[Show abstract][Hide abstract] ABSTRACT: Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.
[Show abstract][Hide abstract] ABSTRACT: Mycobacterium tuberculosis Beijing strains represent targets of special importance for molecular surveillance of tuberculosis (TB), especially because they are associated with spread of multi-drug resistance in some world regions. Standard 24-locus mycobacterial interspersed repetitive-unit-variable-number of tandem-repeat (MIRU-VNTR) typing lacks resolution power for accurately discriminating closely related clones that often compose Beijing strain populations. Therefore, we evaluated a set of 7 additional, hypervariable MIRU-VNTR loci for better resolution and tracing of such strains, using a collection of 535 Beijing isolates from six world regions where these strains are known to be prevalent. The typeability and inter-laboratory reproducibility of these hypervariable loci was lower than that of the 24 standard loci. Three loci (2163a, 3155, 3336) were excluded because of their redundant variability and/or of more frequent non-interpretable results compared to the 4 other markers. The use of the remaining 4-locus set (1982, 3232, 3820 and 4120) increased the number of types by 52 % (from 223 to 340) and reduced the clustering rate from 58.3 to 36.6 %, when combined to the use of the standard 24-locus set. Known major clonal complexes/24-locus-based clusters were all subdivided, although the degree of subdivision varied depending on the complex. Only five single-locus variations were detected among the hypervariable loci of an additional panel of 92 isolates, representing 15 years of clonal spread of a single Beijing strain in a geographically restricted setting. On this calibrated basis, we propose this 4-locus set as a consensus for subtyping Beijing clonal complexes and clusters, after standard typing.
Full-text · Article · Jan 2014 · Journal of clinical microbiology
[Show abstract][Hide abstract] ABSTRACT: Background: Nontuberculous mycobacteria infection is a growing global concern. As mycobacterial cultures are challenging and time-consuming to perform, epidemiological data are useful to guide the choice of empiric antibiotic therapy. Unfortunately, such reports in Asia are scarce. We aim to describe the distribution and antibiotic susceptibility profiles of rapidly growing mycobacterium (RGM) isolates in Singapore.
Methods: This is a retrospective study involving three major hospitals in Singapore. Clinical RGM isolates with antibiotic susceptibility tests performed between 2006 and 2011 were identified using microbiology laboratory databases. For patients with repeat cultures, only unique isolates from the first culture were included. MICs of Amikacin (AMI), Cefoxitin (FOX), Clarithromycin (CLA), Ciprofloxacin (CIP), Doxycycline (DOX), Imipenem (IMP), Linezolid (LZD), Moxifloxacin (MXF), Sulfamethoxazole (SMX), Tigecycline (TGC) and Tobramycin (TOB) were recorded. Linear regression was used to detect changes in antibiotic susceptibility patterns over time.
Results: A total of 427 isolates from 392 patients (median age: 60 years; range: 21-88 years) were included. Of these, 252 (64%) patients had lung infections, 37 (9%) had bacteremia and 26 (7%) had infections related to peritoneal dialysis. The two most common species identified were M. abscessus (73%) and M. fortuitium (22%). Both had similar MIC90 (µg/ml) for AMI (16), FOX (64), DOX (>16) and SMX (>128). The MIC90 for M. abscessus and M. fortuitum differed for CLA (1 vs. 16), CIP (4 vs. 1), IMP (64 vs. 16), LZD (32 vs. 16), MXF (8 vs. 0.25) and TGC (0.5 vs. 0.25). Decreases in the susceptibility of M. abscessus to LZD by 8.8%/year (R2=0.948, p=0.001) and M. fortuitum to IMP by 9.5%/year (R2=0.761, p=0.023) were observed.
Conclusion: M. abscessus lung infection is the most common RGM disease in Singapore. Antibiotic options for treatment of RGM infections are increasingly limited; a combination involving AMI, TGC and CLA may provide the most appropriate regimen for empiric antibiotic therapy.
[Show abstract][Hide abstract] ABSTRACT: The Mycobacteria Growth Indicator Tube (MGIT 960) system was evaluated against Lowenstein-Jensen (LJ) medium and the BACTEC 460 TB system for the recovery of mycobacteria from 1393 consecutive urine specimens. The MGIT had a sensitivity of 91.3% [95% confidence interval (CI), 83.2-99.4] when the combination of BACTEC 460 and LJ medium was used as the reference method. The mean time for positivity for MGIT and BACTEC 460 was 19.3 days and 20 days, respectively, while that for LJ medium was 35 days.The incidence of contamination was highest for LJ medium (n=148), followed by MGIT 960 (n=81), and BACTEC 460 had the lowest incidence of contamination (n=50). In conclusion, the isolation of mycobacteria from urine specimens by the MGIT 960 is comparable to that of the BACTEC 460 TB system and solid media.
Full-text · Article · Nov 2008 · Journal of Medical Microbiology
[Show abstract][Hide abstract] ABSTRACT: We reevaluated the BACTEC MGIT 960 antimicrobial susceptibility testing system (MGIT 960 AST) by using 1,112 isolates of Mycobacterium tuberculosis. When the results of MGIT 960 AST were compared with that of the proportion method using Ogawa medium (Ogawa PM), discrepant
results were obtained for 30 strains with isoniazid, all resistant by MGIT 960 AST but susceptible by Ogawa PM. For 93% of
the strains that produced discrepant results, the MIC was 0.4 or 0.8 μg/ml, showing resistance by the proportion method using
Middlebrook agar plates. Furthermore, it was also established by analyses of the katG and inhA genes that strains resistant only by MGIT 960 AST have a low level of isoniazid (INH) resistance, indicating that MGIT 960
AST is a reliable method. Ninety-six strains were resistant to 0.1 μg/ml INH by MGIT 960 AST. When they were divided into
three groups, Low-S (susceptible at 0.2 μg/ml), Low-R (resistant at 0.2 μg/ml), and High-R (resistant at 1.0 μg/ml), by Ogawa
PM, 43.3% of the Low-S strains had mutations in the promoter region of inhA and no mutations were detected in katG codon 315, while 61.7% of the High-R strains had katG codon 315 mutations or a gross deletion of katG. These results suggest that mutations in inhA are associated with low-level resistance to INH and katG codon 315 mutations are associated with high-level resistance to INH. In addition, the analyses demonstrated some relationship
of mutations in the inhA gene with ethionamide resistance for the Low-S strains, but not for the High-R strains.
Preview · Article · Aug 2008 · Journal of clinical microbiology
[Show abstract][Hide abstract] ABSTRACT: To compare the incidence of carbapenemase genes in Acinetobacter baumannii between two time periods.
We studied 114 isolates of imipenem-resistant A. baumannii collected over two 5 month periods (in 1996 and 2001). Isolates showing carbapenemase activity by plate bioassay were screened for carbapenemase genes using PCR. Chromosomal DNA from strains carrying carbapenemase genes was subjected to PFGE after digestion with ApaI.
The incidence of imipenem-resistant A. baumannii in our hospital rose from 1.1 per 1000 admissions in 1996 to 2.3 per 1000 admissions in 2001. However, the number of carbapenemase-producing A. baumannii rose only slightly in 2001 (0.8 per 1000 admissions) compared to 1996 (0.5 per 1000 admissions). Of 44 isolates with carbapenemase activity, 4 isolates carried bla(IMP-4), 5 carried bla(OXA-58), and 40 carried bla(OXA-23). In addition, most isolates carried a bla(OXA-51)-type beta-lactamase gene. All strains with bla(IMP-4), also carried bla(OXA-58) and bla(PSE-1), but not bla(OXA-51)-type beta-lactamase genes. PCR analysis repeated on seven recent isolates of susceptible A. baumannii showed only the presence of bla(OXA-51)-type beta-lactamase genes. A total of five novel bla(OXA-51)-type beta-lactamase genes (bla(OXA-88),-91,-93,-94, and -95) and one new bla(OXA-58)-type beta-lactamase gene (bla(OXA-96)) were found.
The incidence of carbapenemase genes did not vary significantly between the two study periods. There is a wide diversity of OXA genes in A. baumannii in Singapore. The most common carbapenemase gene found in our study was bla(OXA-23).
Preview · Article · May 2007 · Journal of Antimicrobial Chemotherapy
[Show abstract][Hide abstract] ABSTRACT: We report the first outbreak of vancomycin-resistant Enterococcus faecium colonization and infection among inpatients in the hematology ward of an acute tertiary care public hospital in Singapore. Two cases of bacteremia and 4 cases of gastrointestinal carriage were uncovered before implementation of strict infection control measures resulted in control of the outbreak.
No preview · Article · Oct 2006 · Infection Control and Hospital Epidemiology
[Show abstract][Hide abstract] ABSTRACT: Gordonia species have been recognized as pathogens in immunocompromised and immunocompetent patients. We report the first case of
bacteremia due to Gordonia bronchialis in a diabetic patient with a sequestrated lung. Species identification was confirmed with mycolic acid analysis by high-performance
liquid chromatography and sequencing of the 16S rRNA gene.
[Show abstract][Hide abstract] ABSTRACT: Four carbapenem-resistant Pseudomonas spp. were isolated from patients in Singapore. One Pseudomonas putida isolate contained a bla(IMP-1) identical to that first described in Japan. The sequence of a variant bla(IMP-1) in Pseudomonas fluorescens contained four silent mutations compared with the original sequence. The remaining P. putida isolates contained bla(VIM-6), a novel VIM gene variant.