Abstract:
:Use of whole-genome sequencing (WGS) for routine mycobacterial species identification and drug susceptibility testing (DST) is becoming a reality. We compared the performances of WGS and standard laboratory workflows prospectively, by parallel processing at a major mycobacterial reference service over the course of 1 year, for species identification, first-line Mycobacterium tuberculosis resistance prediction, and turnaround time. Among 2,039 isolates with line probe assay results for species identification, 74 (3.6%) failed sequencing or WGS species identification. Excluding these isolates, clinically important species were identified for 1,902 isolates, of which 1,825 (96.0%) were identified as the same species by WGS and the line probe assay. A total of 2,157 line probe test results for detection of resistance to the first-line drugs isoniazid and rifampin were available for 728 M. tuberculosis complex isolates. Excluding 216 (10.0%) cases where there were insufficient sequencing data for WGS to make a prediction, overall concordance was 99.3% (95% confidence interval [CI], 98.9 to 99.6%), sensitivity was 97.6% (91.7 to 99.7%), and specificity was 99.5% (99.0 to 99.7%). A total of 2,982 phenotypic DST results were available for 777 M. tuberculosis complex isolates. Of these, 356 (11.9%) had no WGS comparator due to insufficient sequencing data, and in 154 (5.2%) cases the WGS prediction was indeterminate due to discovery of novel, previously uncharacterized mutations. Excluding these data, overall concordance was 99.2% (98.7 to 99.5%), sensitivity was 94.2% (88.4 to 97.6%), and specificity was 99.4% (99.0 to 99.7%). Median processing times for the routine laboratory tests versus WGS were similar overall, i.e., 20 days (interquartile range [IQR], 15 to 31 days) and 21 days (15 to 29 days), respectively (P = 0.41). In conclusion, WGS predicts species and drug susceptibility with great accuracy, but work is needed to increase the proportion of predictions made.
journal_name
J Clin Microbioljournal_title
Journal of clinical microbiologyauthors
Quan TP,Bawa Z,Foster D,Walker T,Del Ojo Elias C,Rathod P,MMM Informatics Group.,Iqbal Z,Bradley P,Mowbray J,Walker AS,Crook DW,Wyllie DH,Peto TEA,Smith EGdoi
10.1128/JCM.01480-17subject
Has Abstractpub_date
2018-01-24 00:00:00issue
2eissn
0095-1137issn
1098-660Xpii
JCM.01480-17journal_volume
56pub_type
杂志文章abstract::The performance of the Amplified Mycobacterium Tuberculosis Direct (AMTD) test (Gen-Probe Inc., San Diego, Calif.) was assessed in a large tertiary care mycobacteriology laboratory. Both acid-fast smear-positive and smear-negative respiratory and nonrespiratory clinical specimens were analyzed. From February 1998 to 4...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.40.5.1723-1727.2002
更新日期:2002-05-01 00:00:00
abstract::Pseudomonas gladioli was isolated from 11 patients with cystic fibrosis. It resembled Pseudomonas cepacia on the selective and differential medium OFPBL, producing yellow colonies after 48 to 72 h of incubation. Isolates were characterized biochemically, by DNA hybridization, and by cellular fatty acid analysis. A rev...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.27.2.270-273.1989
更新日期:1989-02-01 00:00:00
abstract::Rapid identification and differentiation of orthopoxviruses by PCR were achieved with primers based on genome sequences encoding the hemagglutinin (HA) protein, an infected-cell membrane antigen that distinguishes orthopoxviruses from other poxvirus genera. The initial identification step used a primer pair of consens...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.33.8.2069-2076.1995
更新日期:1995-08-01 00:00:00
abstract::The indirect immunoperoxidase antibody technique (IPA) has been applied to determine immunoglobulin (Ig)G to humans cytomegalovirus (CMV) antibodies in 114 blood donor sera, four cases of congenital cytomegalic inclusion disease, and four cases of acquired CMV infection. The results have been compared with those obtai...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:
更新日期:1976-03-01 00:00:00
abstract::Rose Bengal and counterimmunoelectrophoresis, two tests that detect antibodies against different structural antigens, when carried out on spinal fluid permitted rapid diagnosis of human Brucella meningitis. The Rose Bengal test was positive in five out of five patients studied, and counterimmunoelectrophoresis was pos...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:
更新日期:1978-02-01 00:00:00
abstract::A hemolysin produced by Aeromonas hydrophila CA-11, isolated from an environmental source, was purified by sulfopropyl-Sephadex C-25 chromatography at pH 5.0. This hemolysin caused fluid accumulation in infant mouse intestines and rabbit intestinal loops and killed Vero cells, as did the hemolysin produced by strain A...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.24.2.228-232.1986
更新日期:1986-08-01 00:00:00
abstract::A genotyping study of 285 Hybrid Capture 2 low-risk probe cocktail-positive specimens showed cross-reactivity with several untargeted human papillomavirus genotypes. Cross-reactivity was often clinically beneficial due to the detection of untargeted low-risk genotypes. A total of 8.4% of positive results, usually weak...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.00278-09
更新日期:2009-08-01 00:00:00
abstract::Yersinia enterocolitica biotype 1, serotype O:21 was isolated from feces or rectal washings of three members of one family in northwestern Saskatchewan. The three isolates gave positive pathogenicity tests in guinea pigs with cultures grown at 22 degrees C as inoculum. All three cases showed clinical symptoms consiste...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.16.4.622-626.1982
更新日期:1982-10-01 00:00:00
abstract::During a taxonomic investigation of Nocardia spp. and Streptomyces spp., we received 658 isolates from laboratories of both human and veterinary medicine. Our procedure leading to the identification of 92% of these isolates, the species that they represented, and a characteristic pattern of properties of the strains o...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.11.6.728-736.1980
更新日期:1980-06-01 00:00:00
abstract::The past 2 decades have brought worrying increases in severe Streptococcus pyogenes diseases globally. To investigate and compare the epidemiological patterns of these diseases within Europe, data were collected through a European Union FP-5-funded program (Strep-EURO). Prospective population-based surveillance of sev...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.00422-08
更新日期:2008-07-01 00:00:00
abstract::The prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBLEC) in Spain increased 8-fold from 2000 to 2006. ESBL type, clonal relationship, antimicrobial susceptibility, and clinical data about infections caused by ESBLEC are evaluated in a second nationwide study developed in 2006. From...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.02147-09
更新日期:2010-08-01 00:00:00
abstract::Rothia spp. are Gram-positive cocco-bacilli that cause a wide range of serious infections, especially in immunocompromised hosts. Risk factors for Rothia mucilaginosa (previously known as Stomatococcus mucilaginosus) bacteremia include prolonged and profound neutropenia, malignancy, and an indwelling vascular foreign ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.01270-14
更新日期:2014-09-01 00:00:00
abstract::In vitro studies established that neither cloth nor disposable diapers demonstrably contributed to the growth of Escherichia coli, Proteus vulgaris, Staphylococcus aureus, or Candida albicans when urine was present as a growth medium. In a clinical study of 166 children, the microbial skin flora of children with atopi...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.25.2.216-221.1987
更新日期:1987-02-01 00:00:00
abstract::We investigated a method to reduce oxygen tension and produce anaerobic conditions conveniently by coculture with a nonfermentative organism. The biochemical reactions of 94 strains representing 41 different species were determined using prereduced media and gas chromatography according to standard methods. The standa...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.19.2.215-217.1984
更新日期:1984-02-01 00:00:00
abstract::Paired serum samples from 93 patients suspected of having measles were assayed for measles virus-specific immunoglobulin M (IgM) antibodies by an enzyme immunoassay (EIA), and the results were compared with results from a complement fixation assay and an EIA for measles virus IgG. By using significant serologic rises ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.29.12.2865-2867.1991
更新日期:1991-12-01 00:00:00
abstract::Reference strains of serotypes 1 to 12 of Actinobacillus (Haemophilus) pleuropneumoniae were cultured in Eagle minimal essential medium with 10% Serum Plus. Culture supernatants were examined for cytotoxicity to alveolar macrophages and for the ability to hemolyze sheep erythrocytes. All strains except the reference s...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.27.6.1187-1191.1989
更新日期:1989-06-01 00:00:00
abstract::Antisera prepared against the eight recognized serotypes of Ureaplasma urealyticum were tested against the homologous and heterologous antigens by a modified metabolic inhibition test that used bromothymol blue broth in microtiter plates. The method gives clear endpoint determinations which are usually maintained on c...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:
更新日期:1979-06-01 00:00:00
abstract::Cell-free and cell-associated human immunodeficiency virus cultures suspended in 10% serum remained infectious for several weeks at room temperature. The stability was further increased when cell-associated virus was suspended in neat serum. When dried onto a glass coverslip, virus remained infectious for several days...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.32.2.571-574.1994
更新日期:1994-02-01 00:00:00
abstract::Serratia plymuthica was isolated from the blood and from a central venous catheter tip in a 54-year-old man with alcoholic cirrhosis and clinical signs of sepsis. This was the seventh reported isolate of S. plymuthica from a clinical specimen and the first in which the organism was clearly a significant pathogen. ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.25.8.1562-1563.1987
更新日期:1987-08-01 00:00:00
abstract::Actinomyces naeslundii is a saprophyte, sometimes a pathogen, of the human oral cavity. Very few extra-oral infections related to this agent have been described. We report the first instance of A. naeslundii as an etiological agent of pelvic actinomycosis in a user of an intrauterine device, an infection so far exclus...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.21.2.273-275.1985
更新日期:1985-02-01 00:00:00
abstract::Bacteroides fragilis is an obligatory anaerobic, gram-negative bacterium found among the normal intestinal flora of humans. Enterotoxigenic strains of B. fragilis (ETBF) have been associated with diarrheal diseases in humans and animals. The enterotoxin of ETBF induces fluid changes in ligated intestinal segments and ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.36.12.3545-3548.1998
更新日期:1998-12-01 00:00:00
abstract::Yarrowia lipolytica is a weakly pathogenic yeast that is rarely isolated from the blood. We observed transient recurrent catheter-related fungemia attributable to this organism in a leukemic patient. The fungemia and accompanying fever subsided spontaneously. The data suggest that it might be possible to withhold spec...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.39.3.1200-1201.2001
更新日期:2001-03-01 00:00:00
abstract::An evaluation of the serotyping system for Proteus rettgeri has been performed through its application to 561 human isolates of this species. Of these, 545 were typable and could be separated into 58 O serotypes. A group of isolates from one hospital, and clinically implicated in cross-infections, was found to belong ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:
更新日期:1976-04-01 00:00:00
abstract::Rapid identification and typing of methicillin (meticillin)-resistant Staphylococcus aureus (MRSA) is important for understanding the molecular epidemiology and evolution of MRSA and offers many advantages for controlling transmission in both health care and community settings. We developed a rapid molecular beacon re...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.00766-09
更新日期:2009-11-01 00:00:00
abstract::Nosocomial oxacillin-resistant Staphylococcus aureus (ORSA) bloodstream isolates were tested to determine the prevalence of vancomycin heteroresistance. We screened 619 ORSA nosocomial bloodstream isolates from 36 hospitals between 1997 and 2000. Only one isolate exhibiting heterotypic resistance was detected. Thus, v...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.40.6.2249-2250.2002
更新日期:2002-06-01 00:00:00
abstract::Herpes simplex virus type 1 (HSV-1) encodes 11 envelope glycoproteins, of which glycoprotein G-1 (gG-1) induces a type-specific antibody response. Variability of the gG-1 gene among wild-type strains may be a factor of importance for a reliable serodiagnosis and typing of HSV-1 isolates. Here, we used a gG-1 type-spec...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.40.9.3245-3251.2002
更新日期:2002-09-01 00:00:00
abstract::In this study we describe a multiplex PCR assay for the detection of nine clinically relevant antibiotic resistance genes of Staphylococcus aureus. Conditions were optimized to amplify fragments of mecA (encoding methicillin resistance), aacA-aphD (aminoglycoside resistance), tetK, tetM (tetracycline resistance), erm(...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.41.9.4089-4094.2003
更新日期:2003-09-01 00:00:00
abstract::Nocardia isolations increased from 0.7 to 11.7/1,000 acid-fast bacillus and mycological cultures (P less than 0.000001). Only three isolations from one patient represented infection. Pseudoepidemic strain identity was confirmed by DNA fingerprinting; the isolate causing infection was distinct. The end of the pseudoepi...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.30.5.1357-1360.1992
更新日期:1992-05-01 00:00:00
abstract::We describe a multiplex reverse transcription-PCR (m-RT-PCR) assay that is able to detect and differentiate all known human parainfluenza viruses (HPIVs). Serial dilution experiments with reference strains that compared cell culture isolation and m-RT-PCR showed sensitivities ranging from 0.0004 50% tissue culture inf...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.38.3.1191-1195.2000
更新日期:2000-03-01 00:00:00
abstract::Blood isolates of Salmonella enterica serovar Typhi from two recently returned Bangladeshi patients in Kuwait were ciprofloxacin resistant, with ciprofloxacin MICs of 12 mg/liter for both isolates. Both isolates had three novel gyrA mutations (55-Leu-->Trp, 87-Asp-->Ala, and 106-Gln-->Arg) and three novel parC mutatio...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.01161-08
更新日期:2009-01-01 00:00:00