PulseNet International Survey on the Implementation of Whole Genome Sequencing in Low and Middle-Income Countries for Foodborne Disease Surveillance

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.

The emergence of antibiotic resistant Mycoplasma genitalium as the cause of non-gonococcal urethritis in male sexually transmitted infection clinic patients

Mycoplasma genitalium (MG) is the cause of an emerging sexually-acquired infection with high propensity for antimicrobial resistance development. In a prevalence study conducted at the public sexually transmitted infection (STI) service in Hong Kong, the first void urine (FVU) samples of 38 (8%) out of 493 male non-gonococcal urethritis (NGU) patients were tested positive by RT-PCR. Patients with MG were younger in age (31 vs 33, OR=0.96, 95% 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 longer symptom duration of over 2 weeks (14% vs 6%, OR=2.34, 95% CI 1.10-4.97; P=0.03). The prevalence of MG was lower in patients co-infected with Chlamydia trachomatis than as isolated infection (4% vs 10%, OR=0.38, 95% CI 0.17-0.84; P=0.02). Men who have sex with men (MSM) did not give a higher prevalence of MG. Antimicrobial resistance-conferring mutation was present in 24 (63%) patients with MG - 23S rRNA 18 (47%) and parC 19 (53%). Similar to neigbouring Asia Pacific countries, concurrent resistance mutation against both macrolide and fluoroquinolone was demonstrated in 14 (37%). Histories of azithromycin and moxifloxacin use were significantly associated with MG diagnosis. Characteristically, NGU in Hong Kong featured the co-existence of mono-resistance against macrolide or fluoroquinolone, and the presence of dual class resistance. The geographic variability of antimicrobial resistance against MG is attributed to not just the different transmission networks formed in separate population groups but the antimicrobial prescriptions in the treatment of urethritis in the community.

Evolving Epidemiological Characteristics of COVID-19 in Hong Kong From January to August 2020: Retrospective Study

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 (Rt), 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). Rt 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. Rt 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.

Utility of GeneXpert in analysis of bronchoalveolar lavage samples from patients with suspected tuberculosis in an intermediate-burden setting

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.

A systematic review of transmission dynamic studies of methicillin-resistant Staphylococcus aureus in non-hospital residential facilities

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.

PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies. WGS data are suitable for surveillance and outbreak purposes and for answering scientific questions pertaining to source attribution, antimicrobial resistance, transmission patterns, and virulence, which will further enable the protection and improvement of public health with respect to food-borne disease.

Insights into intercontinental spread of Zika virus

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.

Concurrent Outbreaks of Tuberculosis in a School and the Wider Community in Macau

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.

Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong

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.

Multicenter Evaluation of the Molecular Line Probe Assay for Multidrug Resistant Mycobacterium Tuberculosis Detection in China

In order to evaluate the performance of a molecular Hain line probe assay (Hain LPA) for rapid detection of rifampicin and isoniazid resistance of Mycobacterium tuberculosis in China, 1612 smear positive patients were consecutively enrolled in this study. Smear positive sputum specimens were collected for Hain LPA and conventional drug susceptibility testing (DST). The sensitivity and specificity of Hain LPA were analyzed by using conventional DST as golden reference. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for rifampicin resistance detection were 88.33%, 97.66%, 81.54%, and 98.62%, respectively. The sensitivity, specificity, PPV and NPV for isoniazid resistance detection were 80.25%, 98.07%, 87.25%, and 96.78%, respectively. These findings suggested that Hain LPA can be an effective method worthy of broader use in China.

Cost-effectiveness analysis of the Xpert MTB/RIF assay for rapid diagnosis of suspected tuberculosis in an intermediate burden area

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.

Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus

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.

First proficiency testing of second-line anti-tuberculosis drug susceptibility testing in 12 provinces of China

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.

Diagnostic accuracy of the PURE-LAMP test for pulmonary tuberculosis at the county-level laboratory in China

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.

Use of the INNO-LIA syphilis score assay in the resolution of discordant positive screening enzyme immunoassay results for the serological diagnosis of syphilis

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.

Development of an ICR mouse bioassay for toxicity evaluation in neurotoxic poisoning toxins-contaminated shellfish

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.

Association of polymorphisms in the Chr18q11.2 locus with tuberculosis in Chinese population

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.

Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing

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.

A pilot external quality assurance programme for line-probe assay detection of anti-tuberculosis drug resistance

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.

Emerging resistance in Salmonella enterica serotype Typhi in Hong Kong

A total of 182 Salmonella enterica serotype Typhi isolated from three hospitals in Hong Kong from 1986 to 1992 were tested for their susceptibility to 21 antimicrobial agents. Four percent or less were resistant to chloramphenicol, ampicillin, some of the cephalosporins, nalidixic acid, tetracycline and trimethoprim and 6% to 1024 mg/l sulfamethoxazole. All were susceptible to the aminoglycosides and the 4-quinolones. Nineteen isolates were resistant to at least 1, and up to 9, antibiotics. Of 8 chloramphenicolor multiply-resistant isolates studied, only 3 could transfer their resistances while resistance of one could only be mobilized. Four of 5 ampicillin-resistant strains produced a beta-lactamase of pI 5.5. Antibiotic resistances were mediated by plasmids of 106, 116 or 221 kb of incompatibility groups H, I1 and K. Three resistant isolates did not harbour any plasmid. A total of 43 (24%) S. Typhi harboured plasmids ranging in size from 4.3 to 221 kb. Plasmids of 106 kb and 8.5 kb were found in 17 and 10 isolates, respectively. Restriction enzyme digestion of these two plasmids showed that each could be differentiated into 3 types. Of 89 isolates that were phage typed, 38% were untypable, while 17% and 12% were of phage types E1 and A, respectively, and the rest belonged to 17 other types.

Random blinded rechecking of sputum acid-fast bacilli smear using fluorescence microscopy: 8 years' experience

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.

Transmission of multidrug-resistant and extensively drug-resistant tuberculosis in a metropolitan city

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.

Standardization and international multicenter validation of a PulseNet pulsed-field gel electrophoresis protocol for subtyping Shigella flexneri isolates

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.

A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation

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.

Methodological issues in quantifying the magnitude of the tuberculosis problem in a prison population

SETTING

Correctional settings and remand prisons.

OBJECTIVE

To critically discuss calculations for epidemiological indicators of the tuberculosis (TB) burden in prisons and to provide recommendations to improve study comparability.

METHODS

A hypothetical data set illustrates issues in determining incidence and prevalence. The appropriate calculation of the incidence rate is presented and problems arising from cross-sectional surveys are clarified.

RESULTS

Cases recognized during the first 3 months should be classified as prevalent at entry and excluded from any incidence rate calculation. The numerator for the incidence rate includes persons detected as having developed TB during a specified period of time subsequent to the initial 3 months. The denominator is person-time at risk from 3 months onward to the end point (TB or end of the observation period). Preferably, entry time, exit time and event time are known for each inmate to determine person-time at risk. Failing that, an approximation consists of the sum of monthly head counts, excluding prevalent cases and those persons no longer at risk from both the numerator and the denominator.

CONCLUSIONS

The varying durations of inmate incarceration in prisons pose challenges for quantifying the magnitude of the TB problem in the inmate population. Recommendations are made to measure incidence and prevalence.

Role of whole-blood interferon-gamma release assay in the diagnosis of smear-negative tuberculosis

SETTING

Hong Kong Chest Clinics.

OBJECTIVES AND METHODS

To conduct a prospective study investigating the role of a whole-blood interferon-gamma release assay, QuantiFERON®-TB Gold In-Tube (QFT-GIT), in the diagnosis of smear-negative tuberculosis (TB). The QFT-GIT result was compared with the final confirmed diagnosis after 12 months.

RESULTS

Of 262 smear-negative subjects, 188 had active TB, 167 (88.8%) of whom were QFT-GIT-positive; 74 had inactive/non-TB, 30 (40.5%) of whom were QFT-GIT-negative. The positive (PPV) and negative predictive values for active TB were respectively 79.1% and 58.8%. For this target group with high TB prevalence (71.8%), a positive test increased the chance of active disease by only 7.3%. Despite a positive likelihood ratio (LR) of 1.49, the negative LR was 0.28, making the diagnosis of active TB much less likely after a negative test. Although sensitivity and specificity showed no difference across different age groups, the PPV decreased (P < 0.001) with increasing age, likely reflecting the increased prevalence of competing diagnoses.

CONCLUSION

In an area with a high prevalence of latent TB infection, a positive QFT-GIT test does not add much to confirm the diagnosis of smear-negative TB, while a negative test indicates a need for further investigation.

Usefulness of resistant gene markers for predicting treatment outcome on second-line anti-tuberculosis drugs

AIM

Mutations in rrs [nucleotide (nt) 1401], gyrA gene (codons 90, 91 or 94), tlyA, ethA and thyA genes of Mycobacterium tuberculosis (MTB) were evaluated for their usefulness in predicting treatment outcome of kanamycin (KM), capreomycin (CPM), ofloxacin (OFX), ethionamide (ETH) and para-aminosalicylic acid (PAS).

METHODS AND RESULTS

DNA sequence analyses of these genes were performed against 188 MTB isolates obtained from patients put on second-line anti-TB drugs (SLDs) with well-documented clinical history and treatment outcome. Mutations in rrs and gyrA have 100% positive predictive value (PPV) in predicting treatment failure for KM and OFX, while 88·9 and 80% were obtained, respectively, when tlyA and rrs mutations were considered in CPM. For ETH and PAS, the PPV of using ethA and thyA mutations to predict treatment failure was 82·5 and 89·3%, respectively.

CONCLUSIONS

Our study demonstrated high specificities of gene mutations in predicting poor treatment outcome; however, further technical advancement is required to make the molecular detection of resistances to other SLDs feasible in clinical laboratories.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to correlate different polymorphisms of major SLD resistance gene markers with predicted treatment outcome, using an international set of well-documented clinical MTB strains.

Solid-phase extraction clean-up of ciguatoxin-contaminated coral fish extracts for use in the mouse bioassay

Florisil solid-phase extraction (SPE) cartridges were used for purifying ciguatoxin (CTX)-contaminated coral fish extracts, with the aim of removing extracted lipid but retaining optimal level of CTXs in the purified fractions. The CTX-containing fraction (target fraction) in fish ether extract was isolated and purified by eluting through a commercially available Florisil cartridge with hexane-acetone-methanol solvent mixtures of increasing polarity (hexane-acetone (4:1, v/v) < acetone-methanol (7:3, v/v) < 100% methanol). Application of Florisil SPE using acetone-methanol (7:3, v/v) condition facilitated the separation of 4.2 +/- 0.4 mg (mean +/- standard error of the mean (SEM)) of purified target fraction from 20 mg ether extract with good retention of CTXs. The mouse bioassay was used to demonstrate that the average CTX recovery of the target fraction from CTX-spiked samples was 75.8% +/- 3.3%, which was significantly increased by 96.7% +/- 15% when compared with CTX recovery from ether extracts (44.8% +/- 5.2%) without performing SPE purification. Over 70% of non-target lipids were removed in which no CTX toxicity was found. Moreover, the target fractions of both CTX-spiked and naturally CTX-contaminated samples gave more prominent toxic responses of hypothermia and/or induced more rapid death of the mice. The use of acetone-methanol (7:3, v/v) condition in the elution could significantly improve overall recovery of CTXs, while minimizing the possible interferences of lipid matrix from co-extractants on mice.

Determination of critical concentrations of second-line anti-tuberculosis drugs with clinical and microbiological relevance

BACKGROUND

Reliable DST against second-line anti-tuberculosis drugs (SLDs) is crucial for the management of the increasing burden of patients affected by multidrug- and extensively drug-resistant TB.

METHODS

This study utilizes 252 clinical isolates of Mycobacterium tuberculosis from five countries (Hong Kong Special Administrative Region, Korea, Latvia, Peru, Philippines) with documented treatment histories to establish clinically and microbiologically relevant critical concentrations (CCs) of six SLDs for three routine testing methods: the absolute concentration method using Löwenstein-Jensen (LJ) medium, the 1% proportion method using Middlebrook 7H10 agar medium, and the radiometric BACTEC 460 system.

FINDINGS

In LJ medium, CCs of capreomycin, ethionamide, kanamycin, ofloxacin, rho-aminosalicylic acid and cycloserine (CS) were respectively 40.0, 40.0, 30.0, 3.0, 1.0 and 30.0 mg/l. In 7H10 agar medium, the respective CCs for the first five antibiotics (except CS) were 8.0, 2.0-3.0, 3.0-5.0, 1.0-1.5 and 0.5-1.0 mg/l. In BACTEC 460 broth, the respective CCs were 1.5-2.0, 1.0-1.5, 2.0-3.0, 0.5-1.0 and 0.5-1.0 mg/l. Precautions in DST interpretation was also discussed.

INTERPRETATION

By adopting this set of CCs as a global standard to define second-line drug susceptibility and resistance, as well as precautions in result interpretation, the screening, diagnosis and management of patients with drug-resistant TB can be greatly improved.

Comparative evaluation of the INNO-LIA syphilis score and the MarDx Treponema pallidum immunoglobulin G Marblot test assays for the serological diagnosis of syphilis

We evaluated the performance of two immunoblot assays: the INNO-LIA Syphilis Score (LIA) and the MarDx T. pallidum IgG Marblot Test (TWB), as compared with that of the Murex ICE Syphilis enzyme immunoassay (EIA), the Serodia Treponema pallidum particle agglutination (TPPA) assay and the fluorescent treponemal antibody-absorption (FTA-abs) assay, for the serological diagnosis of syphilis using serum samples of 135 attendees of the social hygiene clinics of the Department of Health in Hong Kong newly diagnosed with syphilis and provided with clinical stages (39 in primary, 20 in secondary, 18 in early latent and 58 in latent of unknown duration) and of 43 normal healthy subjects between October and December 2004. The differences in the overall sensitivities of the LIA assay and the EIA/TPPA/FTA-abs assays were not statistically significant ( P > 0.05) whereas the overall sensitivity of the TWB assay was significantly lower ( P < 0.05) than the overall sensitivities of the EIA, the TPPA and the FTA-abs assays. The LIA assay had an overall sensitivity of 94.1% (95% CI 88.7–97.0%) whereas the TWB assay 65.2% (95% CI 56.8–72.7%). Both the LIA and the TWB assays have a specificity of 100%. When consensus results were derived from the most predominant results of the EIA, the TPPA and the FTA-abs assays, the LIA assay had a positive agreement with the consensus results of 98.5% (95% CI 94.5–99.6%) whereas the TWB assay 68.2% (95% CI 59.8–75.6%). Therefore, the LIA assay performed significantly better ( P < 0.05) than the TWB assay. The LIA assay can be considered to be a valid alternative confirmatory test for the serological diagnosis of syphilis.

Bulk acid-fast staining of sputum smears: time to end a taboo

SETTING

A high-throughput laboratory routinely performing fluorescence microscopy for acid-fast bacilli (AFB) smear with automated bulk staining.

OBJECTIVES

To determine the risk of false-positive AFB sputum smears from bulk staining showing as smear-positive, culture-negative specimens, or a decrease in smear- and culture-positives.

DESIGN

Direct AFB smear and Löwenstein-Jensen culture were performed for a total of 39,350 routine sputum specimens. Of these, 6633 were randomly selected for individual AFB staining, while the remaining 32,717 were processed by bulk machine staining. Positives for smear and culture were compared.

RESULTS

Overall, 111 specimens yielded a positive individually stained smear; of these, 100 (90.1%, 95%CI 83.0-95.0) were also culture-positive compared to 504/543 smear-positives after bulk staining (92.8%, 95%CI 90.6-95.0). The proportions of smear-positive, culture-negative and smear- and culture-positive specimens were respectively 1.8% vs. 2.2% and 90.1% vs. 92.8%, for individual and bulk staining (non-significant).

CONCLUSIONS

The risk of transferring AFB from positive to negative smears during bulk AFB staining is negligible, if it occurs at all. Bulk staining should not be discouraged, as even in low-income countries this method will save significant resources, particularly manpower, and improve staining results in laboratories with a high workload.

Genetic association between a chemokine gene CXCL-10 (IP-10, interferon gamma inducible protein 10) and susceptibility to tuberculosis

Background

Previous studies showed that activation of CXCL-10 and other chemokines were prominent in many infectious diseases. These chemokines are components of innate immune response to respiratory tract pathogens. We examined the promoter variants of CXCL-10 and their role in predisposition to tuberculosis (TB).

Methods

The promoter 1.8 kb of CXCL-10 was sequenced in 24 healthy Chinese individuals to identify genetic polymorphisms. Three tagging SNPs in CXCL-10 promoter (− 1447A > G, − 872G > A, − 135G > A) were selected, and genotyping were performed in 240 TB patients and 176 healthy Chinese subjects. Disease associations were examined by χ² and Fisher exact test.

Results

A promoter SNP (− 135G > A) with minor allele frequency of 0.1 showed a moderate association with TB both in genotype analysis (p = 0.01) and allelic analysis (p = 0.03); other tagging SNPs (− 1447A > G, − 872G > A) were not associated with TB. The odd ratio of the protective allele − 135G > A was 0.51(C.I 0.29 − 0.91) for homozygotes and heterozygotes carriers of the A allele.

Conclusion

A new potential protective SNP (− 135G > A) for TB is identified in the promoter of chemokine gene, CXCL-10. Interestingly, the exact same allele has been shown to enhance IP-10 transactivation and susceptibility to Hepatitis B virus infection in a recent publication. This SNP, located at 14 bp upstream of a NF-kB binding site, might also account for the susceptibility to TB. Our results expanded the clinical significance of this SNP in CXCL-10 promoter.

Epidemiology of antituberculosis drug resistance 2002-07: an updated analysis of the Global Project on Anti-Tuberculosis Drug Resistance Surveillance

BACKGROUND

The Global Project on Anti-Tuberculosis Drug Resistance has been gathering data since 1994. This study provides the latest data on the extent of drug resistance worldwide.

METHODS

Data for drug susceptibility were gathered from 90 726 patients in 83 countries and territories between 2002 and 2007. Standardised collection of results enabled comparison both between and within countries. Where possible, data for HIV status and resistance to second-line drugs were also obtained. Laboratory data were quality assured by the Supranational Tuberculosis Reference Laboratory Network.

FINDINGS

The median prevalence of resistance to any drug in new cases of tuberculosis was 11.1% (IQR 7.0-22.3). The prevalence of multidrug resistance in new tuberculosis cases ranged from 0% in eight countries to 7% in two provinces in China, 11.1% in Northern Mariana Islands (although reporting only two cases), and between 6.8% and 22.3% in nine countries of the former Soviet Union, including 19.4% in Moldova and 22.3% in Baku, Azerbaijan (median for countries surveyed 1.6%, IQR 0.6-3.9). Trend analysis showed that between 1994 and 2007, the prevalence of multidrug-resistant (MDR) tuberculosis in new cases increased substantially in South Korea and in Tomsk Oblast and Orel Oblast, Russia, but was stable in Estonia and Latvia. The prevalence of MDR tuberculosis in all tuberculosis cases decreased in Hong Kong and the USA. 37 countries and territories reported representative data on extensively drug-resistant (XDR) tuberculosis. Five countries, all from the former Soviet Union, reported 25 cases or more of XDR tuberculosis each, with prevalence among MDR-tuberculosis cases ranging between 6.6% and 23.7%.

INTERPRETATION

MDR tuberculosis remains a threat to tuberculosis control in provinces in China and countries of the former Soviet Union. Data on drug resistance are unavailable in many countries, especially in Africa, emphasising the need to develop easier methods for surveillance of resistance in tuberculosis.

FUNDING

Global Project: United States Agency for International Development and Eli Lilly and Company. Drug resistance surveys: national tuberculosis programmes, the Government of the Netherlands, the Global Fund to Fight AIDS, Tuberculosis and Malaria, Japan International Cooperation Agency, and Kreditanstalt für Wiederaufbau.

Variations in quality of carbol fuchsin stains collected from routine tuberculosis laboratories

SETTING

In-use carbol fuchsin stains were collected from 10 different routine acid-fast bacilli smear microscopy laboratories.

OBJECTIVE

To examine the variations in the composition of carbol fuchsin stains.

METHOD

Carbol fuchsin concentrations were first determined spectrophotometrically by measuring absorbance at 547 nm. High-performance liquid chromatography (HPLC) separated and quantified the four basic fuchsin homologues: para-rosaniline, rosaniline, magenta II and new fuchsin, and identity was confirmed by mass spectrometry (MS).

RESULTS

Absorbance measurement showed that three of 10 (30%) samples contained insufficient carbol fuchsin (<70%). Wide variations in relative proportions of fuchsin homologues were found.

CONCLUSION

The relative abundance of rosaniline + new fuchsin was quite stable among the different laboratories. Spectrophotometry and HPLC/MS are necessary and sensitive tools for monitoring fuchsin quality.

Risk factors for multidrug-resistant tuberculosis in Hong Kong

SETTING

Previous anti-tuberculosis treatment is a widely reported risk factor for multidrug-resistant tuberculosis (MDR-TB), whereas other risk factors are less well described. In Hong Kong, the clinical characteristics of MDR-TB have not been systematically evaluated.

OBJECTIVE

To explore the risk factors for MDR-TB in Hong Kong.

DESIGN

MDR-TB patients treated between 1999 and 2003 were compared with non-MDR-TB patients by stratification of previous anti-tuberculosis treatment.

RESULTS

One hundred and fifty-six MDR-TB patients, including 93 with and 63 without a previous history of anti-tuberculosis treatment, were identified. Among the 322 non-MDR-TB controls, respectively 192 and 130 patients did and did not have a previous history of anti-tuberculosis treatment. Using logistic regression analysis, non-permanent residents (OR 6.85, 95%CI 1.38-34.09), frequent travel (OR 2.48, 95%CI 1.07-5.74) and younger age were found to be independent predictors of MDR-TB in previously treated patients, whereas living on financial assistance just failed to reach statistical significance (OR 2.75, 95%CI 0.98-7.68, P=0.05). In the treatment-naïve group, despite significant differences in baseline characteristics among MDR-TB and non-MDR-TB patients, no independent predictor variables could be identified.

CONCLUSION

In Hong Kong, non-permanent residents, frequent travel and young age were independent predictors of MDR-TB among previously treated patients.

Rapid detection of pathogenic Vibrio parahaemolyticus by a sensitive and specific duplex PCR-hybridization probes assay using LightCycler

AIMS

To develop a real-time polymerase chain reaction (PCR) hybridization probe assay for rapid and specific detection of thermostable direct haemolysin-producing Vibrio parahaemolyticus.

METHODS AND RESULTS

Primers and hybridization probes were designed to target the toxR and tdh2 genes. Mismatches were introduced in the tdh2 primers for specific amplification of the target. The 3' ends of donor probes for both genes were labelled with fluorescein. The 5' ends of recipient probes for tdh2 and toxR were labelled with LC Red 640 and LC Red 705, respectively. The real-time assay was evaluated against conventional biochemical tests and the KAP-RPLA kit (Kanagawa phenomenon detection kit by reverse passive latex agglutination). toxR and tdh2 were detected in 100% and 91% of clinical V. parahaemolyticus isolates (n = 118), respectively. Specificity and sensitivity of the real-time assay for toxR and tdh2 were 100%, respectively. Dynamic range of detection for toxR was 10(7)-10(1) CFU ml(-1) and that for tdh2 was 10(7)-10(4) CFU ml(-1).

CONCLUSIONS

The LightCycler assay described is sensitive and highly specific for detection of pathogenic V. parahaemolyticus in a single reaction tube within 80 min.

SIGNIFICANCE AND IMPACT OF THE STUDY

The assay developed allows accurate detection of pathogenic V. parahaemolyticus, which is valuable for rapid tracing of infection source during outbreaks.

Application of BAX system, Tecra Unique Salmonella test, and a conventional culture method for the detection of Salmonella in ready-to-eat and raw foods

AIMS

To compare the BAX system, the Tecra Unique Salmonella test, and a conventional culture method for the detection of Salmonella in various foods.

METHODS AND RESULTS

Ready-to-eat and raw foods were inoculated with Salmonella serotype Typhimurium, Salmonella serotype Enteritidis, Salmonella serotype Typhi, or Salmonella serotype Derby. Incubated pre-enrichment cultures were examined using the BAX system, the Tecra Unique Salmonella test, and a conventional culture method. Salmonella could be detected in all ready-to-eat food samples inoculated with S. Typhimurium, S. Enteritidis, or S. Derby, with any of the three test methods. However, false negatives were obtained with the Tecra test and the culture method when samples with higher background flora were inoculated with S. Typhi. Sensitivity test results suggested the two rapid tests performed as well as the culture method in the detection of 10(1) CFU of S. Typhimurium in 25-g cooked or raw food.

CONCLUSIONS

The BAX system and the Tecra Unique Salmonella test demonstrated results comparable with those of the culture method in the detection of Salmonella serotypes used except S. Typhi.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first evaluation of the BAX system, the Tecra Unique Salmonella test, and a culture method in the detection of Salmonella in a variety of western and oriental foods.

TB surveillance in correctional institutions in Hong Kong, 1999-2005

OBJECTIVE

To understand the epidemiology of tuberculosis (TB) inside the prison system of Hong Kong.

METHOD

Prospective territory-wide TB surveillance was conducted among prisoners in 24 correctional institutions.

RESULTS

From 1999 to 2005, 622 prevalent TB cases diagnosed before or within 3 months of incarceration and 214 incident cases diagnosed after 3 months were reported by prison staff to a paper-based central prison TB registry. Both crude prevalence and incidence were falling (chi(2) for trend, both P < 0.001), despite a higher sex- and age-adjusted prison TB incidence as compared to the general population (indirectly standardised rate [ISR] 280.6 vs. 108.0/100000, P < 0.001). Illegal immigrants (odds ratio [OR] 3.6, 95% confidence interval [CI] 1.8-7.4) and drug addicts (OR 2.04, 95%CI 1.13-3.7) were two major risk groups. The TB incident risk disappeared after their exclusion (ISR 117.1 vs. 108.0/100000, P = 0.52). No significant difference in the multidrug-resistant rate was found when comparing the group with the general population (3.5% vs. 1.0%, OR 3.6, 95%CI 0.5-28.4). No extensively drug-resistant (XDR) cases were identified.

CONCLUSION

TB remains a significant disease in local prisons. Further strengthening of TB control programmes in prisons, especially targeting the higher risk groups, is recommended.

Roles of laboratories and laboratory systems in effective tuberculosis programmes

Laboratories and laboratory networks are a fundamental component of tuberculosis (TB) control, providing testing for diagnosis, surveillance and treatment monitoring at every level of the health-care system. New initiatives and resources to strengthen laboratory capacity and implement rapid and new diagnostic tests for TB will require recognition that laboratories are systems that require quality standards, appropriate human resources, and attention to safety in addition to supplies and equipment. To prepare the laboratory networks for new diagnostics and expanded capacity, we need to focus efforts on strengthening quality management systems (QMS) through additional resources for external quality assessment programmes for microscopy, culture, drug susceptibility testing (DST) and molecular diagnostics. QMS should also promote development of accreditation programmes to ensure adherence to standards to improve both the quality and credibility of the laboratory system within TB programmes. Corresponding attention must be given to addressing human resources at every level of the laboratory, with special consideration being given to new programmes for laboratory management and leadership skills. Strengthening laboratory networks will also involve setting up partnerships between TB programmes and those seeking to control other diseases in order to pool resources and to promote advocacy for quality standards, to develop strategies to integrate laboratories functions and to extend control programme activities to the private sector. Improving the laboratory system will assure that increased resources, in the form of supplies, equipment and facilities, will be invested in networks that are capable of providing effective testing to meet the goals of the Global Plan to Stop TB.

Feasibility of using interpolated contours of targets and organs at risk in intensity-modulated radiation therapy treatment planning for advanced-stage nasopharyngeal carcinoma

To assess the dosimetric effect of using interpolated contours in planning intensity-modulated radiation therapy (IMRT) for advanced T-stage nasopharyngeal carcinoma. The present study focused on T3-T4 tumours where the proximity of targets to neurological organs poses a stringent test on the feasibility of such an approach. Contours of targets and organs were delineated on CT images of 2.5-mm interval and a reference IMRT plan was generated. An investigative (INV) IMRT plan was then generated with the same planning protocol, but based on interpolated contours that replaced deleted contours on alternate slices. The reference and INV plans were compared. Regarding target coverage, all targets in the INV plans met the acceptance criteria except for the PTV in one case. Regarding organs, the mean dose to 1% volume of the brainstem and spinal cord in the INV plans were kept below their dose limits. No significant differences in the mean doses to others organs were found. Satisfactory target coverage and protection of critical organs to a degree similar to full-scale contouring could be achieved with use of interpolated contours. The saving in manpower time for contouring is expected to significantly improve the throughput of the IMRT planning process.

Association between RANTES functional polymorphisms and tuberculosis in Hong Kong Chinese

Chemokines play a major role in leukocyte recruitment during the formation of tuberculous granulomas. We studied the association between genetic polymorphisms of three chemokines, monocyte chemoattractant protein-1 (MCP-1), RANTES (regulated on activation, normal T cell expressed and secreted) and macrophage inflammatory protein-1alpha (MIP-1alpha), and tuberculosis (TB). The distribution of five functionally significant single-nucleotide polymorphisms (SNPs), MCP-1 -2518A/G, RANTES -403G/A, -28C/G and In1.1T/C as well as MIP-1alpha +459C/T was not found to be different between patients with TB and healthy control subjects of the Hong Kong Chinese population. However, differences in linkage disequilibrium (LD) of the SNPs of RANTES and in distribution of the haplotypes of RANTES between patients with TB and healthy controls (P<0.0001) were found. Two risk haplotypes of RANTES, A-C-T and G-C-C, at positions -403, -28 and In1.1, respectively, were identified. Furthermore, combining the genotypes of RANTES -403 and In1.1, two diplotypes GA/TT (P<0.001) and GG/TC (P<0.0001) showed strong association with TB. Our findings support the association between RANTES functional polymorphisms and TB.