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We studied the use of the INNO-LIA syphilis score assay in the resolution of discordant positive screening results of the Murex ICE Syphilis enzyme immunoassay (EIA) with the confirmatory results of both the Serodia Treponema pallidum particle agglutination (TPPA) and the fluorescent treponemal antibody-absorption (FTA-Abs) assays, for the serological diagnosis of syphilis. This was an observational study on the serum samples received by the Syphilis Laboratory, Hong Kong, during the period from January 2006 to December 2012. A total of 801 serum samples with discordant positive screening EIA results were used. Consensus results of such serum samples were derived from results of the EIA, TPPA and FTA-abs assays. The age range of the individuals was 14 to 104 years (median of 52). There were 369 males and 432 females. Of 378 serum samples, 139 showed agreement among positive results, 23 of 310 showed agreement among indeterminate results and 277 of 465 showed agreement among negative results. The proportions of agreement among positive, indeterminate and negative results were 0.37 (95% CI 0.32–0.42), 0.07 (95% CI 0.05–0.11) and 0.60 (95% CI 0.55–0.64), respectively; kappa 0.55 (95% CI 0.49–0.60). There were 60 serum samples with positive consensus results but negative INNO-LIA syphilis score results and 10 with negative consensus results but positive INNO-LIA syphilis score results. Although the INNO-LIA syphilis score assay can be considered a valid alternative confirmatory test for the serological diagnosis of syphilis, the present study showed that its use in the resolution of discordant positive screening EIA results was moderate. A more extensive characterization of serum samples with discordant reactive screening treponemal test results is necessary. [ABSTRACT FROM PUBLISHER]

We conducted a 31-month retrospective review of all laboratory-confirmed Streptococcus suis infections admitted to public hospitals in Hong Kong. Strain identification, serotyping and antibiotic susceptibility tests were conducted on S. suis isolates. Twenty-one sporadic cases were identified, comprising 18 (86%) males and 3 (14%) females. About half were patients aged 65 years. More cases occurred during summer. Occupational exposure was documented in five (24%) cases. The estimated annual incidence was 0.09/100 000 in the general population and 32/100 000 in people with occupational exposure to pigs and raw pork. The primary clinical manifestations were meningitis (48%), septicaemia (38%) and endocarditis (14%). The case-fatality rate was 5%. All available isolates from 15 patients were serotype 2, sensitive to penicillin, ampicillin, ceftriaxone, but resistant to tetracycline. Injury prevention and proper handling of pigs or raw pork should be advocated to both at-risk occupational groups and the general population. [ABSTRACT FROM AUTHOR]

Context: No large-scale study has investigated the impact of multidrug-resistant tuberculosis (TB) on the outcome of standard short-course chemotherapy under routine countrywide TB control program conditions in the World Health Organization's (WHO) directly observed treatment short-course strategy for TB control.Objective: To assess the results of treatment with first-line drugs for patients enrolled in the WHO and the International Union Against Tuberculosis and Lung Disease's global project on drug-resistance surveillance.Design and Setting: Retrospective cohort study of patients with TB in the Dominican Republic, Hong Kong Special Administrative Region (People's Republic of China), Italy, Ivanovo Oblast (Russian Federation), the Republic of Korea, and Peru.Patients: New and retreatment TB cases who received short-course chemotherapy with isoniazid, rifampicin, pyrazinamide, and either ethambutol or streptomycin between 1994 and 1996.Main Outcome Measure: Treatment response according to WHO treatment outcome categories (cured; died; completed, defaulted, or failed treatment; or transferred).Results: Of the 6402 culture-positive TB cases evaluated, 5526 (86%) were new cases and 876 (14%) were retreatment cases. A total of 1148 (20.8%) new cases and 390 (44.5%) retreatment cases were drug resistant, including 184 and 169 cases of multidrug-resistant TB, respectively. Of the new cases 4585 (83%) were treated successfully, 138 (2%) died, and 151 (3%) experienced short-course chemotherapy failure. Overall, treatment failure (relative risk [RR], 15.4; 95% confidence interval [CI], 10.6-22.4; P<.001) and mortality (RR, 3.73; 95% CI, 2.13-6.53; P<.001) were higher among new multidrug-resistant TB cases than among new susceptible cases. Even in settings using 100% direct observation, cases with multidrug resistance had a significantly higher failure rate than those who were susceptible (9/94 [10%] vs 8/1410 [0.7%]; RR, 16.9; 95% CI, 6.6-42.7; P<.001). Treatment failure was also higher among patients with any rifampicin resistance (n=115) other than multidrug resistance (RR, 5.48; 95% CI, 3.04-9.87; P<.001), any isoniazid resistance (n=457) other than multidrug resistance (RR, 3. 06; 95% CI, 1.85-5.05; P<.001), and among patients with TB resistant to rifampicin only (n=76) (RR, 5.47; 95% CI, 2.68-11.2; P<.001). Of the retreatment cases, 497 (57%) were treated successfully, 51 (6%) died, and 124 (14%) failed short-course chemotherapy treatment. Failure rates among retreatment cases were higher in those with multidrug-resistant TB, with any isoniazid resistance other than multidrug resistance, and in cases with TB resistant to isoniazid only.Conclusions: These data suggest that standard short-course chemotherapy, based on first-line drugs, is an inadequate treatment for some patients with drug-resistant TB. Although the directly observed treatment short-course strategy is the basis of good TB control, the strategy should be modified in some settings to identify drug-resistant cases sooner, and to make use of second-line drugs in appropriate treatment regimens. JAMA. 2000;283:2537-2545 [ABSTRACT FROM AUTHOR]

PulseNet International (PNI) is a global network of 88 countries who work together through their regional and national public health laboratories to track foodborne disease around the world. The vision of PNI is to implement globally standardized surveillance using whole genome sequencing (WGS) for real-time identification and subtyping of foodborne pathogens to strengthen preparedness and response and lower the burden of disease. Several countries in North America and Europe have experienced significant benefits in disease mitigation after implementing WGS. To broaden the routine use of WGS around the world, challenges and barriers must be overcome. We conducted this study to determine the challenges and barriers countries are encountering in their attempts to implement WGS and to identify how PNI can provide support to improve and become a better integrated system overall. A survey was designed with a set of qualitative questions to capture the status, challenges, barriers, and successes of countries in the implementation of WGS and was administered to laboratories in Africa, Asia-Pacific, Latin America and the Caribbean, and Middle East. One-third of respondents do not use WGS, and only 8% reported using WGS for routine, real-time surveillance. The main barriers for implementation of WGS were lack of funding, gaps in expertise, and training, especially for data analysis and interpretation. Features of an ideal system to facilitate implementation and global surveillance were identified as an all-in-one software that is free, accessible, standardized and validated. This survey highlights the minimal use of WGS for foodborne disease surveillance outside the United States, Canada, and Europe to date. Although funding remains a major barrier to WGS-based surveillance, critical gaps in expertise and availability of tools must be overcome. Opportunities to seek sustainable funding, provide training, and identify solutions for a globally standardized surveillance platform will accelerate implementation of WGS worldwide.

Mycoplasma genitalium is the cause of an emerging sexually transmitted infection (STI) with high propensity for development of antimicrobial resistance. In a prevalence study conducted at the public STI service in Hong Kong, the first void urine samples of 38 (8%) of 493 male patients with non-gonococcal urethritis (NGU) tested positive for M. genitalium using reverse transcription polymerase chain reaction. Patients with M. genitalium infection were younger [31 vs 33 years, odds ratio (OR) 0.96, 95% confidence interval (CI) 0.93-0.996; P=0.03], more likely to present with urethral discharge (12% vs 6%, OR 2.16, 95% CI 1.10-4.23; P=0.02) and had symptom duration >2 weeks (14% vs 6%, OR 2.34, 95% CI 1.10-4.97; P=0.03) compared with patients without M. genitalium infection. The prevalence of M. genitalium infection was lower in patients co-infected with Chlamydia trachomatis compared with patients with isolated infection (4% vs 10%, OR 0.38, 95% CI 0.17-0.84; P=0.02). The prevalence of M. genitalium infection was not higher in men who have sex with men. Antimicrobial-resistance-conferring mutations were present in 24 (63%) patients with M. genitalium - 23S rRNA 18 (47%) and parC 19 (53%). Similar to neighbouring countries in the Asia Pacific region, concurrent resistance mutations against both macrolides and fluoroquinolones were demonstrated in 14 (37%) patients. Histories of azithromycin and moxifloxacin use were significantly associated with a diagnosis of M. genitalium infection. Characteristically, NGU in Hong Kong featured the co-existence of mono-resistance against macrolides or fluoroquinolones, and the presence of dual class resistance. The geographic variability of antimicrobial resistance against M. genitalium is attributed not just to the different transmission networks formed in separate population groups, but the antimicrobial prescriptions for the treatment of urethritis in the community., Competing Interests: Competing interests None declared., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Background: COVID-19 has plagued the globe, with multiple SARS-CoV-2 clusters hinting at its evolving epidemiology. Since the disease course is governed by important epidemiological parameters, including containment delays (time between symptom onset and mandatory isolation) and serial intervals (time between symptom onsets of infector-infectee pairs), understanding their temporal changes helps to guide interventions., Objective: This study aims to characterize the epidemiology of the first two epidemic waves of COVID-19 in Hong Kong by doing the following: (1) estimating the containment delays, serial intervals, effective reproductive number (R t ), and proportion of asymptomatic cases; (2) identifying factors associated with the temporal changes of the containment delays and serial intervals; and (3) depicting COVID-19 transmission by age assortativity and types of social settings., Methods: We retrieved the official case series and the Apple mobility data of Hong Kong from January-August 2020. The empirical containment delays and serial intervals were fitted to theoretical distributions, and factors associated with their temporal changes were quantified in terms of percentage contribution (the percentage change in the predicted outcome from multivariable regression models relative to a predefined comparator). R t was estimated with the best fitted distribution for serial intervals., Results: The two epidemic waves were characterized by imported cases and clusters of local cases, respectively. R t peaked at 2.39 (wave 1) and 3.04 (wave 2). The proportion of asymptomatic cases decreased from 34.9% (0-9 years) to 12.9% (≥80 years). Log-normal distribution best fitted the 1574 containment delays (mean 5.18 [SD 3.04] days) and the 558 serial intervals (17 negative; mean 4.74 [SD 4.24] days). Containment delays decreased with involvement in a cluster (percentage contribution: 10.08%-20.73%) and case detection in the public health care sector (percentage contribution: 27.56%, 95% CI 22.52%-32.33%). Serial intervals decreased over time (6.70 days in wave 1 versus 4.35 days in wave 2) and with tertiary transmission or beyond (percentage contribution: -50.75% to -17.31%), but were lengthened by mobility (percentage contribution: 0.83%). Transmission within the same age band was high (18.1%). Households (69.9%) and social settings (20.3%) were where transmission commonly occurred., Conclusions: First, the factors associated with reduced containment delays suggested government-enacted interventions were useful for achieving outbreak control and should be further encouraged. Second, the shorter serial intervals associated with the composite mobility index calls for empirical surveys to disentangle the role of different contact dimensions in disease transmission. Third, the presymptomatic transmission and asymptomatic cases underscore the importance of remaining vigilant about COVID-19. Fourth, the time-varying epidemiological parameters suggest the need to incorporate their temporal variations when depicting the epidemic trajectory. Fifth, the high proportion of transmission events occurring within the same age group supports the ban on gatherings outside of households, and underscores the need for residence-centered preventive measures., (©Kin On Kwok, Wan In Wei, Ying Huang, Kai Man Kam, Emily Ying Yang Chan, Steven Riley, Ho Hin Henry Chan, David Shu Cheong Hui, Samuel Yeung Shan Wong, Eng Kiong Yeoh. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 16.04.2021.)

Shigella spp. are a leading cause of human diarrheal disease worldwide, with Shigella flexneri being the most frequently isolated species in developing countries. This serogroup is presently classified into 19 serotypes worldwide. We report here a multicenter validation of a multiplex-PCR-based strategy previously developed by Q. Sun, R. Lan, Y. Wang, A. Zhao, et al. (J Clin Microbiol 49:3766-3770, 2011) for molecular serotyping of S. flexneri This study was performed by seven international laboratories, with a panel of 71 strains (researchers were blind to their identity) as well as 279 strains collected from each laboratory's own local culture collections. This collaborative work found a high extent of agreement among laboratories, calculated through interrater reliability (IRR) measures for the PCR test that proved its robustness. Agreement with the traditional method (serology) was also observed in all laboratories for 14 serotypes studied, while specific genetic events could be responsible for the discrepancies among methodologies in the other 5 serotypes, as determined by PCR product sequencing in most of the cases. This work provided an empirical framework that allowed the use of this molecular method to serotype S. flexneri and showed several advantages over the traditional method of serological typing. These advantages included overcoming the problem of availability of suitable antisera in testing laboratories as well as facilitating the analysis of multiple samples at the same time. The method is also less time-consuming for completion and easier to implement in routine laboratories. We recommend that this PCR be adopted, as it is a reliable diagnostic and characterization methodology that can be used globally for laboratory-based shigella surveillance., (Copyright © 2019 American Society for Microbiology.)

Objectives: To explore the clinical role of GeneXpert in managing pulmonary tuberculosis (TB) in an intermediate burden city., Methods: Sputum acid-fast-bacilli (AFB) smear negative patients underwent bronchoscopy for bronchial alveolar lavage (BAL). Fluids collected were examined for AFB smear, TB culture, TB polymerase chain reaction (PCR) (Cobas Taqman) and for GeneXpert., Results: From October 2015 to February 2017, 227 BAL samples were collected. Cough and haemoptysis were the presenting symptoms in 70.0% and 37.4%, respectively. Apical shadows on chest X-rays (CXR) and apical cavitations on computed tomography (CT) were commoner in GeneXpert positive cases (p = 0.01 and 0.02, respectively). Sensitivity and specificity of GeneXpert for TB diagnosis was 80% and 98% respectively. Positive and negative predictive value of the test was 92.3 and 95.1%, respectively. There were 9 false negative GeneXpert samples (8 were Cobas Taqman TB PCR negative): 6 were diagnosed by BAL culture, 2 by biopsy and one by Cobas Taqman TB PCR. There were 3 false positive cases with negative culture; 2 were put on empirical treatment with favourable clinical responses, while one defaulted follow-p., Conclusion: GeneXpert in BAL samples has high sensitivity and specificity. It enabled timely initiation of anti-TB treatment in clinical suspicious cases., (Copyright © 2018 The British Infection Association. Published by Elsevier Ltd. All rights reserved.)

Background: Non-hospital residential facilities are important reservoirs for MRSA transmission. However, conclusions and public health implications drawn from the many mathematical models depicting nosocomial MRSA transmission may not be applicable to these settings. Therefore, we reviewed the MRSA transmission dynamics studies in defined non-hospital residential facilities to: (1) provide an overview of basic epidemiology which has been addressed; (2) identify future research direction; and (3) improve future model implementation., Methods: A review was conducted by searching related keywords in PUBMED without time restriction as well as internet searches via Google search engine. We included only articles describing the epidemiological transmission pathways of MRSA/community-associated MRSA within and between defined non-hospital residential settings., Results: Among the 10 included articles, nursing homes (NHs) and correctional facilities (CFs) were two settings considered most frequently. Importation of colonized residents was a plausible reason for MRSA outbreaks in NHs, where MRSA was endemic without strict infection control interventions. The importance of NHs over hospitals in increasing nosocomial MRSA prevalence was highlighted. Suggested interventions in NHs included: appropriate staffing level, screening and decolonizing, and hand hygiene. On the other hand, the small population amongst inmates in CFs has no effect on MRSA community transmission. Included models ranged from system-level compartmental models to agent-based models. There was no consensus over the course of disease progression in these models, which were mainly featured with NH residents /CF inmates/ hospital patients as transmission pathways. Some parameters used by these models were outdated or unfit., Conclusions: Importance of NHs has been highlighted from these current studies addressing scattered aspects of MRSA epidemiology. However, the wide variety of non-hospital residential settings suggest that more work is needed before robust conclusions can be drawn. Learning from existing work for hospitals, we identified critical future research direction in this area from infection control, ecological and economic perspectives. From current model deficiencies, we suggest more transmission pathways be specified to depict MRSA transmission, and further empirical studies be stressed to support evidence-based mathematical models of MRSA in non-hospital facilities. Future models should be ready to cope with the aging population structure.

Background: In countries with high tuberculosis (TB) burden, there is urgent need for rapid, large-scale screening to detect smear-positive patients. We developed a computer-aided whole smear screening system that focuses in real-time, captures images and provides diagnostic grading, for both bright-field and fluorescence microscopy for detection of acid-fast-bacilli (AFB) from respiratory specimens., Objectives: To evaluate the performance of dual-mode screening system in AFB diagnostic algorithms on concentrated smears with auramine O (AO) staining, as well as direct smears with AO and Ziehl-Neelsen (ZN) staining, using mycobacterial culture results as gold standard., Methods: Adult patient sputum samples requesting for M. tuberculosis cultures were divided into three batches for staining: direct AO-stained, direct ZN-stained and concentrated smears AO-stained. All slides were graded by an experienced microscopist, in parallel with the automated whole smear screening system. Sensitivity and specificity of a TB diagnostic algorithm in using the screening system alone, and in combination with a microscopist, were evaluated., Results: Of 488 direct AO-stained smears, 228 were culture positive. These yielded a sensitivity of 81.6% and specificity of 74.2%. Of 334 direct smears with ZN staining, 142 were culture positive, which gave a sensitivity of 70.4% and specificity of 76.6%. Of 505 concentrated smears with AO staining, 250 were culture positive, giving a sensitivity of 86.4% and specificity of 71.0%. To further improve performance, machine grading was confirmed by manual smear grading when the number of AFBs detected fell within an uncertainty range. These combined results gave significant improvement in specificity (AO-direct:85.4%; ZN-direct:85.4%; AO-concentrated:92.5%) and slight improvement in sensitivity while requiring only limited manual workload., Conclusion: Our system achieved high sensitivity without substantially compromising specificity when compared to culture results. Significant improvement in specificity was obtained when uncertain results were confirmed by manual smear grading. This approach had potential to substantially reduce workload of microscopists in high burden countries.

The epidemic of Zika virus (ZIKV) infection in South America has led to World Health Organization's declaration of a Public Health Emergency of International Concern. To further inform effective public health policy, an understanding of ZIKV's transmission mechanisms is crucial. To characterize the intercontinental transmission of ZIKV, we compiled and analyzed more than 250 gene sequences together with their sequence-related geographic and temporal information, sampled across 27 countries spanning from 1947 to 2016. After filtering and selecting appropriate sequences, extensive phylogenetic analyses were performed. Although phylogeographic reconstruction supported the transmission route of the virus in Africa, South-eastern Asia, Oceania and Latin America, we discovered that the Eastern Africa origin of ZIKV was disputable. On a molecular level, purifying selection was found to be largely responsible for the evolution of non-structural protein 5 and envelope protein E. Our dataset and ancestral sequences reconstruction analysis captured previously unidentified amino acid changes during evolution. Finally, based on the estimation of the time to the most recent common ancestors for the non-structural protein 5 gene, we hypothesized potential specific historic events that occurred in the 1940s and might have facilitated the spread of Zika virus from Africa to South-eastern Asia. Our findings provide new insights into the transmission characteristics of ZIKV, while further genetic and serologic studies are warranted to support the design of tailored prevention strategies.

Objective: To assess the potential risk of dengue transmission in a non-endemic city using a spatial epidemiological approach., Methods: Past dengue exposure of the general population was examined by dengue virus (DENV) IgG testing of archived samples from voluntary blood donors. Vector intensities were determined by local ovitrap index (OI). Analyses were made in the context of population statistics at both the district and sub-district level., Results: The overall prevalence of DENV IgG was low at 2.25%. Positive donors were more likely to be older, non-Chinese, and female. Neither the OI nor the location of residence was associated with DENV serology. The sub-district level OI was clustered, but no correlation could be confirmed with the location of residence of positive blood donors., Conclusions: The cumulative exposure of Hong Kong residents to dengue has so far been low. Coupled with the lack of a spatial relationship between exposed cases and vector intensities, a high risk of local transmission of DENV is not supported. The apparently higher exposure likelihood of females could be explained by past infection in workers from dengue endemic countries, while frequent travel could have exposed older adults to DENV. Continued surveillance, risk assessment, and intensive vector control remain essential to prevent the transformation of a non-endemic to an endemic city., (Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The aim of this study is to investigate the mutation pattern of the folC gene in drug-resistant Mycobacterium tuberculosis (MTB) clinical isolates of global and Hong Kong cohorts. The public sequence read archives of 1,124 MTB genomes from three independent studies were retrieved and folC mutations existing solely in drug-resistant MTB strains were identified. A phylogenetic tree was constructed to analyze the segregation of mutation-related amino acid residues in the FolC structure. These mutation sites were further supported by direct Sanger sequencing of the folC gene among 254 clinical MTB isolates in a Hong Kong cohort. Homology modeling of wild-type and mutated FolC was performed, and the predicted structures were docked with hydroxydihydropteroate, the metabolic derivative of para-aminosalicylic acid (PAS), to evaluate the resultant binding affinity changes. Combining the results of three previous cohorts and our cohort, E40, I43, S150, and E153 are the most frequently affected amino acid residues in resistant isolates. Based on the distribution of mutations in the genome-based phylogenetic tree, lineage-specific mutation patterns were observed. Regarding the segregation of affected amino acid residues, the four most frequently affected residues are all in close proximity of the binding pocket for the PAS derivative. Molecular modeling results showed that mutations at E40, I43, and S150 can alter the structure of FolC putative binding pocket, causing the PAS derivative to bind outside of the now deformed pocket. This might ablate the interaction between the protein and the PAS derivative. To conclude, this study is the first comprehensive mutation pattern and bioinformatics analysis of the folC gene in MTB drug-resistant isolates. The distribution of mutations in phylogenetic lineages and protein structure is reported, analyzed, and discussed.

Between 2009 and 2012, 22 adolescents of age 15-20 from a day school in Macau were diagnosed with tuberculosis. Detection of multiple molecular clusters may suggest the presence of concurrent outbreaks, and could reflect also ongoing transmissions in the community. Careful interpretation of molecular epidemiology data is crucial in contact investigations., (© The Author 2014. Published by Oxford University Press on behalf of the Pediatric Infectious Diseases Society. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Background: Salmonella Typhimurium is frequently isolated from foodborne infection cases in Hong Kong, but the lack of genome sequences has hindered in-depth epidemiological and phylogenetic studies. In this study, we sought to reconstruct the phylogenetic relationship and investigate the distribution and mutation patterns of virulence determinants among local S. Typhimurium clinical isolates using their genome sequences., Results: We obtained genome sequences of 20 S. Typhimurium clinical isolates from a local hospital cluster using a 454 GS FLX Titanium sequencing platform. Phylogenetic analysis was performed based on single nucleotide polymorphism positions of the core genome against the reference strain LT2. Antimicrobial susceptibility was determined using minimal inhibitory concentration for five antimicrobial agents and analyses of virulence determinants were performed through referencing to various databases. Through phylogenetic analysis, we revealed two distinct clades of S. Typhimurium isolates and three outliers in Hong Kong, which differ remarkably in antimicrobial susceptibility and presentation and mutations of virulence determinants. The local isolates were not closely related to many of the previously sequenced S. Typhimurium isolates, except LT2. As the isolates in the two clades spanned over 10 years of isolation, they probably represent endemic strains. The outliers are possibly introduced from outside of Hong Kong. The close relatedness of members in one of the clades to LT2 and the Japanese stool isolate T000240 suggests the potential reemergence of LT2 progeny in regions nearby., Conclusions: Our study demonstrated the utility of next-generation sequencing coupled to traditional microbiological testing method in a retrospective epidemiological study involving multiple clinical isolates. The evolution of multidrug- and ciprofloxacin-resistant strains among the more virulent clade is also an increasing concern.

Objectives: We examined, from a Hong Kong healthcare providers' perspective, the cost-effectiveness of rapid diagnosis with Xpert in patients hospitalized for suspected active pulmonary tuberculosis (PTB)., Methods: A decision tree was designed to simulate outcomes of three diagnostic assessment strategies in adult patients hospitalized for suspected active PTB: conventional approach, sputum smear plus Xpert for acid-fast bacilli (AFB) smear-negative, and a single sputum Xpert test. Model inputs were derived from the literature. Outcome measures were direct medical cost, one-year mortality rate, quality-adjusted life-years (QALYs) and incremental cost per QALY (ICER)., Results: In the base-case analysis, Xpert was more effective with higher QALYs gained and a lower mortality rate when compared with smear plus Xpert by an ICER of USD99. A conventional diagnostic approach was the least preferred option with the highest cost, lowest QALYs gained and highest mortality rate. Sensitivity analysis showed that Xpert would be the most cost-effective option if the sensitivity of sputum AFB smear microscopy was ≤74%. The probabilities of Xpert, smear plus Xpert and a conventional approach to be cost-effective were 94.5%, 5.5% and 0%, respectively, in 10,000 Monte Carlo simulations., Conclusions: The Xpert sputum test appears to be a highly cost-effective diagnostic strategy for patients with suspected active PTB in an intermediate burden area like Hong Kong., (Copyright © 2015 The British Infection Association. Published by Elsevier Ltd. All rights reserved.)

Objective: To evaluate the performance of Xpert MTB/RIF (MTB/RIF) in the county-level tuberculosis (TB) laboratory in China., Methods: From April 2011 to January 2012, patients with suspected multidrug-resistant tuberculosis (MDR-TB) and non-MDR-TB were enrolled consecutively from four county-level TB laboratories. The detection of Mycobacterium tuberculosis (MTB) by MTB/RIF was compared to detection by Löwenstein-Jensen culture. The detection of rifampin resistance was compared to detection by conventional drug-susceptibility testing. The impact of multiple specimens on the performance of MTB/RIF was also evaluated., Results: A total of 2142 suspected non-MDR-TB cases and 312 suspected MDR-TB cases were enrolled. For MTB detection in suspected non-MDR-TB cases, the sensitivity and specificity of MTB/RIF were 94.4% and 90.2%, respectively. The sensitivity in smear-negative patients was 88.8%. For the detection of rifampin resistance in suspected non-MDR-TB cases, the sensitivity and specificity of MTB/RIF were 87.1% and 97.9%, respectively. For the detection of rifampin resistance in suspected MDR-TB cases, the sensitivity and specificity of MTB/RIF were 87.1% and 91.0%, respectively. Using multiple sputum specimens had no significant influence on the performance of MTB/RIF for MTB detection., Conclusions: The introduction of MTB/RIF could increase the accuracy of detection of MTB and rifampin resistance in peripheral-level TB laboratories in China. One single specimen is adequate for TB diagnosis by MTB/RIF., (Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: Vibrio parahaemolyticus is a Gram-negative halophilic bacterium. Infections with the bacterium could become systemic and can be life-threatening to immunocompromised individuals. Genome sequences of a few clinical isolates of V. parahaemolyticus are currently available, but the genome dynamics across the species and virulence potential of environmental strains on a genome-scale have not been described before., Results: Here we present genome sequences of four V. parahaemolyticus clinical strains from stool samples of patients and five environmental strains in Hong Kong. Phylogenomics analysis based on single nucleotide polymorphisms revealed a clear distinction between the clinical and environmental isolates. A new gene cluster belonging to the biofilm associated proteins of V. parahaemolyticus was found in clincial strains. In addition, a novel small genomic island frequently found among clinical isolates was reported. A few environmental strains were found harboring virulence genes and prophage elements, indicating their virulence potential. A unique biphenyl degradation pathway was also reported. A database for V. parahaemolyticus (http://kwanlab.bio.cuhk.edu.hk/vp) was constructed here as a platform to access and analyze genome sequences and annotations of the bacterium., Conclusions: We have performed a comparative genomics analysis of clinical and environmental strains of V. parahaemolyticus. Our analyses could facilitate understanding of the phylogenetic diversity and niche adaptation of this bacterium.

Although second-line anti-tuberculosis (TB) injectable drugs have been widely used to improve treatment outcomes of multidrug-resistant TB (MDR-TB), little is known about the prevalence and mechanism of second-line injectable drug resistance among MDR Mycobacterium tuberculosis isolates in China. Here, we found that 12.7 % (20/158) of isolates showed resistance to at least one second-line injectable drug among 158 MDR isolates. At the same time, there were 16 (10.1 %) strains resistant to kanamycin (KAN), 9 (5.7 %) to amikacin (AMK), and 12 (7.6 %) to capreomycin (CAP). In addition, our data revealed no significant difference in the drug resistance patterns for Beijing versus non-Beijing genotype strains (p > 0.05). The most frequently observed mutation was A-to-G substitution at position 1401 of the rrs gene, conferring high-level resistance to KAN and AMK, but had varying minimum inhibitory concentrations (MICs) for CAP. The mutations in the eis promoter and tlyA gene were responsible for low-level resistance to CAP. 83.3 % of A1401G substitutions in the rrs gene was observed in Beijing genotype strains, while the difference was not significant (p = 0.157). Our data demonstrated that the hot-spot regions localized in the rrs gene serve as excellent markers for AMK, but is not a sensitive marker for KAN and CAP. In addition, the cross-resistance patterns and MICs differed among different genetic mutation types, which challenge the practice in China of generalizing resistance to AMK and CAP based on the resistance to KAN alone. Our findings suggested that the individualized drug susceptibility to three major second-line injectable drugs is essential in order to generate more effective treatment regimens for MDR patients.

Neurosyphilis is a difficult clinical stage of syphilis as there is no ideal method for diagnosis and workup requires lumbar puncture which may sometimes provide ambiguous results especially in HIV co-infected patients. Enzyme immunoassay is a widely used screening test for syphilis in serum, but its test performance was not well studied in cerebrospinal fluid. To examine the diagnostic performance of cerebrospinal fluid-enzyme immunoassay (CSF-EIA) in neurosyphilis, we conducted a prospective study for two years. All consecutive patients admitted for workup of neurosyphilis under the Social Hygiene Service, in Hong Kong, were included. Laboratory tests on CSF included several serological tests, CSF cell count, and protein. Forty-five patients were prospectively recruited, of which 29 people were living with HIV / AIDS. Using diagnostic case definition standard stipulated in the IUSTI 2008 guidelines, 17 patients satisfied the diagnosis of neurosyphilis. The CSF-EIA test provided 100% in both sensitivity and negative predictive value; its specificity was 46.4% (13/28, 95% CI 31.8-61%). Specificity improved to 80.8% (95% CI: 68.4-93.2%) with optical density cut-off value at 1.4 for cases with CSF red cell counts <600/mm(3) This is the first study on use of CSF-EIA in neurosyphilis. CSF-EIA showed high sensitivity and high negative predictive value in the study population and the presence of CSF red cells < 600/mm(3)might not affect its accuracy., (© The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.)

Background: Early and effective detection of Mycobacterium tuberculosis (MTB), particularly in smear-negative tuberculosis (TB), is a priority for global TB control. Loop-mediated isothermal amplification with a procedure for ultra rapid DNA extraction (PURE-LAMP) can detect TB in sputum samples rapidly and with high sensitivity and specificity. However, the PURE-LAMP test has not been effectively evaluated, especially in resource-limited laboratories. In this study, we evaluated the performance of the PURE-LAMP test for TB detection in TB suspects from two county-level TB dispensaries in China., Methodology/principal Findings: From April 2011 to February 2012, patients with suspected TB were continuously enrolled from two county-level TB laboratories in China. Three sputum samples (spot, night, and morning sputum) were collected from each recruited patient. Detection of MTB by PURE-LAMP was compared to a reference standard L-J culture. The results showed that the sensitivity of the PURE-LAMP test based on spot sputum for MTB detection was 70.67%, while the sensitivity of the PURE-LAMP test based on spot sputum for MTB detection in smear positive and culture positive patients and smear negative and culture positive patients was 92.12% and 53.81%, respectively. The specificity of PURE-LAMP based on spot sputum for MTB detection was 98.32%. The sensitivity and specificity of the PURE-LAMP test based on three sputa combination for MTB detection was 88.80% and 96.86%, respectively. The results also showed that the PURE-LAMP test had a significantly lower contamination rate than did solid culture., Conclusions/significance: The study suggested that, in peripheral-level TB laboratories in China, the PURE-LAMP test showed high sensitivity and specificity for TB detection in TB suspects, making it a more effective, rapid, and safe method worthy of broader use in the future.

We evaluated the correlation of phenotypic ethambutol (EMB) susceptibility as determined by two drug susceptibility methods with embB mutations in multidrug-resistant (MDR) Mycobacterium tuberculosis strains. The concordance rate for EMB resistance between broth dilution method and sequencing results (83.6%) was significantly higher than between the proportion method and sequencing results (61.7%) (P = 0.004). Of the embB mutants, 75.4% (46/61) possessed a mutation at embB306. Our results demonstrated that ethambutol resistance determined by broth dilution method reveals better correlation with embB mutations than the proportion method in MDR isolates.

Objective: To evaluate the performance of drug susceptibility testing (DST) against the main second-line (SL) anti-tuberculosis drugs in tuberculosis (TB) laboratories in China., Method: The supranational TB reference laboratory issued 30 Mycobacterium tuberculosis isolates to the participating laboratories. Each participating laboratory performed DST against kanamycin (KM), amikacin (AMK), capreomycin (CPM) and ofloxacin (OFX) using the proportion method in Löwenstein-Jensen medium per World Health Organization recommendations. Reported results were checked and compared with the judicial results., Result: The main performance indicators for the four anti-tuberculosis drugs evaluated (KM, AMK, CPM, OFX) were as follows: accordance rates: 91.62%, 99.16%, 96.93% and 96.37%; reproducibility: 99.16%, 99.16%, 94.96% and 94.12%; specificity: 99.12%, 99.64%, 98.00% and 98.41%; sensitivity: 78.03%, 97.62%, 94.44% and 91.51%. The accordance rates and sensitivity values of the four drugs showed statistically significant differences, while specificities showed no significant differences., Conclusion: Eight (66.7%) participating laboratories met the set requirement criteria; however, DST in four (33.3%) laboratories requires greater attention. Of the four drugs tested, the results for KM were lower than those for the other drugs. External quality assessment can lead to effective evaluation of laboratory performance in SL DST.

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.

A GWAS study has reported that two single nucleotide polymorphisms (SNPs) were associated with predisposition to tuberculosis (TB) in African populations. These two loci represented the long-waited GWAS hits for TB susceptibility. To determine whether these two SNPs are associated with TB in Chinese population, we attempted an replication in a cohort of over one thousand Chinese TB patients and 1,280 healthy controls using melting temperature shift allele-specific genotyping analysis. We found that only SNP rs4331426 was significantly associated with TB in Chinese population (p = 0.011). However, the effect was opposite. The G allele of the SNP in Chinese population is a protective allele (OR = 0.62, 95 % CI 0.44-0.87), while it was the risk allele for African population (OR = 1.19, 95 % CI 1.12-1.26). No significance was found for SNP rs2335704. The results provided an independent support for a role in susceptibility to TB for SNP rs4331426. However, it also indicated that direct predisposition element to TB and the association effects may vary across ethnic groups.

Drug-resistant tuberculosis (TB), especially multidrug-resistant TB (MDR-TB), is still one of the most serious threats to TB control worldwide. Early diagnosis of MDR-TB is important for effectively blocking transmission and establishing an effective protocol for chemotherapy. Genechip is a rapid diagnostic method based on molecular biology that overcomes the poor biosafety, time consumption, and other drawbacks of traditional drug sensitivity testing (DST) that can detect MDR-TB. However, the Genechip approach has not been effectively evaluated, especially in limited-resource laboratories. In this study, we evaluated the performance of Genechip for MDR-TB in 1,814 patients in four prefectural or municipal laboratories and compared its performance with that of traditional DST. The results showed that the sensitivity and specificity of Genechip were 87.56% and 97.95% for rifampin resistance and 80.34% and 95.82% for isoniazid resistance, respectively. In addition, we found that the positive grade of the sputum smears influenced the judgment of results by Genechip. The test judged only 75% of the specimens of "scanty" positive grade. However, the positive grade of the specimens showed no influence on the accuracy of Genechip. Overall, the study suggests that, in limited-resource laboratories, Genechip showed high sensitivity and specificity for rifampin and isoniazid resistance, making it a more effective, rapid, safe, and cost-beneficial method worthy of broader use in limited-resource laboratories in China.

Objective: To develop an ICR (female) mouse bioassay (MBA) for toxicity confirmation and evaluation of neurotoxins (brevetoxins)-contaminated shellfish., Methods: Brevetoxins (BTX-B) as a causative agent of neurotoxic shellfish poisoning (NSP) under different shellfish matrices were intraperitoneally injected at different doses into mice to study their toxic effects and to differentiate the range of lethal and sublethal dosages. Their sensitivity and specificity were analyzed with 2 competitive ELISA kits for quantitative determination of standard BTX-B and dihydroBTX-B under different shellfish matrix-diluent combinations. Detection rates of MBA and two antibody-based assays for BTX-B from field NSP-positive shellfish samples were compared., Results: BTX-B could be detected in shellfish tissues at concentration of 50-400 μg/100 g under shellfish matrix-Tween-saline media, which were appropriate to identify toxic shellfish at or above the regulatory limit (80 μg/100 g shellfish tissues). The LD50 identified was 455 mg/kg for BTX-B under general shellfish matrices (excluding oyster matrices) dissolved in Tween-saline. The presence of shellfish matrices, of oyster matrices in particular, retarded the occurrence of death and toxicity presentation in mice. Two antibody-based assays, even in the presence of different shellfish matrix-diluent combinations, showed acceptable results in quantifying BTX-B and dihydroBTX-B well below the regulatory limit., Conclusion: The two ELISA analyses agree favorably (correlation coefficient, r³⋝0.96; Student's t-tests, P>0.05) with the developed bioassay., (Copyright © 2013 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.)

We report 9 cases of exit-site infection and continuous ambulatory peritoneal dialysis peritonitis associated with atypical mycobacteria. All patients had been using topical gentamicin cream as prophylaxis for exit-site infection before the onset of these infections. Gentamicin cream is postulated to be a potential risk factor for atypical mycobacterial infection because of selective pressure on other micro-organisms. The microbiology of atypical mycobacteria and the treatment for atypical mycobacterial infections are discussed.

Multidrug-resistant (MDR)- tuberculosis (TB) and extensively drug resistant (XDR)-TB reportedly lead to increased household transmission. This is a retrospective cohort study of active TB occurring among household contacts exposed to MDR-TB. Of 704 contacts in 246 households, initial screening identified 12 (1.7%) TB cases (prevalent cases) and 17 (2.4%) contacts that subsequently developed active TB (secondary cases) after a median (range) duration of 17 (5-62.5) months. Eight prevalent cases and three secondary cases had MDR-TB. TB incidence rates per 100,000 person-years were 254.9 overall and 45.0 for MDR-TB. XDR-TB in the index MDR-TB patient significantly increased the odds of identifying a prevalent TB case to 4.8 (95% CI 1.02-22.5), and the hazard of finding a secondary TB case to 4.7 (95% CI 1.7-13.5). Molecular fingerprinting confirmed household transmission of MDR-TB. Of 20 retrievable isolates from 27 XDR-TB index cases, restriction fragment length polymorphism analysis showed clustering among 13 (65%), with 11 (55%) due to recent transmission by n-1 method and an identifiable household source in only three (27.2%) of the 11 cases. XDR-TB relative to MDR-TB significantly increases household transmission of TB, probably reflecting prolonged/higher infectivity, and indicating a need for prolonged household surveillance. XDR-TB may largely transmit outside of the household settings.

Background: Multidrug-resistant tuberculosis (MDR-TB; resistance to isoniazid and rifampicin) is difficult to detect and control. Line-probe assays (LiPA) are widely used for the rapid detection of MDR-TB., Objective: To ensure the quality of the test, a pilot external quality assurance (EQA) programme was initiated to assess the feasibility of running such a programme and the possibility of improving the proficiency of TB laboratories in performing the test., Design: Prepared filter-paper-based Mycobacterium tuberculosis DNA samples were shipped to participant laboratories for LiPA EQA. The tests were performed blind, and the results were returned to the organising laboratory for comparison and analysis., Results: A total of four rounds of EQA samples were dispatched to five laboratories in four countries. Overall inter- and intra-laboratory reproducibility was respectively 97% and 96%. The strengths and weaknesses of the participant laboratories in performing the test were discussed., Conclusion: A LiPA EQA programme can ensure quality and improve the performance of TB laboratories. This is a critical step during the initial stages at the time of setting up this method of testing.

Background: Tuberculosis (TB) remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen Mycobacterium tuberculosis. Recent studies have revealed associations of some diseases with an imbalance in the microbial community. Characterization of the TB microbiota could allow a better understanding of the disease., Methodology/principal Findings: Here, the sputum microbiota in TB infection was examined by using 16S rRNA pyrosequencing. A total of 829,873 high-quality sequencing reads were generated from 22 TB and 14 control sputum samples. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were the five major bacterial phyla recovered, which together composed over 98% of the microbial community. Proteobacteria and Bacteroidetes were more represented in the TB samples and Firmicutes was more predominant in the controls. Sixteen major bacterial genera were recovered. Streptococcus, Neisseria and Prevotella were the most predominant genera, which were dominated by several operational taxonomic units grouped at a 97% similarity level. Actinomyces, Fusobacterium, Leptotrichia, Prevotella, Streptococcus, and Veillonella were found in all TB samples, possibly representing the core genera in TB sputum microbiota. The less represented genera Mogibacterium, Moryella and Oribacterium were enriched statistically in the TB samples, while a genus belonging to the unclassified Lactobacillales was enriched in the controls. The diversity of microbiota was similar in the TB and control samples., Conclusions/significance: The composition and diversity of sputum microbiota in TB infection was characterized for the first time by using high-throughput pyrosequencing. It lays the framework for examination of potential roles played by the diverse microbiota in TB pathogenesis and progression, and could ultimately facilitate advances in TB treatment.

Objective: To assess the feasibility of using light-emitting diode fluorescence microscopy (LED-FM) in peripheral laboratories in China., Design: The performance of LED-FM and Ziehl-Neelsen (ZN) microscopy was compared on slides directly prepared from the sputum of tuberculosis (TB) suspects and follow-up patients on treatment. The examination time, fading of fluorescence-stained slides, average unit cost and qualitative user appraisal of LED-FM were also analysed., Results: Among 11 276 slides, the smear-positive rate for LED-FM was 11.2% (1263/11 276), 2.6% (294/11 276) higher than that of ZN (8.6%, 969/11 276; χ(2) 263.5, P < 0.05). The examination time for LED-FM (120.0 ± 38.9 seconds) was shorter than that for ZN (206.3 ± 75.9 s; t = 28.12, P < 0.05). For smear fading, quantitative and qualitative errors occurred within respectively 7.8 and 7.7 weeks. The average unit costs for ZN and LED-FM were respectively US$2.20 ± 0.58 and US$1.97 ± 0.71 (t = 5.08, P < 0.05). LED-FM was accepted by most laboratory technicians., Conclusion: LED-FM compared favourably with ZN, with a higher smear-positive detection rate, a shorter examination time and lower unit examination cost. LED-FM may be an alternative to ZN as a cost-effective method for detecting bacilli in peripheral laboratories in China.

Salmonella enterica serovar Typhimurium is one of the most prevalent serovars of Salmonella that causes human gastroenteritis. Here, we report the draft genome sequence of the S. Typhimurium multidrug-resistant strain ST1660/06. Comparative genomic analysis unveiled three strain-specific genomic islands that potentially confer the multidrug resistance and virulence of the strain.

Primary cervical spine osteosarcoma is rare and is considered to have a poor prognosis. We describe an adolescent patient suffering from primary cervical spine osteosarcoma with delayed diagnosis. Nineteen months deficit and symptom-free survival was achieved after an aggressive multi-modality treatment comprising surgery and adjuvant chemoradiotherapy., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Shigella flexneri is one of the agents most frequently linked to diarrheal illness in developing countries and often causes outbreaks in settings with poor hygiene or sanitary conditions. Travel is one of the means by which S. flexneri can be imported into developed countries, where this pathogen is not commonly seen. A robust and discriminatory subtyping method is needed for the surveillance of S. flexneri locally and regionally, and to aid in the detection and investigation of outbreaks. The PulseNet International network utilizes standardized pulsed-field gel electrophoresis (PFGE) protocols to carry out laboratory-based surveillance of foodborne pathogens in combination with epidemiologic data. A multicenter validation was carried out in nine PulseNet laboratories located in North and South America, Europe, and Asia, and it demonstrated that a new protocol is highly robust and reproducible for subtyping of S. flexneri. This protocol, already approved for PulseNet laboratories, applies NotI and XbaI as primary and secondary restriction enzymes, respectively, under electrophoresis conditions of initial switch time of 5 s to final switch time of 35 s, at 6 volts/cm.

Background: Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes., Findings: Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ~90% of 100 assemblies with < 10 scaffolds and ~95% of 100 assemblies with < 150 contigs; 2) average contig N50 size is over 331 kb; 3) average single base accuracy is > 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%., Conclusions: A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks.

Background: The Hong Kong TB Reference Laboratory is a high volume laboratory examining around 400 sputum acid-fast bacilli smears daily using fluorescence microscopy (FM)., Objective: To assess the effectiveness of blinded rechecking applied to FM in a high-throughput laboratory., Method: From 2003, 2.5% (5% in 2003 and 2004) of all smears were randomly selected, relabelled and assigned to each technician (rechecker) in turn. These smears were restained and re-examined. Discordance between initial screener and rechecker was resolved by a controller., Results: From 2003 to 2010, low false-negative (LFN) errors (0.10-0.27%) were within the critical values, at 85% (1 year) and 90% (7 years) sensitivity. However, LFN error (0.28-0.62%) among recheckers was prominent. There were also low false-positive (LFP) cases (0.13-0.75%), but subsequent cultures showed these to be mycobacteria culture-positive. This relatively poor performance among the recheckers might be due to background fluorescence increase after restaining and/or inefficiency of the rechecking procedure., Conclusion: In a high-throughput laboratory, blind rechecking is a good means of quality assurance. To minimise false LFP, problems due to restaining should be resolved before blinded rechecking can be generally applied in the field for FM where mycobacterial cultures are not routinely performed.

Setting: Patients infected with non-tuberculous mycobacteria usually fail treatment due to erroneous diagnoses. Early detection of mycobacterial species is essential for adequate case management., Objective: To conduct a multicentre, prospective evaluation of the recently developed biochip test and to determine its sensitivity and specificity in three clinical hospitals in China., Results: A total of 1565 clinical isolates obtained from three hospitals were identified as 19 mycobacterial species by 16S sequencing. The same 53 reference strains were detected in all three hospitals as quality control and to evaluate the reproducibility of the assay. The overall accuracy of the species identification assay among all strains was 99.9% (1722/1724). The two unidentified samples, belonging to Mycobacterium parascrofulaceum and M. monacense, were not included among the 17 mycobacterial species. The reference strains demonstrated that the reproducibility of the assay was 100%., Conclusion: The biochip test provided cost-effective and highly sensitive identification of mycobacterial species in less than 6 h. This will help clinical staff carry out more efficient and personalized clinical treatment without delay.