resistance to the principal first-line antituberculosis drugs. Further optimization of test conditions would be useful in order to increase its performance.

Bacterial culture through selective and non-selective conditions: the evolution of culture media in clinical microbiology

Microbiology has been largely developed thanks to the discovery and optimization of culture media. The first liquid artificial culture medium was created by Louis Pasteur in 1860. Previously, bacterial growth on daily materials such as some foods had been observed. These observations highlighted the importance of the bacteria's natural environment and their nutritional needs in the development of culture media for their isolation. A culture medium is essentially composed of basic elements (water, nutrients), to which must be added different growth factors that will be specific to each bacterium and necessary for their growth. The evolution of bacterial culture through the media used for their culture began with the development of the first solid culture medium by Koch, allowing not only the production of bacterial colonies, but also the possibility of purifying a bacterial clone. The main gelling agent used in solid culture media is agar. However, some limits have been observed in the use of agar because of some extremely oxygen-sensitive bacteria that do not grow on agar media, and other alternatives were proposed and tested. Then, the discovery of antimicrobial agents and their specific targets prompted the emergence of selective media. These inhibiting agents make it possible to eliminate undesirable bacteria from the microbiota and select the bacteria desired. Thanks to a better knowledge of the bacterial environment, it will be possible to develop new culture media and new culture conditions, better adapted to certain fastidious bacteria that are difficult to isolate.

Reduction of turnaround time for non-tuberculous mycobacteria detection in heater-cooler units by propidium monoazide-real-time polymerase chain reaction

BACKGROUND

Invasive non-tuberculous mycobacteria (NTM) infections are emerging worldwide in patients undergoing open-chest cardiac bypass surgery exposed to contaminated heater-cooler units (HCUs). Although this outbreak has been investigated by culturing bacteria isolated from HCU aerosol and water samples, these conventional methods have low-analytic sensitivity, high rates of sample contamination, and long turnaround time.

AIM

To develop a simple and effective method to detect NTM in HCUs by real-time polymerase chain reaction (PCR), with a short laboratory turnaround time and reliable culture results.

METHODS

A total of 281 water samples collected from various HCUs at seven Italian hospitals were simultaneously screened for NTM by a propidium monoazide (PMA)-PCR assay and by conventional culture testing. The results were analysed with culture testing as the reference method.

FINDINGS

(i) The agreement between culture testing and PMA-PCR was 85.0% with a cycle threshold (C_T) cut-off value of <38 vs 80.0% with a C_T of <43, with a moderate Cohen's κ-coefficient; (ii) the C_T cut-off value of <42 was deemed more suitable for predicting positive specimens; (iii) given the low concentration of target DNA in water samples, the minimum volume to be tested was 1 L.

CONCLUSION

The use of PMA-PCR for fast detection of NTM from environmental samples is highly recommended in order to ascertain whether HCUs may represent a potential source of human exposure to NTM. This reliable and simple method reduces laboratory turnaround time compared to conventional methods (one to two days vs eight weeks, respectively), thereby improving control strategies and effective management of HCUs.

Identification of spore-forming bacteria isolated from contaminated Lowenstein Jensen media and effectiveness of Vancomycin to reduce Mycobacterial culture contamination in Burkina-Faso

The type of commensal microorganisms can influence the efficiency of sputum decontamination for TB diagnosis. A basic characterization of contaminants from LJ contaminated media showed that Gram positive Spore Forming Bacteria (SFB) were the major contaminants. This study aims to identify the species of this contaminants and to evaluate the effectiveness of VCNT at 10 µg of vancomycin to reduce mycobacterial culture contamination mainly linked to SFB. Fifty-three SFB isolated between February 2016 and May 2017 were used. The effectiveness of LJ with VCNT at 10 µg of Vancomycin were evaluated with sputum collected in the same period. SFB had been stored at -20 °C and identified after subculture onto 5% sheep blood Columbia agar and incubated at 37 °C during 24 h. Bacteria cells and isolated colonies were described. API 50CH/B was performed and MALDI-TOF MS was used for external quality control. Thirty- five (66%) isolates representing 4 genera (Bacillus, Paenibacillus, Brevisbacillus and Lysinibacillus) including 10 species were identified. The most important species were Bacillus cereus (30%) and Bacillus licheniformis (21%). Eighteen (34%) isolates were non-reactive Bacillus. The overall contamination rate on LJ with VCNT at 10 µg of vancomycin was statistically lower than which without VCNT (18.7% versus 43.8%) (p = 0.01). The most important SFB identified were B. cereus and B. licheniformis. Almost all identified strains were similar to those currently isolated in fermented traditional food suggesting in part food related contaminants. VCNT containing 10 µg of vancomycin is a good alternative method to reduce mycobacterial culture contamination.

Centrifugation and decontamination procedures selectively impair recovery of important populations in Mycobacterium smegmatis

Diagnosis and treatment monitoring of patients with tuberculosis (TB) requires detection of all viable mycobacteria in clinical samples. Quantitation of Mycobacterium tuberculosis (Mtb) in sputum is commonly performed by culture after sample decontamination to prevent overgrowth by contaminant organisms. Exponentially growing cultures have cells that predominately lack non-polar lipid bodies whereas stationary cultures have a predominance of cells with non-polar lipid bodies. This may reflect rapidly growing 'active' and non-replicating 'persister' sub-populations respectively in sputum from TB patients. We investigated the effect of decontamination on culture-based quantitation of exponential and stationary phase cultures of Mycobacterium smegmatis in an artificial sputum model. Exponentially growing populations were between 89 and 50 times more susceptible to decontamination than stationary phase cultures when quantified by most probable number and colony forming units. These findings suggest that decontamination selectively eliminates the 'active' population. This may impair diagnostic sensitivity, treatment monitoring, and compromise clinical trials designed to identify new antibiotic combinations with activity against all mycobacterial cell states.

Automatic microscopic detection of mycobacteria in sputum: a proof-of-concept

The laboratory diagnosis of lung mycobacterioses including tuberculosis comprises the microscopic examination of sputum smear after appropriate staining such as Ziehl-Neelsen staining to observe acid-fast bacilli. This standard procedure is operator-dependant and its sensitivity depends on the duration of observation. We developed and evaluated an operator-independent microscopic examination of sputum smears for the automated detection and enumeration of acid-fast bacilli using a ZEISS Axio Scan.Z1 microscope. The sensitivity, specificity, positive predictive value, negative predictive values and accuracy were calculated using standard formulations by comparison with standard microscopic examination. After in-house parameterization of the automatic microscope and counting software, the limit of detection evaluated by seeding negative sputa with Mycobacterium bovis BCG or Mycobacterium tuberculosis H37Rv (10⁰–10⁵ bacilli/mL) was of 10² bacilli/mL of sputum with a 100% positivity rate. Then, the evaluation of 93 sputum specimens including 34 smear-positive and 59 smear-negative specimens yielded a sensitivity of 97.06% [84.67–99.93%], a specificity of 86.44% [73.01–92.78%]. Up to 100 smear slides could be stocked for reading in the microscope magazine and results are exportable into the laboratory information system. Based on these preliminary results, we are implanting this automatic protocol in the routine workflow so that only smears detected positive by automatic microscopy are confirmed by standard microscopic examination.

A protocol for culturing environmental strains of the Buruli ulcer agent, Mycobacterium ulcerans

Contaminations and fastidiousness of M. ulcerans may have both hamper isolation of strains from environmental sources. We aimed to optimize decontamination and culture of environmental samples to circumvent both limitations. Three strains of M. ulcerans cultured onto Middlebrook 7H10 at 30 °C for 20 days yielded a significantly higher number of colonies in micro-aerophilic atmosphere compared to ambient atmosphere, 5% CO₂ and anaerobic atmosphere. In a second step, we observed that M. ulcerans genome uniquely encoded chitinase, fucosidase and A-D-GlcNAc-diphosphoryl polyprenol A-3-L-rhamnosyl transferase giving M. ulcerans the potential to metabolize chitine, fucose and N-acetyl galactosamine (NAG), respectively. A significant growth-promoting effect of 0.2 mg/mL chitin (p < 0.05), 0.01 mg/mL N-acetyl galactosamine (p < 0.05), 0.01 mg/mL fucose (p < 0.05) was observed with M. ulcerans indicating that NAG alone or combined with fucose and chitin could complement Middlebrook 7H10. Finally, the protocol combining 1% chlorhexidine decontamination with micro-aerophilic incubation on Middlebrook 7H10 medium containing chitin (0.2%), NAG (0.01%) and fucose (0.01%) medium and auto-fluorescence detection of colonies allowed for the isolation of one mycolactone-encoding strain from Thryonomys swinderianus (aulacode) feces specimens collected near the Kossou Dam, Côte d'Ivoire. We propose that incubation of chlorhexidine-decontaminated environmental specimens on Middlebrook 7H10-enriched medium under micro-aerophilic atmosphere at 30 °C may be used for the tentative isolation of M. ulcerans strains from potential environmental sources.

In Vitro Evaluation of Povidone-Iodine and Chlorhexidine against Outbreak and Nonoutbreak Strains of Mycobacterium abscessus Using Standard Quantitative Suspension and Carrier Testing

Povidone-iodine (PI) and chlorhexidine (CHX) are widely used antiseptics active against conventional Staphylococcus aureus, Enterobacteriaceae, Candida species, and viruses, but their efficacy against Mycobacterium abscessus remains unproven. We determined the in vitro potency of alcoholic PI and CHX against M. abscessus subsp. abscessus (ATCC 19977), M. abscessus subsp. bolletii (BCRC 16915), and our outbreak strain of M. abscessus subsp. massiliense (TPE 101) in reference to Staphylococcus aureus (ATCC 29213) by standard quantitative suspension and carrier methods (EN 14563). By suspension, all mycobacterial strains compared to S. aureus were significantly more resistant to CHX, but not PI. By carrier, the mean logarithmic reductions (LR) achieved by PI under clean (dirty) conditions were 6.575 (2.482), 5.540 (2.298), 4.595 (1.967), and 1.173 (0.889), while those achieved by CHX under clean (dirty) conditions were 3.164 (5.445), 5.307 (2.564), 3.844 (2.232), and 0.863 (0.389) for S. aureus, M. abscessus subsp. bolletii, M. abscessus subsp. abscessus, and M. abscessus subsp. massiliense, respectively. M. abscessus subsp. massiliense (outbreak strain) was significantly more resistant than the other tested strains to PI and CHX. By both methods, the mean LR achieved by PI was higher than for CHX for all mycobacterial strains, but under dirty conditions, neither antiseptic was effectively mycobactericidal (LR < 5). These preliminary findings caution against the universal replacement of PI with CHX as the first-line skin antiseptic, since all M. abscessus isolates were resistant to CHX. More studies are needed to establish the best practice for skin antisepsis if mycobacterial infections are also to be prevented.

A novel sputum transport solution eliminates cold chain and supports routine tuberculosis testing in Nepal

This preliminary study evaluated the transport reagent OMNIgene SPUTUM (OMS) in a real-world, resource-limited setting: a zonal hospital and national tuberculosis (TB) reference laboratory, Nepal. The objectives were to: (1) assess the performance of OMS for transporting sputum from peripheral sites without cold chain stabilization; and (2) compare with Nepal's standard of care (SOC) for Mycobacterium tuberculosis smear and culture diagnostics. Sixty sputa were manually split into a SOC sample (airline-couriered to the laboratory, conventional processing) and an OMS sample (OMS added at collection, no cold chain transport or processing). Smear microscopy and solid culture were performed. Transport was 0-8days. Forty-one samples (68%) were smear-positive using both methods. Of the OMS cultures, 37 (62%) were positive, 22 (36%) were negative, and one (2%) was contaminated. Corresponding SOC results were 32 (53%), 21 (35%), and seven (12%). OMS "rescued" six (i.e., missed using SOC) compared with one rescue using SOC. Of smear-positives, six SOC samples produced contaminated cultures whereas only one OMS sample was contaminated. OMS reduced culture contamination from 12% to 2%, and improved TB detection by 9%. The results suggest that OMS could perform well as a no cold chain, long-term transport solution for smear and culture testing. The findings provide a basis for larger feasibility studies.

A Chlorhexidine- Agar Plate Culture Medium Protocol to Complement Standard Broth Culture of Mycobacterium tuberculosis

The culture of Mycobacterium tuberculosis using parallel inoculation of a solid culture medium and a liquid broth provides the gold standard for the diagnosis of tuberculosis. Here, we evaluated a chlorhexidine decontamination-MOD9 solid medium protocol versus the standard NALC-NaOH-Bactec 960 MGIT protocol for the diagnosis of pulmonary tuberculosis by culture. Three-hundred clinical specimens comprising 193 sputa, 30 bronchial aspirates, 10 broncho-alveolar lavages, 47 stools, and 20 urines were prospectively submitted for the routine diagnosis of tuberculosis. The contamination rates were 5/300 (1.7%) using the MOD9 protocol and 17/300 (5.7%) with the Bactec protocol, respectively (P < 0.05, Fisher exact test). Of a total of 50 Mycobacterium isolates (48 M. tuberculosis and two Mycobacterium abscessus) were cultured. Out of these 50, 48 (96%) isolates were found using the MOD9 protocol versus 35 (70%) when using the Bactec protocol (P < 0.05, Fisher exact test). The time to positivity was 10.1 ± 3.9 days versus 14.7 ± 7.3 days, respectively, (P < 0.05, Student’s t-test). These data confirmed the usefulness of parallel inoculation of a solid culture medium with broth for the recovery of M. tuberculosis in agreement with current recommendations. More specifically, chlorhexidine decontamination and inoculation of the MOD9 solid medium could be proposed to complement the standard Bactec 960 MGIT broth protocol.

Rapid culture-based diagnosis of pulmonary tuberculosis in developed and developing countries

Culturing Mycobacterium tuberculosis remains the gold standard for the laboratory diagnosis of pulmonary tuberculosis, with 9 million new cases and 1.5 million deaths mainly in developing countries. Reviewing data reported over 20 years yields a state-of-the-art procedure for the routine culture of M. tuberculosis in both developed and developing countries. Useful specimens include sputum, induced sputum, and stools collected in quaternary ammonium preservative-containing sterile cans. The usefulness of other non-invasive specimens remains to be evaluated. Specimens can be collected in a diagnosis kit also containing sampling materials, instructions, laboratory requests, and informed consent. Automated direct LED fluorescence microscopy after auramine staining precedes inoculation of an egg-lecithin-containing culture solid medium under microaerophilic atmosphere, inverted microscope reading or scanning video-imaging detection of colonies and colonies identification by recent molecular methods. This procedure should result in a diagnosis of pulmonary tuberculosis as fast as 5 days. It may be implemented in both developed and developing countries with automated steps replaceable by manual steps depending on local resources.