Conventional methods versus 16S ribosomal DNA sequencing for identification of nontuberculous mycobacteria: cost analysis

Contamination rate of rare bacterial species detected by MALDI-TOFMS: a retrospective cohort study

When rare bacterial species are identified in blood cultures, determining the clinical significance is sometimes difficult. This study aimed to analyze the clinical significance of rare bacterial species detected in blood cultures using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOFMS) by comparing their contamination rates with those of common species. We retrospectively analyzed medical records of adult patients with positive blood cultures at Kyoto City Hospital from 2014 to 2022. Rare species were defined by low detection rates and few PubMed reports. Of 4880 microorganisms identified from 3441 individuals, 1150 (23.6%) were classified as contamination. Meanwhile, 24 rare microorganisms were identified, of which 14 (58.3%) were classified as contamination, which was significantly higher than common species (odds ratio 4.56, 95% confidence Interval 1.88-11.50, P < 0.001). These findings may help in determining the clinical significance of rare bacterial species in blood cultures with few reported cases.

Application of MALDI-TOF MS for enumerating bacterial constituents of defined consortia

Characterization of live biotherapeutic product (LBP) batches typically includes a measurement of viability, such as colony forming units (CFU). However, strain-specific CFU enumeration assays can be complicated by the presence of multiple organisms in a single product with similar growth requirements. To overcome specific challenges associated with obtaining strain-specific CFU values from multi-strain mixtures, we developed a method combining mass spectrometry-based colony identification with a traditional CFU assay. This method was assessed using defined consortia made from up to eight bacterial strains. Among four replicate batches of an eight-strain mixture, observed values differed from expected values by less than 0.4 log₁₀ CFU among all strains measured (range of differences, -0.318 to + 0.267). The average difference between observed and expected values was + 0.0308 log₁₀ CFU, with 95% limits of agreement from -0.347 to 0.408 (Bland-Altman analysis). To estimate precision, a single batch of eight-strain mixture was assayed in triplicate by three different users, for a total of nine measurements. Pooled standard deviation values ranged from 0.067 to 0.195 log₁₀ CFU for the eight strains measured, and user averages did not differ significantly. Leveraging emerging mass-spectrometry-based colony identification tools, a novel method for simultaneous enumeration and identification of viable bacteria from mixed-strain consortia was developed and tested. This study demonstrates the potential for this approach to generate accurate and consistent measurements of up to eight bacterial strains simultaneously and may provide a flexible platform for future refinements and modifications. KEY POINTS: • Enumeration of live biotherapeutics is essential for product quality and safety. • Conventional CFU counting may not differentiate between strains in microbial products. • This approach was developed for direct enumeration of mixed bacterial strains simultaneously.

Mycobacteriophage Derived Lipoarabinomannan Binding Protein for Recognizing Non-Tuberculosis Mycobacteria

Non-tuberculosis mycobacteria (NTM) is one family of pathogens usually leading to nosocomial infections. Exploration of high-performance biological recognition agent plays a pivotal role for the development of point-of-care testing device and kit for detecting NTM. Mycobacterium smegmatis (M. smegmatis) is a NTM which has been frequently applied as an alternative model for highly pathogenic mycobacteria. Herein, a recombinant tail protein derived from mycobacteriophage SWU1 infecting M. smegmatis was expressed with Escherichia coli system and noted as GP89. It shows a fist-like structure according to the results of homology modeling and ab initio modeling. It is confirmed as a lipoarabinomannan (LAM) binding protein, which can recognize studied NTM genus since abundant LAM constructed with d-mannan and d-arabinan is distributed over the mycobacterial surface. Meanwhile an enhanced green fluorescent protein (eGFP)-fused GP89 protein was acquired with a fusion expression technique. Then GP89 and eGFP-fused GP89 were applied to establish a sensitive and rapid method for fluorescent detection of M. smegmatis with a broad linear range of 1.0 × 10² to 1.0 × 10⁶ CFU mL^-1 and a low detection limit of 69 CFU mL^-1. Rapid and reliable testing of antimicrobial susceptibility was achieved by the GP89-based fluorescent method. The present work provides a promising recognition agent for studied NTM and opens an avenue for clinical diagnosis of NTM-induced infections.

Unnecessary Routine Use of Mycobacterial Cultures in Patients with Periprosthetic Joint Infections

Accurate diagnosis ensures appropriate therapy of periprosthetic joint infection (PJI). Since mycobacterial PJI is rare, routine testing is inappropriate. We reviewed hip and knee PJI at our institution over 28 months. Mycobacterial cultures were routinely sent with rare positivity. Mycobacterial cultures should be sent only when there is clinical suspicion.

Osteomyelitis Due to Mycobacterium goodii in an Adolescent, United States

Osteomyelitis is a rare clinical manifestation of infection with nontuberculous mycobacteria (NTM). We report an adolescent with femoral osteomyelitis associated with prosthetic material due to an emerging pathogen, Mycobacterium goodii. Application of secA1 and 16S ribosomal RNA gene sequencing reliably determined the NTM species, enabling targeted antimicrobial therapy.

Differential diagnosis of disseminated Mycobacterium avium and Mycobacterium tuberculosis infection in HIV patients using duplex PCR

Background: Disseminated Mycobacterium avium complex (MAC) and Mycobacterium tuberculosis infections have almost similar clinical presentations but require different therapeutic management. Materials & methods: A duplex PCR was designed based on the sequence variation between the genes encoding catalase-peroxidase (KatG) of M. avium complex and M. tuberculosis, so as to discriminate MAC, M. tuberculosis and mixed mycobacterial (MAC + M. tuberculosis) infections in HIV patients. Results: An accurate, single-step differential diagnosis of disseminated mycobacterial infections in HIV patients was achieved with specific detection of a single band each for M. avium (120 bp) and M. tuberculosis (90 bp) and two bands for the mixed (120 and 90 bp) infections. Conclusion: katG gene-based duplex PCR can facilitate quick differential diagnosis of disseminated MAC and M. tuberculosis infections in HIV patients.

Isolation and Molecular Identification of Nontuberculous Mycobacterium from Different Species of Fish in Karbala Province, Iraq

This study was designed for isolation and molecular identification of Nontuberculous Mycobacterium (NTM) from fish during the period between October and December 2017 from Karbla province, Iraq. This study included 200 fresh fish samples from four different species including Spondyliosoma cantharus, Liza abu, Carassius carassius and Cyprinuscarpio. Three samples of each fish were taken including gills, muscles and all internal organs. The samples were processed by decontamination, concentration of 4% sodium hydroxide, and 0.1 ml of sediment was streaking on Löwenstein Johnson (LJ) media; then the bacterial cultures were incubated at 28-30 °C for 3days up to 4 weeks and suspected colonies were stained with acid fast stain to confirm the presence of Mycobacterium. Further identification, biochemical tests were carried out to confirm the diagnosis of isolates, PCR was done using 16s RNA gene for all isolates, hsp65 gene was used in unidentified NTM spp and to confirm the others. Results revealed that out of 200 fish samples, 19 isolates 9.5% were identified as NTM belonged to Rapid Growth Mycobacterium (RGM). of the total isolates, 18.26 % was investigated from Liza abu (Kishni, Abu khraiza). NTM (RGM) isolates on spp level identified six spp of these isolates. M. porcinum was 26.32% which was followed by M. fortuitum of 21.05%, others included M. neworleansense and M. mucogenicum 10.5% of each, M. cosmeticum and M. pallens 5.26% of each. The distribution of NTM spp in the fish organs, nine out of 19 (47.37%) NTM isolate were recovered from gills followed by muscles 36.84 %, while 15.79% from internal organs. These results were the first study concerning isolation of these spp of NTM from fish in Iraq, and some spp are not reported in other studies. This study concluded that the fish is an importance source or reservoir for NTM, especially the pathogenic spp.

The role of infectious pathogens in exacerbation of chronic obstructive pulmonary disease in Dakahlia Governorate

Background

Exacerbations of chronic obstructive pulmonary disease (COPD) represent important events in the management of COPD because of its negative impact on health status and disease progression. The etiology of acute exacerbations of chronic obstructive pulmonary disease (COPDAE) is heterogeneous and still under discussion. So, this study was planned to investigate the role of infectious pathogens (fungi and atypical mycobacteria in addition to the well-known bacteria) in patients with COPD exacerbation in our locality.

Results

This observational cross-sectional study was conducted on 100 patients with acute exacerbation of COPD. Sputum specimens were collected for mycobacterial and fungal examination in addition to routine sputum bacteriology. All sputum samples were negative for typical and atypical mycobacteria whereas sputum samples of 18 patients (18%) were negative for fungi. Mixed fungal growth was found in 19 patients (19%).Candidawas isolated from 67 patients (67%),Aspergilluswas isolated from 27 patients (27%),Alternariawas isolated from 3 patients (3%), and other fungi were isolated from 4 patients (4%). As regards sputum bacteriology, sputum samples of 49 patients (49%) have bacterial growth.Streptococcus pneumoniaewas isolated from 16 samples (16%) and represents the most frequent bacterial isolate in this study.

Conclusion

The present study indicates that typical and atypical mycobacteria have no role in COPD exacerbations in our locality. However, fungi and bacteria may have a role in COPD exacerbations.

Impact of host genetics on gut microbiome: Take-home lessons from human and mouse studies

The intestinal microbiome has emerged as an important component involved in various diseases. Therefore, the interest in understanding the factors shaping its composition is growing. The gut microbiome, often defined as a complex trait, contains diverse components and its properties are determined by a combination of external and internal effects. Although much effort has been invested so far, it is still difficult to evaluate the extent to which human genetics shape the composition of the gut microbiota. However, in mouse studies, where the environmental factors are better controlled, the effect of the genetic background was significant. The purpose of this paper is to provide a current assessment of the role of human host genetics in shaping the gut microbiome composition. Despite the inconsistency of the reported results, it can be estimated that the genetic factor affects a portion of the microbiome. However, this effect is currently lower than the initial estimates, and it is difficult to separate the genetic influence from the environmental effect. Additionally, despite the differences between the microbial composition of humans and mice, results from mouse models can strengthen our knowledge of host genetics underlying the human gut microbial variation.

Isolation, identification and associated risk factors of non-tuberculous mycobacteria infection in humans and dromedary camels in Samburu County, Kenya

Non-tuberculous mycobacteria are of public health significance, and zoonotic infection is attributed to the sociocultural practice of consumption of raw milk and the close human-livestock contact in pastoral communities. This study aimed at isolation, identification of mycobacteria from human sputum and camel milk and risk factors assessment in Samburu East, Kenya. Six hundred and twelve camels and 48 people presumed to have tuberculosis (TB) from 86 households in Wamba and Waso regions were screened. Camels were categorized into Somali, Turkana and Rendile breeds. Single intradermal comparative tuberculin test (SICTT) was used as a herd-screening test on lactating camels and a milk sample collected from reactive camels. Sputum samples were collected from eligible members of participating households. A standard questionnaire on possible risk factors for both humans and camels was administered to respective household heads or their representatives. Total camel skin test reactors were 238/612 (38.9%). Milk and sputum samples were analysed at KEMRI/TB research laboratory for microscopy, GeneXpert^® , culture and identification. Isolates were identified using 16S rRNA gene sequencing at Inqaba biotec in South Africa. Sixty-four isolates were acid-fast bacilli (AFB) positive of which M. fortuitum (3), M. szulgai (20), M. monacense (5), M. lehmanni (4), M. litorale (4), M. elephantis (3), M. duvalii (3), M. brasiliensis (1), M. arcueilense (1) and M. lentiflavum (1) were from milk; M. fortuitum (1), M. szulgai (2) and M. litorale (1) were from humans. Risk factors included the following: Turkana breed (OR = 3.4; 95% CI: 1.2-9.3), replacements from outside the County (OR = 2.1; 95% CI: 0.3-12.3), presence of other domestic species (small stock; OR = 4.6) and replacement from within the herd (OR = 3.2; 95% CI: 0.7-14.7). Zoonotic risk practices included raw milk consumption, shared housing and handling camels. Monitoring of zoonotic NTM through surveillance and notification systems is required.

Current significance of the Mycobacterium chelonae-abscessus group

Organisms of the Mycobacterium chelonae-abscessus group can be significant pathogens in humans. They produce a number of diseases including acute, invasive and chronic infections, which may be difficult to diagnose correctly. Identification among members of this group is complicated by differentiating at least eleven (11) known species and subspecies and complexity of identification methodologies. Treatment of their infections may be problematic due to their correct species identification, antibiotic resistance, their differential susceptibility to the limited number of drugs available, and scarcity of susceptibility testing.

Polymerase Chain Reaction Assay Using the Restriction Fragment Length Polymorphism Technique in the Detection of Prosthetic Joint Infections: A Multi-Centered Study

BACKGROUND

PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) techniques have been used for the diagnosis of bacteria in some infections. In this study, we aimed to evaluate the diagnostic accuracy of PCR for the diagnosis of prosthetic joint infections (PJI) and to identify isolated microorganisms, using the RFLP method.

METHODS

During January 2015 to January 2018, patients who were suspected of having PJI after arthroplasty surgery or were candidates for revision surgery due to loosening of implant entered the study. Patients who had 1 major criterion or 3 minor criteria for PJI based on the Philadelphia Consensus Criteria (PCC) on Periprosthetic Joint Infection were considered as cases of PJI. Both culture results and PCR findings, were cross compared with results of the PCC (as the gold standard criteria).

RESULTS

Overall, 76 samples were included in the study. Mean (standard deviation) age of patients was 66.72 ± 11.82 years. Overall, 57.9% of patients were females. Prevalence of PJI was 50% based on the PCC. Sensitivity, specificity, positive predictive value, negative predictive value, and general efficacy of PCR for detection of PJI was 97.4%, 100%, 100%, 97.4%, and 98.7%, respectively. Sensitivity, specificity, positive predictive value, negative predictive value, and general efficacy of culture was 31.6%, 100%, 65.7%, 100%, and 59.4%, respectively. We isolated a broad range of bacteria using PCR-RFLP including Gram-positive cocci such as Staphylococcus sp., Streptococcus sp., and Enterococcus sp., and Gram-negative bacilli such as Enterobacteriaceae sp., Pseudomonas sp. Citrobacter sp., as well as Chlamydophila pneumonia, Stenotrophomonas maltophilia, Brucella melitensis, non-gonococcal Neisseria, Kingella kingae, Bacteroides ovatus, and Proteus mirabilis from PJI patients.

CONCLUSION

Inhere, for the first time, we showed that PCR-RFLP is a powerful tool for identifying the type of bacteria involved in PJI, and can be used for follow-up of patients suspected of PJI and those with a history of antibiotic use. PCR-RFLP may be able to substantially decrease detection time of PJI among PCR-based methods, while allowing more accurate identification of the bacteria involved.

Management of Mycobacterium Other than Tuberculosis in Solid Organ Transplantation

Mycobacteria other than tuberculosis are important pathogens to consider in solid organ transplant recipients. Delay in recognition and treatment may incur significant morbidity and mortality. Management of mycobacteria other than tuberculosis requires a knowledge of treatment specific for each species and drug-drug interactions between antimicrobial and immunosuppressive drugs. Therapy in solid organ transplant can be prolonged and may require a reduction in immunosuppression to improve outcomes.

Prevalence and species spectrum of both pulmonary and extrapulmonary nontuberculous mycobacteria isolates at a tertiary care center

OBJECTIVE/BACKGROUND

Nontuberculous mycobacteria (NTM) infection associated with pulmonary and extrapulmonary disease has been increasing globally. Despite an increase in incidence rate of NTM infection, its prevalence, species diversity, and circulation pattern in India is largely unknown. This study sought to investigate the overall burden and diversity of NTM among both pulmonary and extrapulmonary clinical isolates from a Northern Indian population.

METHODS

The study was conducted in the Department of Microbiology, from January 2013 to December 2015. A total of 4620 clinical samples were collected from patients suspected to have pulmonary and extrapulmonary tuberculosis. Preliminary diagnosis was performed using Ziehl-Neelsen staining followed by liquid culture in BacT/ALERT three-dimensional system. A total of 906 positive cultures obtained were differentiated as either NTM or Mycobacterium tuberculosis complex using a biochemical and MPT64 antigen test. Further identification of NTM species was confirmed with a line probe assay.

RESULTS

Out of 906 cultures isolates, 263 (29.0%) were confirmed as NTM and 643 (71.0%) were identified as Mycobacterium tuberculosis complex. A total of 79.4% of the NTM were recovered from pulmonary and 18.2% from extrapulmonary specimens. The diversity of NTM species was high (13 species) and predominated by Mycobacterium abscessus (31.3%) followed by Mycobacterium fortuitum (22%), Mycobacterium intracellulare (13.6%), Mycobacterium chelonae (9.1%), however, M. abscessus and M. fortuitum were the predominant species in both types of clinical isolates. Men (60.4%) and older patients aged greater than 55years were the predominated risk group for NTM infection.

CONCLUSION

The high prevalence and species diversity of NTM suggests the need for immediate and accurate characterization of NTM for proper treatment and management of patients.

Sequence-based identification of microbial contaminants in non-parenteral products

ABSTRACT Phenotypic profiles for microbial identification are unusual for rare, slow-growing and fastidious microorganisms. In the last decade, as a result of the widespread use of PCR and DNA sequencing, 16S rRNA sequencing has played a pivotal role in the accurate identification of microorganisms and the discovery of novel isolates in microbiology laboratories. The 16S rRNA region is universally distributed among microorganisms and is species-specific. Accordingly, the aim of our study was the genotypic identification of microorganisms isolated from non-parenteral pharmaceutical formulations. DNA was separated from five isolates obtained from the formulations. The target regions of the rRNA genes were amplified by PCR and sequenced using suitable primers. The sequence data were analyzed and aligned in the order of increasing genetic distance to relevant sequences against a library database to achieve an identity match. The DNA sequences of the phylogenetic tree results confirmed the identity of the isolates as Bacillus tequilensis, B. subtilis, Staphylococcus haemolyticus and B. amyloliqueficians. It can be concluded that 16S rRNA sequence-based identification reduces the time by circumventing biochemical tests and also increases specificity and accuracy.

Novel Mycobacterium avium Complex Species Isolated From Black Wildebeest (Connochaetes gnou) in South Africa

A study was undertaken to isolate and characterize Mycobacterium species from black wildebeest suspected of being infected with tuberculosis in South Africa. This led to the discovery of a new Mycobacterium avium complex species, provisionally referred to as the Gnou isolate from black wildebeest (Connochaetes gnou). Sixteen samples from nine black wildebeest were processed for Mycobacterium isolation. Following decontamination, samples were incubated in an ordinary incubator at 37°C on Löwenstein-Jensen slants and in liquid medium tubes using the BACTEC^™ MGIT^™ 960 system, respectively. Identification of the isolate was carried out by standard biochemical tests and using the line probe assay from the GenoType^® CM/AS kit (Hain Lifescience GmbH, Nehren, Germany). The DNA extract was also analysed using gene sequencing. Partial gene sequencing and analysis of 16S rRNA gene, and 16S-23S rRNA (ITS), rpoB and hsp65 and phylogenetic analyses by searching GenBank using the BLAST algorithm were conducted. Phylogenetic trees were constructed using four methods, namely Bayesian inference, maximum likelihood, maximum parsimony and neighbour-joining methods. The isolate was identified as Mycobacterium intracellulare using the GenoType^® CM/AS kit and as Mycobacterium avium complex (MAC) by gene sequencing. The gene sequence targeting all the genes, ITS, 16S rRNA, rpoB and hsp65 and phylogenetic analyses indicated that this isolate presented a nucleotide sequence different from all currently published sequences, and its position was far enough from other MAC species to suggest that it might be a new species.

Non-tuberculous mycobacteria (NTM) in Zambia: prevalence, clinical, radiological and microbiological characteristics

Background

Non-tuberculous mycobacteria (NTM) infection is an emerging health problem. We present here the Zambia-specific national level data of prevalence, symptomatic, radiological and microbiological characteristics of NTM, using results from a national Tuberculosis (TB) prevalence survey.

Methods

This was a cross-sectional study of the prevalence of NTM among adults aged 15 years and above, who were participants in a national TB prevalence survey. Participants who had either an abnormal chest x-ray or were symptomatic were considered presumptive TB cases and submitted sputum for smear and culture analysis. HIV testing was performed on an opt-out basis. Symptomatic NTM prevalence was estimated from individual level analysis.

Results

Of the 6,123 individuals with presumptive TB, 923 (15.1 %) were found to have NTM, 13 (0.2 %) were MTB/NTM co-infected and 338 (5.5 %) were contaminated (indeterminate). The prevalence of symptomatic NTM was found to be 1,477/100,000 [95 % CI 1010–1943]. Smear positivity, history of cough or chest pain and HIV positivity were risk factors for NTM.

Conclusion

This first study to estimate the national prevalence of NTM in Zambia indicates that the burden is high. The NTM occurrence in Zambia constitutes both a public health and ethical issue requiring action from health managers.

16S rRNA gene sequencing is a non-culture method of defining the specific bacterial etiology of ventilator-associated pneumonia

Ventilator-associated pneumonia (VAP) is an acquired respiratory tract infection following tracheal intubation. The most common hospital-acquired infection among patients with acute respiratory failure, VAP is associated with a mortality rate of 20-30%. The standard bacterial culture method for identifying the etiology of VAP is not specific, timely, or accurate in identifying the bacterial pathogens. This study used 16S rRNA gene metagenomic sequencing to identify and quantify the pathogenic bacteria in lower respiratory tract and oropharyngeal samples of 55 VAP patients. Sequencing of the 16S rRNA gene has served as a valuable tool in bacterial identification, particularly when other biochemical, molecular, or phenotypic identification techniques fail. In this study, 16S rRNA gene sequencing was performed in parallel with the standard bacterial culture method to identify and quantify bacteria present in the collected patient samples. Sequence analysis showed the colonization of multidrug-resistant strains in VAP secretions. Further, this method identified Prevotella, Proteus, Aquabacter, and Sphingomonas bacterial genera that were not detected by the standard bacterial culture method. Seven categories of bacteria, Streptococcus, Neisseria, Corynebacterium, Acinetobacter, Staphylococcus, Pseudomonas and Klebsiella, were detectable by both 16S rRNA gene sequencing and standard bacterial culture methods. Further, 16S rRNA gene sequencing had a significantly higher sensitivity in detecting Streptococcus and Pseudomonas when compared to standard bacterial culture. Together, these data present 16S rRNA gene sequencing as a novel VAP diagnosis tool that will further enable pathogen-specific treatment of VAP.

Evaluation and management of patients with pulmonary nontuberculous mycobacterial infections

Nontuberculous mycobacteria (NTM) are emerging pathogens increasingly associated with chronic pulmonary disease. NTM are environmental saprophytes found in soil, dust and water and, unlike Mycobacterium tuberculosis, NTM are not transmitted from person to person. Pulmonary disease caused by NTM is a particular problem in older people without underlying immune compromise. The diagnosis of NTM pulmonary disease usually requires either multiple respiratory cultures that grow NTM or heavy growth of NTM from a single bronchoscopy or lung-biopsy specimen. High resolution computed tomography is the most useful radiographic study for diagnosis and to determine the extent of disease. Treatment includes multiple medications with activity against the particular NTM species, as single-drug therapy is likely to select for resistant organisms. Data demonstrating the effectiveness of specific drug regimens for NTM pulmonary disease are limited. Clarithromycin and azithromycin form the backbone of most treatment regimens because these drugs are active against many NTM species. Drug tolerability and cost are the major barriers to successful treatment of NTM pulmonary disease. Adjunctive therapies, including mucus clearance techniques and appetite stimulants, are unproven but may be of value in management of NTM pulmonary disease. Multicenter, randomized trials of macrolide-based therapies are sorely needed to determine the safest and most effective treatments for NTM pulmonary disease.

Cost-effectiveness comparison of Genechip and conventional drug susceptibility test for detecting multidrug-resistant tuberculosis in China

BACKGROUND

Genechip (CapitalBio, Beijing, China) is a system for diagnosing resistance to rifampin and isoniazid, which shows high efficiency in detecting drug-resistant tuberculosis. Here, we firstly evaluated the costs of Genechip for detecting the drug susceptibility of Mycobacterium tuberculosis, compared to conventional drug susceptibility test (DST) in laboratories in China.

METHODOLOGY/PRINCIPAL FINDINGS

Data on the costs of the two tests were collected at four hospitals. Costs were calculated using the essential factor cost calculation method. The costs of diagnosing a single case of multidrug-resistant tuberculosis (MDR-TB) using Genechip and DST were US$22.38 and $53.03, respectively. Taking into account the effect on costs from failure of a certain number of tests to accurately diagnose MDR-TB, the costs of Genechip and DST increased by 17.65% and 5.22%, respectively. The cost of both tests decreased with the increasing prevalence of MDR-TB disease, and the cost of Genechip at a sensitivity of more than 50% was lower than that of DST. When price of Genechip was varied to 50%, 80%, 150%, and 200% of the original price, the cost of Genechip at sensitivities of more than 30%, 40%, 60%, and 70%, respectively, was also lower than that of DST.

CONCLUSIONS/SIGNIFICANCE

This study showed that Genechip was a more cost-effective method of diagnosing MDR-TB compared to conventional DST.

Bovine tuberculosis in South Darfur State, Sudan: an abattoir study based on microscopy and molecular detection methods

Bovine tuberculosis (BTB) is a widespread zoonosis in developing countries but has received little attention in many sub-Saharan African countries including Sudan and particularly in some parts such as Darfur states. This study aimed to detect bovine tuberculosis among caseous materials of cattle slaughtered in abattoirs in South Darfur State, Sudan by using microscopic and PCR-based methods. The study was a cross-sectional abattoir-based study which examined a total of 6,680 bovine carcasses for caseous lesions in South Darfur State between 2007 and 2009. Collected specimens were examined for the presence of acid-fast bacilli (AFB) by using microscopic and culture techniques. Isolated mycobacteria were identified by selected conventional cultural and biochemical tests in comparison to a single tube multiplex PCR (m-PCR) assay which detect Mycobacterium bovis-specific 168-bp amplicons. Of the total 6,680 slaughtered cattle examined in South Darfur, 400 (6 %) showed caseations restricted to lymph nodes (86.8 %) or generalized (13.2 %). Bovine tuberculosis was diagnosed in 12 (0.18 %), bovine farcy in 59 (0.88 %), unidentified mycobacteria in 6 (0.09 %), and missed or contaminated cultures in 7 (0.1 %). Out of 18 cultures with nonbranching acid-fast rods, 12 amplified unique 168-bp sequence specific for M. bovis and subsequently confirmed as M. bovis. With the exception of the reference M. tuberculosis strains, none of the remaining AFB amplified the 337-bp amplicon specific for M. tuberculosis. It could be concluded that bovine tuberculosis is prevalent among cattle in South Darfur representing 4.5 % from all slaughtered cattle with caseous lesions. The study sustains microscopy as a useful and accessible technique for detecting AFB. m-PCR assay proved to be valuable for confirmation of BTB and its differentiation from other related mycobacteriosis, notably bovine farcy.

Electronic fingerprints of DNA bases on graphene

We calculate the electronic local density of states (LDOS) of DNA nucleotide bases (A,C,G,T), deposited on graphene. We observe significant base-dependent features in the LDOS in an energy range within a few electronvolts of the Fermi level. These features can serve as electronic fingerprints for the identification of individual bases in scanning tunneling spectroscopy (STS) experiments that perform image and site dependent spectroscopy on biomolecules. Thus the fingerprints of DNA-graphene hybrid structures may provide an alternative route to DNA sequencing using STS.

Novel real-time simultaneous amplification and testing method to accurately and rapidly detect Mycobacterium tuberculosis complex

The aim of this study was to establish and evaluate a simultaneous amplification and testing method for detection of the Mycobacterium tuberculosis complex (SAT-TB assay) in clinical specimens by using isothermal RNA amplification and real-time fluorescence detection. In the SAT-TB assay, a 170-bp M. tuberculosis 16S rRNA fragment is reverse transcribed to DNA by use of Moloney murine leukemia virus (M-MLV) reverse transcriptase, using specific primers incorporating the T7 promoter sequence, and undergoes successive cycles of amplification using T7 RNA polymerase. Using a real-time PCR instrument, hybridization of an internal 6-carboxyfluorescein-4-[4-(dimethylamino)phenylazo] benzoic acid N-succinimidyl ester (FAM-DABCYL)-labeled fluorescent probe can be used to detect RNA amplification. The SAT-TB assay takes less than 1.5 h to perform, and the sensitivity of the assay for detection of M. tuberculosis H37Rv is 100 CFU/ml. The TB probe has no cross-reactivity with nontuberculous mycobacteria or other common respiratory tract pathogens. For 253 pulmonary tuberculosis (PTB) specimens and 134 non-TB specimens, the SAT-TB results correlated with 95.6% (370/387 specimens) of the Bactec MGIT 960 culture assay results. The sensitivity, specificity, and positive and negative predictive values of the SAT-TB test for the diagnosis of PTB were 67.6%, 100%, 100%, and 62.0%, respectively, compared to 61.7%, 100%, 100%, and 58.0% for Bactec MGIT 960 culture. For PTB diagnosis, the sensitivities of the SAT-TB and Bactec MGIT 960 culture methods were 97.6% and 95.9%, respectively, for smear-positive specimens and 39.2% and 30.2%, respectively, for smear-negative specimens. In conclusion, the SAT-TB assay is a novel, simple test with a high specificity which may enhance the detection rate of TB. It is therefore a promising tool for rapid diagnosis of M. tuberculosis infection in clinical microbiology laboratories.

Mass spectrometry based methods for the discrimination and typing of mycobacteria

Identification and typing of mycobacteria is very important for epidemiology, susceptibility testing and diagnostic purposes. This paper describes the development and validation of the alternative methods for species identification and typing of mycobacteria based on a matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-ToF MS). Altogether there were 383 clinical isolates analyzed which include 348 strains of Mycobacterium tuberculosis complex (MTBC) (342 strains of M. tuberculosis and 6 strains of M. bovis) and 35 strains of nontuberculous mycobacteria (NTM) represented by 16 different species. Direct bacterial profiling (DBP) by means of MALDI-ToF MS was carried out. Cluster analysis of DBP mass spectra divided them into two large separate groups corresponding to MTBC and NTM, and also demonstrated the possibility of isolate identification at the species level. Spoligotyping protocol based on mass spectrometry was developed and validated, it matched completely to classical spoligotyping data. Our results suggest that MALDI-ToF MS has potential as a rapid and reproducible platform for the identification and typing of Mycobacterium species.

Biochip system for rapid and accurate identification of mycobacterial species from isolates and sputum

The accurate detection of mycobacterial species from isolates and clinical samples is important for pathogenic diagnosis and treatment and for disease control. There is an urgent need for the development of a rapid, simple, and accurate detection method. We established a biochip assay system, including a biochip, sample preparation apparatus, hybridization instrument, chip washing machine, and laser confocal scanner equipped with interpretation software for automatic diagnosis. The biochip simultaneously identified 17 common mycobacterial species by targeting the differences in the 16S rRNA. The system was assessed with 64 reference strains and 296 Mycobacterium tuberculosis and 243 nontuberculous mycobacterial isolates, as well as 138 other bacteria and 195 sputum samples, and then compared to DNA sequencing. The entire biochip assay took 6 h. The concordance rate between the biochip assay and the DNA sequencing results was 100%. In conclusion, the biochip system provides a simple, rapid, reliable, and highly accurate clinical assay for determination of mycobacterial species in a 6-h procedure, from either culture isolates or sputum samples, allowing earlier pathogen-adapted antimicrobial therapy in patients.

Comparison of traditional phenotypic identification methods with partial 5' 16S rRNA gene sequencing for species-level identification of nonfermenting Gram-negative bacilli

Correct identification of nonfermenting Gram-negative bacilli (NFB) is crucial for patient management. We compared phenotypic identifications of 96 clinical NFB isolates with identifications obtained by 5' 16S rRNA gene sequencing. Sequencing identified 88 isolates (91.7%) with >99% similarity to a sequence from the assigned species; 61.5% of sequencing results were concordant with phenotypic results, indicating the usability of sequencing to identify NFB.

Phenotypic and molecular typing of tuberculous and nontuberculous Mycobacterium species from slaughtered pigs in Egypt

A total of 745 slaughtered pigs were examined during routine meat inspection for suspected tuberculous lesions. Specimens from suspected lesions were collected for conventional mycobacteriologic examinations. Suspected mycobacterial colonies were subjected to molecular typing based on the Mycobacterium species-specific intergenic spacer (IGS) target. The study resulted in detection of suspected lesions in 110 (14.8%) carcasses, from which only 67 specimens produced suspected mycobacterial colonies. Conventional examination was only able to identify 56 isolates as Mycobacterium species, which was confirmed by polymerase chain reaction amplification of the IGS target. Interestingly, out of these, 18 and 12 isolates were Mycobacterium tuberculosis and Mycobacterium bovis, respectively. Sequence analysis of IGS resolved the identities of 10 of the 11 conventionally unidentified isolates as being 4 different nontuberculous Mycobacterium species. The last isolate was proposed as a non-Mycobacterium species and was confirmed by its identification as Rhodococcus equi based on the 16S ribosomal DNA sequence analysis. The study described the isolation of Mycobacterium tuberculosis from pigs and revealed high burden of infection with both tuberculous and nontuberculous mycobacterial species among pigs in Egypt. In addition, the study showed the usefulness of IGS sequence analysis as a reliable molecular tool that would be useful for further epidemiologic and public health studies.

Pyrosequencing of a short hypervariable 16S rDNA fragment for the identification of nontuberculous mycobacteria--a comparison with conventional 16S rDNA sequencing and phenotyping

Conventional methods for identification of nontuberculous mycobacteria (NTM) are often inexact and time consuming. Sequencing of bacterial 16S rDNA is accurate, rapid and effective. We have retrospectively evaluated the discriminative power of pyrosequencing of a short hypervariable 16S rDNA fragment as a simple and rapid tool for NTM characterization. A series of 312 clinical NTM isolates, excluding the M. avium/intracellulare complex, was investigated. When species could not be resolved by sequencing alone, growth rate and pigment production were also examined. 54% (170/312) of the isolates were unambiguously identified by both methods. An additional 14% (45/312) were directly identified to species by conventional 16S rDNA sequencing but needed complementary phenotypic analysis when examined by pyrosequencing. The remaining 31% (97/312) needed additional phenotypic analysis for both sequencing methods. We consider the pyrosequencing procedure to be a useful alternative for the identification of several NTM species, and a versatile tool for the characterization of clinical NTM isolates. At times it requires additional tests for definite species diagnosis and correct identification.

Reliable identification of mycobacterial species by PCR-restriction enzyme analysis (PRA)-hsp65 in a reference laboratory and elaboration of a sequence-based extended algorithm of PRA-hsp65 patterns

BACKGROUND

Identification of nontuberculous mycobacteria (NTM) based on phenotypic tests is time-consuming, labor-intensive, expensive and often provides erroneous or inconclusive results. In the molecular method referred to as PRA-hsp65, a fragment of the hsp65 gene is amplified by PCR and then analyzed by restriction digest; this rapid approach offers the promise of accurate, cost-effective species identification. The aim of this study was to determine whether species identification of NTM using PRA-hsp65 is sufficiently reliable to serve as the routine methodology in a reference laboratory.

RESULTS

A total of 434 NTM isolates were obtained from 5019 cultures submitted to the Institute Adolpho Lutz, Sao Paulo Brazil, between January 2000 and January 2001. Species identification was performed for all isolates using conventional phenotypic methods and PRA-hsp65. For isolates for which these methods gave discordant results, definitive species identification was obtained by sequencing a 441 bp fragment of hsp65. Phenotypic evaluation and PRA-hsp65 were concordant for 321 (74%) isolates. These assignments were presumed to be correct. For the remaining 113 discordant isolates, definitive identification was based on sequencing a 441 bp fragment of hsp65. PRA-hsp65 identified 30 isolates with hsp65 alleles representing 13 previously unreported PRA-hsp65 patterns. Overall, species identification by PRA-hsp65 was significantly more accurate than by phenotype methods (392 (90.3%) vs. 338 (77.9%), respectively; p < .0001, Fisher's test). Among the 333 isolates representing the most common pathogenic species, PRA-hsp65 provided an incorrect result for only 1.2%.

CONCLUSION

PRA-hsp65 is a rapid and highly reliable method and deserves consideration by any clinical microbiology laboratory charged with performing species identification of NTM.

A novel identification scheme for genus Mycobacterium, M. tuberculosis complex, and seven mycobacteria species of human clinical impact

Recently, the incidence of human mycobacterial infections due to species other than M. tuberculosis has increased worldwide. Since disease control depends on appropriate antimicrobial therapy, the precise identification of these species of clinical importance has become a major public health concern. Identification of mycobacteria has been hampered because of the lack of specific, rapid, and inexpensive methods. Therefore, we aimed at designing and validating a bacterial lysate-based polymerase chain reaction identification scheme. This scheme can classify clinical isolates into: (1) the genus Mycobacterium, (2) the M. tuberculosis complex, (3) the nontuberculous mycobacteria, and (4) the species M. avium, M. intracellulare, M. abscessus, M. chelonae, M. fortuitum and M. bovis of clinical importance, and M. gordonae, the most commonly encountered nonpathogenic species in clinical laboratories. By using M. fortuitum and M. avium lysates as models, the method sensitivity was determined to be 372 pg of DNA. In a blind parallel comparison between our approach and conventional biochemical tests, both assays correctly categorized 75 patient's mycobacterial isolates. However, our approach only required 4-9 h for categorization compared with at least 15 days by conventional tests. Furthermore, our methodology could also detect M. fortuitum and M. avium from liquid cultures, after only 2 and 6 days, respectively, of incubation. Our new identification scheme is therefore sensitive, specific, rapid, and economic. Additionally, it can help to provide proper treatment to patients, to control these diseases, and to improve our knowledge of the epidemiology of mycobacteriosis, all urgently needed, particularly in developing countries.

Evaluation of the PCR method for identification of Bifidobacterium species

AIMS

Bifidobacterium species are known for their beneficial effects on health and their wide use as probiotics. Although various polymerase chain reaction (PCR) methods for the identification of Bifidobacterium species have been published, the reliability of these methods remains open to question.

METHODS AND RESULTS

In this study, we evaluated 37 previously reported PCR primer sets designed to amplify 16S rDNA, 23S rDNA, intergenic spacer regions, or repetitive DNA sequences of various Bifidobacterium species.

CONCLUSIONS

Ten of 37 experimental primer sets showed specificity for B. adolescentis, B. angulatum, B. pseudocatenulatum, B. breve, B. bifidum, B. longum, B. longum biovar infantis and B. dentium.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results suggest that published Bifidobacterium primer sets should be re-evaluated for both reproducibility and specificity for the identification of Bifidobacterium species using PCR. Improvement of existing PCR methods will be needed to facilitate identification of other Bifidobacterium strains, such as B. animalis, B. catenulatum, B. thermophilum and B. subtile.

Comparison of three methods for rapid identification of mycobacterial clinical isolates to the species level

A new PCR-reverse dot blot hybridization (RDBH) assay was developed for the rapid identification of Mycobacterium species in clinical isolates. The assay, which targets the 16S rRNA, was evaluated for 27 mycobacterial reference strains and 340 clinical isolates that were simultaneously identified by DNA sequencing and conventional methods, including growth characteristics, pigment production, colony morphology, and biochemical tests. All reference strains and clinical isolates hybridized to the Mycobacterium genus probe (probe M) on the membrane (100% sensitivity). Each probe had only one hybridization signal with the corresponding Mycobacterium species or complex (100% specificity). Compared with DNA sequencing, the RDBH assay correctly identified 337 (99.1% accuracy) of the 340 isolates tested. One M. asia isolate and one M. neoaurum isolate were not identified by the RDBH assay due to the absence of specific probes for the two species on the membrane. Three isolates with different nucleotide sequences from M. intracellulare reference strains had a negative hybridization signal with probe c, which is specific for M. intracellulare. The whole procedure can be completed within 2.5 h post-PCR processing. A total of 32 of 340 isolates were erroneously identified by conventional methods (90.6% accuracy). Molecular identification based on the 16S rRNA sequence was superior to the conventional approaches in speed, sensitivity, and specificity. Therefore, the RDBH assay can be considered a rapid, simple, and reliable method for routine identification of frequently occurring and clinically relevant mycobacteria.

First report of Mycobacterium nebraskense as a cause of human infection

Newly described nontuberculous Mycobacterium species have emerged as causes of opportunistic infection in compromised patients. This report describes the first case of Mycobacterium nebraskense isolated from a patient with a history of emphysema and details the need for adequate diagnostic capabilities to manage patients with infections caused by slow-growing pathogens.

[New methods for mycobacteria identification]

Currently, the genus Mycobacterium comprises more than 100 different species, many of which cause significant clinical infections with high morbidity and mortality. Mycobacteria identification by conventional methods (rate and optimal temperature of growth, pigment production, colony morphology, and biochemical characteristics) has been the standard in most clinical microbiology laboratories. However, this phenotypic approach has considerable limitations, since numerous species cannot be differentiated. Moreover, because of the slow growth of these microorganisms, the results may not be available until 2-4 weeks after the initial isolation. Therefore, one of the most important challenges for clinical mycobacteriology laboratories is rapid and accurate identification of this variety of microorganism. This review aims to briefly describe several alternative procedures for mycobacterial identification. Although analysis of cell wall lipids (mycolic acids) by high-performance liquid chromatography is an interesting and well-known option, the most promising innovation for mycobacteria identification is the use of rapid molecular methods such as nucleic acid probes and, especially, genomic amplification methods.

Sequencing and staphylococci identification

The emerging clinical importance of staphylococcal infections prompted us to establish a reference database for partial RNA polymerase B (rpoB; nucleotides 1444-1928) gene sequences from type strains of all staphylococcal species and subspecies. This database correctly identified 55 clinical staphylococcal isolates; all were correctly identified at the species level. At the subspecies level, rpoB misidentified only 2 isolates.

Nucleic acid-based methods for the detection of bacterial pathogens: Present and future considerations for the clinical laboratory

BACKGROUND

Recent advances in nucleic acid-based methods to detect bacteria offer increased sensitivity and specificity over traditional microbiological techniques. The potential benefit of nucleic acid-based testing to the clinical laboratory is reduced time to diagnosis, high throughput, and accurate and reliable results.

METHODS

Several PCR and hybridization tests are commercially available for specific organism detection. Furthermore, hundreds of nucleic acid-based bacterial detection tests have been published in the literature and could be adapted for use in the clinical setting. Contamination potential, lack of standardization or validation for some assays, complex interpretation of results, and increased cost are possible limitations of these tests, however, and must be carefully considered before implementing them in the clinical laboratory.

CONCLUSIONS

A major area of advancement in nucleic acid-based assay development has been for specific and broad-range detection of bacterial pathogens.

Computational approach involving use of the internal transcribed spacer 1 region for identification of Mycobacterium species

The rapid and reliable identification of clinically significant Mycobacterium species is a challenge for diagnostic laboratories. This study evaluates a unique sequence-dependent identification algorithm called MycoAlign for the differential identification of Mycobacterium species. The MycoAlign system uses pan-Mycobacterium-specific primer amplification in combination with a customized database and algorithm. The results of testing were compared with conventional phenotypic assays and GenBank sequence comparisons using the 16S rRNA target. Discrepant results were retested and evaluated using a third independent database. The custom database was generated using the hypervariable sequences of the internal transcribed spacer 1 (ITS-1) region of the rRNA gene complex from characterized Mycobacterium species. An automated sequence-validation process was used to control quality and specificity of evaluated sequence. A total of 181 Mycobacterium strains (22 reference strains and 159 phenotypically identified clinical isolates) and seven nonmycobacterial clinical isolates were evaluated in a comparative study to validate the accuracy of the MycoAlign algorithm. MycoAlign correctly identified all referenced strains and matched species in 94% of the phenotypically identified Mycobacterium clinical isolates. The ITS-1 sequence target showed a higher degree of specificity in terms of Mycobacterium identification than the 16S rRNA sequence by use of GenBank BLAST. This study showed the MycoAlign algorithm to be a reliable and rapid approach for the identification of Mycobacterium species and confirmed the superiority of the ITS-1 region sequence over the 16S rRNA gene sequence as a target for sequence-based species identification.

Use of the MGB Eclipse system and SmartCycler PCR for differentiation of Mycobacterium chelonae and M. abscessus

Although accurate in the identification of Mycobacterium species, partial 16S rRNA gene sequencing does not distinguish Mycobacterium chelonae from M. abscessus. Thus, we designed a SmartCycler PCR assay targeting the 16S-to-23S internal transcribed spacer (ITS) region with use of MGB Eclipse probes to distinguish each species. Comparison with PCR-restriction enzyme analysis of a 441-bp fragment of the hsp65 gene resulted in 100% correlation with 25 isolates of M. chelonae and 25 isolates of M. abscessus. ITS PCR performed on 90 consecutive isolates identified by partial 16S rRNA gene sequencing (26 isolates of the M. chelonae-M. abscessus complex and 64 remaining isolates, including Mycobacterium species, Nocardia species, and other aerobic actinomycetes) showed 100% specificity and sensitivity. The ITS PCR assay is accurate and specific, easy to perform, and a good supplemental test when using partial 16S rRNA gene sequencing to identify M. chelonae and M. abscessus.

A new method for species identification and differentiation of Mycobacterium chelonae complex based on amplified hsp65 restriction analysis (AHSPRA)

Members of the Mycobacterium chelonae complex (MCC), namely M. chelonae, Mycobacterium abscessus and Mycobacterium immunogenum, have been implicated in nosocomial infections and occupational respiratory illnesses like hypersensitivity pneumonitis (HP) associated with contaminated metalworking fluid (MWF) exposures. Close relationship among these member species makes their differentiation cumbersome using the existing methods. Here we report a simple and rapid method for unambiguous identification and differentiation of the three-member species of the MCC group with PCR-restriction analysis targeting a 667-bp segment of a variable region of the 65-kDa-heat shock protein (hsp65) gene. This assay, described as Amplified hsp65 Restriction Analysis (AHSPRA), can discriminate all the three individual species using a one-step restriction digestion using either BbvI or Eco0109I. The enzyme NarI can differentiate M. immunogenum from the other two MCC species (M. chelonae and M. abscessus). The developed method was validated using several non-MCC reference species of other rapidly growing mycobacteria (RGM) and MCC field isolates from MWF samples. Direct cell-lysis was used instead of the conventional DNA template preparation, which improved the rapidity, simplicity and adaptability of the developed method. The results suggest that the developed method can unambiguously differentiate species of the M. chelonae complex from other RGM species and from one another.

Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases

The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. Problems remain in that the sequences in some databases are not accurate, there is no consensus quantitative definition of genus or species based on 16S rRNA gene sequence data, the proliferation of species names based on minimal genetic and phenotypic differences raises communication difficulties, and microheterogeneity in 16S rRNA gene sequence within a species is common. Despite its accuracy, 16S rRNA gene sequence analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations. Thus, a future challenge is to translate information from 16S rRNA gene sequencing into convenient biochemical testing schemes, making the accuracy of the genotypic identification available to the smaller and routine clinical microbiology laboratories.