Epidemiological studies on tuberculosis control and respiratory viruses - Thesis

Epidemiological studies on tuberculosis control and respiratory viruses

Sloot, R.

Publication date

2015

Document Version

Final published version

Link to publication

Citation for published version (APA):

Sloot, R. (2015). Epidemiological studies on tuberculosis control and respiratory viruses.

General rights

It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons).

Disclaimer/Complaints regulations

If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible.

Epidemiological studies

on tuberculosis control

and respiratory viruses

Rosa Sloot

E

p

id

e

m

io

lo

g

ic

a

l s

tu

d

ie

s o

n

tu

b

e

rc

u

lo

sis

c

o

n

tr

o

l a

n

d

re

sp

ir

a

to

ry

v

ir

u

se

s

R

o

sa

S

lo

Thesis, University of Amsterdam (UvA), the Netherlands ISBN: 978-90-6464-866-3

http://dare.uva.nl/dissertaties

Cover: image by P. Nijenhuis (modified by P. Duijn)

Lay-out: Ferdinand van Nispen, Citroenvlinder-dtp.nl, Bilthoven,

the Netherlands

Printed by: GVO drukkers & vormgevers, Ede, the Netherlands Financial support for printing of this thesis was provided by:

KNCV Tuberculosis Foundation, AMC, Stichting tot Bevordering van de Klinische Epidemiologie Amsterdam, Delft Imaging Systems.

© 2015 Rosa Sloot, Amsterdam, the Netherlands

Published articles were reprinted with permission from the publishers. No part of this thesis may be reproduced, stored or transmitted without the prior permission of the author or, when appropriate, the publishers of the articles.

and respiratory viruses

ACADEMISCH PROEFSCHRIFT

ter verkrijging van de graad van doctor aan de Universiteit van Amsterdam

op gezag van de Rector Magnificus prof. dr. D.C. van den Boom

ten overstaan van een door het College voor Promoties ingestelde commissie, in het openbaar te verdedigen in de Agnietenkapel

op woensdag 10 juni 2015, te 10:00 uur

door Rosa Sloot geboren te Haarlem

Promotores: Prof. dr. M.W. Borgdorff Universiteit van Amsterdam

Prof. dr. M.D. de Jong Universiteit van Amsterdam

Co-promotor: Dr. M.F. Schim van der Loeff Universiteit van Amsterdam

Overige leden: Prof. dr. M.P. Grobusch Universiteit van Amsterdam

Prof. dr. T. van der Poll Universiteit van Amsterdam

Prof. dr. F.G.J. Cobelens Universiteit van Amsterdam

Prof. dr. J.H. Richardus Erasmus Universiteit Rotterdam

Prof. dr. D. van Soolingen Radboud Universiteit Nijmegen

Dr. S. van den Hof KNCV Tuberculosefonds

Chapter 1 Introduction 7

Chapter 2 Clustering of tuberculosis cases based on variable-number

tandem-repeat typing in relation to the population structure of Mycobacterium tuberculosis in the Netherlands.

J Clin Microbiol 2013;51:2427-31

19

Chapter 3 Yield of tuberculosis contact investigations in Amsterdam:

opportunities for improvement.

Eur Respir J 2014;44:714-24

33

Chapter 4 Risk of tuberculosis after recent exposure: a 10-year follow-up study of contacts in Amsterdam.

Am J Respir Crit Care Med 2014;190:1044-52

53

Chapter 5 Biomarkers can identify pulmonary tuberculosis in

HIV-infected drug users months prior to clinical diagnosis.

EBioMedicine 2015;2:172-9

73

Chapter 6 Distribution and viral load of respiratory viruses differ by

illness severity in adults: a comparison between community and hospital populations.

In preparation

93

Chapter 7 General Discussion 119

Chapter 8 Summary 133

Samenvatting Dankwoord About the author Portfolio

Chapter

1

Introduction

Introduction

Tuberculosis epidemiology

Tuberculosis (TB) is a major global health problem; it is the second leading cause of death from an infectious agent worldwide, after the human immunodeficiency virus (HIV). The World Health Organization (WHO) estimated that there were 8.6 million new TB cases in 2012 (1). The global burden of TB is fuelled by high rates of HIV/AIDS; 1.1 million (13%) of the people who developed TB in 2012 were HIV positive; 75% of these HIV-positive TB cases were in the African Region. Out of the 1.3 million estimated deaths due to TB, 320,000 (25%) deaths were among HIV-infected people (1).

Since the start of national recording of TB cases in the Netherlands in 1951, the incidence of TB has steadily declined. In 2001-2005 the TB incidence declined 4% annually to 7.1 per 100,000 (2). Reported rates in 2013 were 5.1 per 100,000 population. Among 848 TB patients in 2013 were 74% foreign-born, of which the largest group were of Somalian origin (147/848, 17%) (3). Although the Netherlands is among the countries with the lowest TB incidence worldwide, it has not yet reached the elimination target, defined as less than 1 sputum smear-positive patient per 1,000,000 inhabitants (4). It is expected that, under the current conditions, elimination in the Netherlands will not be reached in the coming decades, mainly because TB incidence among the first generation immigrants will remain high (5).

TB is more common in the largest cities (>250,000 inhabitants) in the Netherlands than in smaller towns or villages. In 2011, the TB incidence in the urban areas Amsterdam, The Hague, Rotterdam and Utrecht was on average 3 times higher (14.1/100,000) than in rural areas (4.7/100,000) (6). In 2013, the highest rate was recorded in Amsterdam (13.3/100,000), and the majority of cases were among foreign-born (79%) (7).

Tuberculosis – transmission, infection and disease

M. tuberculosis is carried in airborne particles, called droplet nuclei. Aerosol droplets

containing M. tuberculosis bacilli are generated when individuals with pulmonary TB cough, sneeze, talk or otherwise exhale (8). In poorly ventilated environments the bacilli can be kept airborne for prolonged periods of time, resulting in dispersion throughout a room. The presence of acid-fast bacilli in the sputum smear is the

1

increased by the presence of lung cavitation on the chest radiograph. In addition to the infectiousness of the source case, also proximity, frequency and length of exposure can affect transmission of M. tuberculosis.

Infection occurs when an individual inhales droplet nuclei containing M. tuberculosis bacilli that reach the alveoli of the lungs. These bacilli are ingested by alveolar macrophages and dendritic cells and, if not destroyed or inhibited, spread through the lymphatic system or bloodstream to more distant tissues and organs (9) (10). Infection with M. tuberculosis infrequently progresses directly to active disease and is more often contained by the host immune response. The resulting latent infection can be eradicated, or can persist in a dormant state for prolonged periods (latent TB infection). In this state, the immune system prevents active replication but fails to eradicate the bacteria. Any subsequent weakening of the host immune system may result in reactivation of dormant bacilli, causing clinically active disease many years after the infection (reactivation TB) (11). The risk of progression to disease declines steeply with time since infection. About 50%-80% of the individuals who develop TB are believed to do so shortly after infection. When individuals develop active TB more than 2-5 years after infection this is called reactivation (12) (13) (14). Co-infection with HIV and M. tuberculosis is the most important risk factor for both immediate and reactivation TB; the risk of progression to disease for co-infected individuals is 5%-10% each year (15) (16), while in those without HIV co-infection the lifetime risk is believed to be 10% or less.

Molecular fingerprinting as tool for investigating transmission

M. tuberculosis strains recently derived from a common ancestor generally exhibit

an identical DNA fingerprinting pattern. The finding of individuals with identical or highly similar fingerprint patterns suggests epidemiological links between such cases and form a cluster. It is therefore assumed that the proportion of clustered isolates in a population reflects the amount of recent or ongoing transmission of M.

tuberculosis (17). Non-matching, i.e. unique DNA fingerprint patterns, are attributed

to reactivation of infections acquired in the past or recent transmission from patients outside the observed period or geographical area covered by the study (18). In addition to quantification of recent transmission in a population, molecular epidemiological studies have identified risk factors for transmission by comparing characteristics of

clustered and unique patients (19) (20). Knowledge of such risk factors may help to develop strategies to interrupt transmission in high-risk populations. Risk factors identified in molecular epidemiological studies include: male sex, younger age, not being an immigrant, HIV-coinfection, homelessness, injecting drug use and alcohol abuse (21).

In the Netherlands, IS6110 restriction fragment length polymorphism (RFLP) typing has been applied routinely to all M. tuberculosis complex isolates from 1993 until the end of 2008 (22). The analysis of the complex IS6110 RFLP banding patterns is technically demanding, difficult to interpret and unreliable for typing strains with low (<6) IS6110 copy numbers (23). In 2006, 24-locus variable number of tandem repeat (VNTR) typing has gained recognition as the new gold standard for typing of

M. tuberculosis (24) and has been used in the Netherlands since 2008.

Tuberculosis control

In low TB incidence countries (<20 notifications per 100,000 population), which includes most countries in the European Union, TB is concentrated in big cities among risk groups, including immigrants, homeless people and those with drug- or alcohol abuse (25). In contrast to TB control in high-TB burden countries, focussed on the detection and treatment of all TB patients, most low-incidence countries are confronted with very specific challenges as a result of the declining disease incidence in the native population and the increasing relative importance of TB among the immigrant population (26). TB control activities in low-incidence countries include ensuring early detection and treatment of TB patients, reducing the incidence of TB infection by risk group management, prevention of transmission of infection in institutional settings, reducing the incidence of TB through outbreak management, and provision of preventive treatment for specific groups (26).

Diagnosis and treatment

Diagnosis of active TB relies on microscopic examination, chest radiograph and growth of M. tuberculosis on a culture plate or in liquid medium, which are usually performed when individuals are suspected to have pulmonary TB based on clinical symptoms. In the Netherlands, liquid assays, such as Mycobacteria Growth Indicator Tube (MGIT) techniques, are recommended in addition to culture plates, due to the reduced time to detection in liquid medium than in solid medium (27). The most

1

haemoptysis and breathlessness (28).

The tuberculin skin test (TST), introduced in 1890, is the oldest test to diagnose latent TB infection. The TST measures the in vivo cell-mediated immune response to a cocktail of M. tuberculosis antigens, known as purified protein derivative (PPD). If the transverse diameter of the resulting induration is 10 mm or more, measured 48 to 72 hours after injection of PPD, this is considered a positive TST result. PPD shares many antigens with

M. bovis Bacille de Calmette et Guérin (BCG), and several non-tuberculous mycobacteria

(NTM). As a result, the TST has a low specificity in individuals from low- and middle income countries with a high prevalence of infection with NTM, or high coverage of BCG vaccination. Responses to BCG generally last for only a few years after vaccination, so these effects are thought to be of limited influence among immigrants from countries with high BCG coverage (29). The sensitivity of the TST may be low in individuals with depressed immunity such as AIDS or malnutrition. In the last decade more specific tests such as cell-mediated immunity-based interferon-gamma (IFN-γ) release assays (IGRAs) have been developed and include M. tuberculosis specific antigens (ESAT-6 and CFP-10) (30). T-cells of individuals infected with M. tuberculosis produce IFN-γ when they are stimulated in vitro by these M. tuberculosis specific antigens.

Both the IGRA and the TST cannot differentiate between recent or old TB infection, nor between latent TB infection and active TB. Furthermore, both tests are unable to predict which latently infected individuals are at risk for progression to TB; which is a major drawback since the risk to develop active TB in latently infected is small and there may be adverse effects of preventive LTBI treatment. Thus, until such predictive tests become available, the risk of not receiving treatment versus the risk of receiving treatment must be weighed for each individual before deciding on whether to start preventive LTBI treatment (31).

Preventive treatment for LTBI generally consists of six months isoniazid, but LTBI can also be treated with 4 months rifampicin or 3 months isoniazid and rifampicin. Treatment for TB requires daily administration for two months of isoniazid, rifampicin, ethambutol and pyrazinamide, followed by four months of isoniazid and rifampicin. This schedule can be adapted to the drug sensitivity of the strain but treatment of multidrug-resistant TB (resistant to at least isoniazid and rifampicin) is more extensive, less effective and more expensive (32).

Source- and contact investigations in the Netherlands

Source- and contact investigation among infectious pulmonary TB patients is an essential component of TB control in most low-incidence countries. The objectives are reducing transmission and morbidity through early detection and adequate treatment of (secondary) source cases, and by reducing incidence through prompt initiation of preventive treatment among recently infected contacts (33). National guidelines recommend the initiation of a contact investigation for each patient with pulmonary TB, to be performed by public health nurses of the Public Health Services (PHSs) under supervision of a TB specialist. Contacts are prioritized for screening based on a risk assessment, which investigates the infectiousness of the index patient, degree of exposure to the index as determined by duration and intensity of exposure, and risk of progression to TB among infected contacts (33) (34). Subsequently contacts are evaluated according to the stone-in-the-pond principle were screening for TB and/or LTBI starts among the high priority contacts and expands to less prioritized contacts until the infection prevalence resembles the background prevalence of infection in the community, or until all identified contacts have been screened (35). Since the introduction of the IGRA, national guidelines recommend that contacts should be screened according to a two-step strategy in which the IGRA is used to confirm a positive TST result (36).

Respiratory viruses

Acute respiratory tract infections (ARTIs) are a leading cause of morbidity. It is estimated that in the Netherlands, based on a population of 16.9 million individuals, about 920,000 persons annually visit their general practitioner for an ARTI (37). A viral cause of respiratory illness is identifiable in up to 95% of the paediatric cases, but the detection rates decrease steadily by age, to 30-40% in the elderly (38). More than 50% of ARTIs are caused by rhinoviruses and coronaviruses (39). Human rhinoviruses are the most common respiratory pathogens in all ages (>50%), and coronaviruses are estimated to account for 7–26% of all upper respiratory tract infections in adults (38, 39). Influenza viruses account for 5–15% of ARTIs and typically cause mid-winter epidemics. The typical respiratory symptoms (cough, fever and sore throat), however, are poorly associated with confirmed influenza illnesses in older adults (39, 40). Etiologic diagnosis solely based on symptoms is impossible because respiratory viral infections are characterized by a wide range of similar respiratory symptoms including cough, sneezing, fever, myalgia and malaise (41). The recent introduction of

1

has greatly improved the diagnostics for respiratory viral infections (42). However, due to its high sensitivity, the clinical interpretation of a positive result is often difficult. PCR detection of viral nucleic acids in asymptomatic individuals is common, which has raised concerns about establishing a causal link between viral infection and respiratory symptoms in individual patients, especially during high prevalence seasons (43). Furthermore, studies on the burden of viral respiratory infections in critically ill patients give conflicting results regarding the associations between the presence of a viral respiratory tract infection and the clinical outcome (44) (45). Understanding the etiologies and clinical profiles of respiratory viral infections are essential for improving preventive and therapeutic strategies. Most etiological studies have focused on patients presenting in health care settings with respiratory illness. Studies including the general population could provide information on the background prevalence of respiratory infections and thereby contribute to our understanding of the clinical interpretation of a positive PCR in patients with respiratory illness who are seeking healthcare.

Outline of the thesis

The general aim of this thesis was to study the epidemiology of TB and respiratory viruses in the Netherlands, which resulted in the following research questions:

1. Is 24-locus VNTR typing suitable to identify recent transmission between TB cases?

2. What is the impact of source- and contact investigation in Amsterdam regarding TB prevention?

3. Can biomarkers be identified that predict which individuals will progress to TB within a high TB risk population?

4. Could viral load estimations aid in the diagnostic interpretation of respiratory viruses detected in the upper airways by multiplex RT-PCR? The first research question is addressed in chapter 2: it describes the population structure of 3,776 M. tuberculosis isolates from native Dutch and foreign-born TB cases, collected in the period 2004-2008 in the Netherlands, and assesses to what extent clustering based on VNTR typing represents recent transmission. The second research question is addressed by identifying opportunities for improvement of contact

investigation in chapter 3, and by investigating the potential impact of preventive TB treatment among contacts of pulmonary patients in chapter 4. In chapter 3 the success of TB contact investigations in Amsterdam is evaluated by investigating compliance to national guidelines and by determining its coverage and yield between 2008-2011. Chapter 4 estimates the risk of TB among latently infected contacts according to initiation of preventive treatment in a low-incidence, high-income setting, using 10 years of follow-up data. The third research question is addressed in chapter 5. We retrospectively selected blood samples of HIV-infected drug users and compared gene expression profiles in samples of drug users months before clinical TB diagnosis with gene expression in samples of drug users who did not develop TB.

To address the fourth research question, we compared the prevalence, relative distribution and viral load of respiratory viruses among adult populations by approximated illness severity, based on symptom status and health care use. In chapter 6 we investigated nasopharyngeal samples, collected during the influenza seasons of 2011-2013, among a random sample of participants in an adult population-based cohort study and compared results to those obtained during the same period from adult patients presenting at or admitted to various departments of a hospital serving the geographical area of the cohort study population.

Chapter 7 provides a general discussion of the findings and their implications in the context of the literature, and gives some recommendations for TB control in low-incidence high-income settings.

1

References

1- World Health Organization. Global tuberculosis control: WHO report 2013. Geneva, Switzerland: WHO Press, 2013.

2- Erkens CGM, Kalisvaart NA, Slump E, Sebek M, van Soolingen D. Tuberculose in Nederland. Surveillancerapport over de tuberculosesituatie in Nederland. The Hague: KNCV Tuberculosis foundation, 2007.

3- Tuberculosis in the Netherlands 2013. Surveillance rapport. The Hague: KNCV Tuberculosis Foundation, 2013.

4- Styblo K, Broekmans JF, Borgdorff MW. Expected decrease in the tuberculosis incidence during the elimination phase. How to determine its trend. TSRU, progress report. The Hague: KNCV Tuberculosis Foundation, 1997.

5- van Leth F, Kalisvaart N, Erkens CGM, Borgdoff MW. Projection of the number of patients with tuberculosis in the Netherlands in 2030. Eur J Public Health 2009;19:424–7.

6- Tuberculosis in the Netherlands 2011. Surveillance rapport. The Hague: KNCV Tuberculosis Foundation, 2011. 7- Website: http://tbc-online.nl/nederland/index.php?jaar= 2013. Date accessed: 17 February 2015.

8- Riley RL, Mills CC, O’Grady F, Sultan LU, Wittestadt F, Shivipuri DN. Infectiousness of air from a tuberculosis ward-ultraviolet irradiation of infected air: comparative infectiousness of different patients. Am Rev Respir

Dis 1962;85:511–25.

9- Dannenberg AM. Delayed-type hypersensitivity and cell- mediated immunity in the pathogenesis of tuberculosis. Immunol Today 1991;12:228–33.

10- Harries AD, Dye C. Tuberculosis. Ann Trop Med Parasitol 2006;100:415–31.

11- Walzl G, Ronacher K, Hanekom W, Scriba TJ, Zumla A. Immunological biomarkers of tuberculosis. Nat Rev

Immunol 2011;11:343–54.

12- Ferebee SH. Controlled chemoprophylaxis studies in tuberculosis: a general review. Bibl Tuberc 1970;26:28-106.

13- Comstock GW, Livesay VT, Woolpert SF. The prognosis of a positive tuberculin reaction in childhood and adolescence. Am J Epidemiol 1974;99:131-8.

14- Sutherland I. Recent studies in the epidemiology of tuberculosis, based on the risk of being infected with tubercle bacilli. Adv Tuberc Res 1976;19:1-63.

15- Selwyn PA, Hartel D, Lewis VA, Schoenbaum EE, Vermund SH, Klein RS,Walker AT,Friedland GH. A prospective study of the risk of tuberculosis among intravenous drug users with human immunodeficiency virus infection. N Engl J Med 1989;320:545–50.

16- Raviglione MC, Harries AD, Msiska R, Wilkinson D, Nunn P. Tuberculosis and HIV: current status in Africa.

AIDS 1997;11:115–23.

17- Borgdorff MW, Nagelkerke N, van Soolingen D, de Haas PEW, Veen J, van Embden JD. Analysis of tuberculosis transmission between nationalities in the Netherlands in the period 1993-1995 using DNA fingerprinting.

Am J Epidemiol 1998;147:187–95.

18- Glynn JR, Bauer J, Boer AS De, Borgdorff MW, Fine PEM. Interpreting DNA fingerprint clusters of Mycobacterium tuberculosis. Int J Tuberc Lung Dis 1999;3:1055–60.

19- Alland D, Kalkut GE, Moss AR, McAdam RA, Hahn JA, Bosworth W, Drucker E, Bloom BR. Transmission of tuberculosis in New York City. An analysis by DNA fingerprinting and conventional epidemiologic methods.

N Engl J Med 1994;330:1710-6.

20- Small PM, Hopewell PC, Singh SP, Paz A, Parsonnet J, Ruston DC, Schecter GF, Daley CL, Schoolnik GK. The epidemiology of tuberculosis in San Francisco. A population-based study using conventional and molecular methods. N Engl J Med 1994;330:1703–9.

21- Fok A, Numata Y, Schulzer M, Fitzgerald MJ. Risk factors for clustering of tuberculosis cases : a systematic review of population-based molecular epidemiology studies. Int J Tuberc Lung Dis 2008;12:480–92. 22- van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, Hermans P, Martin C, McAdam

R, Shinnick TM, Small PM. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 1993;31:406-9.

23- Kremer K, Soolingen D Van, Frothingham R, Haas WH, Hermans WM, Martín C, Palittapongarnpim P, Riley LW, Yakrus MA, Musser JM. Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility. J Clin Microbiol 1999;37:2607-18.

24- Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, Savine E, de Haas P, van Deutekom H, Roring S, Bifani P, Kurepina N, Kreiswirth B, Sola C, Rastogi N, Vatin V, Gutierrez MC, Fauville M, Niemann S, Skuce R, Kremer K, Locht C, van Soolingen D. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 2006;44:4498–510.

25- de Vries G, Aldridge RW, Caylà JA, Haas WH, Sandgren A, van Hest NA, Abubakar I. Epidemiology of tuberculosis in big cities of the European Union and European Economic Area countries. Euro Surveill 2014;19. 26- Broekmans JF, Migliori GB, Rieder HL, Lees J, Ruutu P, Loddenkemper R, Raviglione MC. European framework for tuberculosis control and elimination in countries with a low incidence: Recommendations of the World Health Organization (WHO), International Union Against Tuberculosis and Lung Disease (IUATLD) and Royal Netherlands Tuberculosis Association. Eur Respir J 2002;19:765–75.

27- NVMM. NVMM-guideline, mycobacterial laboratory diagnostics, Leeuwarden, the Netherlands. Nederlandse Vereniging voor Medische Microbiologie (NVMM), 2006.

28- Campbell IA, Bah-sow O. Pulmonary tuberculosis: diagnosis and treatment. BMJ 2006;332:1194–7. 29- Farhat M, Greenaway C, Pai M, Menzies D. False-positive tuberculin skin tests: what is the absolute effect of

BCG and non-tuberculous mycobacteria? J Clin Microbiol 2006;10:1192–204.

30- Pai M, Riley LW, Colford JM. Jr. Interferon-γ assays in the immunodiagnosis of tuberculosis: a systematic review. Lancet Infect Dis 2004;4:761–6.

31- Lobue P, Menzies D. Treatment of latent tuberculosis infection: An update. Respirology 2010;15:603–22. 32- Diel R, Vandeputte J, de Vries G, Stillo J, Wanlin M, Nienhaus A. Costs of tuberculosis disease in the European

Union: a systematic analysis and cost calculation. Eur Respir J 2014;43:554–65.

33- Erkens CGM, Kamphorst M, Abubakar I, Bothamley GH, Chemtob D, Haas W, Migliori GB, Rieder HL, Zellweger J-P, Lange C. Tuberculosis contact investigation in low prevalence countries: a European consensus.

Eur Respir J 2010;36:925–49.

34- Landelijke Coördinatie Infectieziektebestrijding. Richtlijn Tuberculosecontactonderzoek.[Tuberculosis contact investigation]. Juni 2007. The Hague: KNCV Tuberculosis Foundation, 2007.

35- Veen J. Microepidemics of tuberculosis: the stone-in-the-pond principle. Tuber Lung Dis 1992;73:73–6. 36- IGRA-werkgroep Commissie voor Praktische Tuberculosebestrijding. Richtlijn Interferon Gamma Release

Assays bij de diagnostiek van Tuberculose [Guideline Interferon Gamma Release Assays, for tuberculosis diagnostics]. The Hague: KNCV Tuberculosis Foundation, 2007.

37- van Gageldonk-Lafeber AB, Heijnen MLA, Bartelds AIM, Peeters MF, van der Plas SM, Wilbrink B. A case-control study of acute respiratory tract infection in general practice patients in The Netherlands. Clin Infect

Dis 2005;41:490-7.

38- Jartti T, Jartti L, Ruuskanen O, Söderlund-Venermo M. New respiratory viral infections. Curr Opin Pulm Med 2012;18:271-8.

39- Wat D. The common cold: a review of the literature. Eur J Intern Med 2004;15:79-88.

40- Sullivan SJ, Jacobson RM, Dowdle WR, Poland GA. 2009 H1N1 influenza. Mayo Clin Proc 2010;85:64–76. 41- Heikkinen T, Järvinen A. The common cold. Lancet 2003;361:51–9.

42- Henrickson KJ. Advances in the laboratory diagnosis of viral respiratory disease. Pediatr Infect Dis J 2004;23:S6-10.

43- Jartti T, Söderlund-Venermo M, Hedman K, Ruuskanen O, Mäkelä MJ. New molecular virus detection methods and their clinical value in lower respiratory tract infections in children. Paediatr Respir Rev 2013;14:38–45.

44- Miggins M, Hasan A, Hohmann S, Southwick F, Casella G, Schain D, Liu H, Bihorac A, Moldawer L, Efron P, Ang D. The potential influence of common viral infections diagnosed during hospitalization among critically ill patients in the United States. PloS one 2011;6:e18890.

45- Daubin C, Parienti J-J, Vincent S, Vabret A, du Cheyron D, Ramakers M, Freymuth F, Charbonneau P. Epidemiology and clinical outcome of virus-positive respiratory samples in ventilated patients: a prospective cohort study. Crit Care 2006;10:R142.

Chapter

2

Clustering of tuberculosis cases

based on variable-number

tandem-repeat typing in relation

to the population structure of

Mycobacterium tuberculosis in the

Netherlands

Rosa Sloot Martien W. Borgdorff Jessica L. de Beer Jakko van Ingen Philip Supply Dick van Soolingen

Abstract

The population structure of 3,776 Mycobacterium tuberculosis isolates was determined using variable-number tandem-repeat (VNTR) typing. The degree of clonality was so high that a more relaxed definition of clustering cannot be applied. Among recent immigrants with non-Euro-American isolates, transmission is overestimated if based on identical VNTR patterns.

2

Clustering of Mycobacterium tuberculosis isolates based on identical DNA fingerprints is commonly used as a proxy for recent transmission (1). However, this assumption is not always correct and depends on many factors, such as circulation of genetically similar strains, evolution of M. tuberculosis over time, transmission rate, DNA typing methods applied, duration of the study period, sampling, and effectiveness of TB control (2, 3). Various studies have shown that not all cases in DNA fingerprint clusters have epidemiological links with other cases in the cluster (4, 5). Moreover, epidemiological links have been found between cases caused by bacteria with slightly different DNA fingerprints (6). Clustering results among cases in the immigrant population especially should be interpreted with caution (7, 8), as isolates from these patients often belong to genetically compact strain lineages predominating in the countries of origin (9, 10, 11, 12).

In the Netherlands, more than 70% of all TB cases are found among foreign-born persons, and extensive information on each patient is stored in a national registry. We aimed to investigate the population structure of M. tuberculosis isolates among native and immigrant cases and to determine the consequences for the interpretation of recent transmission based on variable-number tandem- repeat (VNTR) typing results. Culture-confirmed TB cases from October 2003 to December 2008 were included in this study. Patient information was obtained from the Netherlands Tuberculosis Register (NTR), held by the KNCV Tuberculosis Foundation. In total, 3,975 M. tuberculosis isolates were typed by IS6110/PGRS restriction fragment length polymorphism (RFLP) and standard 24-locus VNTR typing (13, 14) at the RIVM or by Genoscreen (Lille). Molecular data were matched with demographic data using the date of birth, sex, postal area code, and year of diagnosis, resulting in 3,793 (95%) matching cases. After exclusion of 17 foreign-born individuals because of incomplete data for several variables, 3,776 (95%) cases remained eligible.

Genotype information was uploaded to the MIRU-VNTRplus web-application (http://www.miru-vntrplus.org) (15) for phylogenetic lineage prediction, which was performed stepwise as described by Allix-Beguec et al. (16). Isolates that were part of the CAS, Beijing, EAI, Mycobacterium bovis, and Mycobacterium africanum lineages were categorized as non-Euro-American and the remaining as a Euro-American superlineage (16).

Clonal complexes, defined as groups of at least two isolates differing in not more than 3/24 loci, were identified on a minimum-spanning tree with BioNumerics software (Applied Maths, Kortrijk, Belgium), using MIRU-VNTR data and the categorical distance, which scores the number of alleles shared or different over the 24 markers used. Multiple imputation was used to account for 184 (5%) and 37 (1%) of 3,776 cases with missing data for the variables “time since immigration at TB diagnosis” and “gender,” respectively. All remaining variables were used to create five imputed data sets, and results are based on pooled statistics. Two different cluster definitions were used to investigate the interpretation of recent transmission; identical VNTR patterns and single-locus variants (SLVs). The theory behind this was that allowing SLVs to be clustered might involve genetically closely related strains that in fact share the same transmission chain. The analyses were performed separately for the Euro-American and non-Euro-American lineages and completed with SPSS 18.0 (SPSS, Chicago, IL) and statistical program R version 2.11.0.

A minimum-spanning tree was produced for all 3,776 isolates included in the analysis. In total 3,377 (89%) isolates were distributed over 83 clonal complexes (Fig. 1), whereas the remaining 399 (11%) isolates did not belong to any clonal complex. Within each complex, all the VNTR patterns represented the same lineage type, except the two largest complexes comprising 84% Haarlem strains and 67% T-specific strains. Of the 3,776 isolates, 1,130 (30%) represented the non-Euro-American lineages (Table 1). We reasoned that recently arrived immigrant cases having nonclustered

M. tuberculosis isolates most likely represent importation of foreign genotypes.

Among the 504 nonclustered recent-immigrant cases, 239 (47%) were caused by isolates of the non-Euro-American lineages, of which EAI (45%), CAS (26%), and Beijing (18%) constituted the majority (Table 1). Cases caused by these non-Euro-American lineages originated from Asia (41%) and Africa (56%). In contrast, recent-immigrant nonclustered cases with Euro-American lineages had a higher diversity in geographical origin. Furthermore, 40 (8%) of the 504 recent-immigrant nonclustered cases originated from European countries, of which the majority (93%) were caused by the Euro-American lineages. Among the 564 native Dutch cases with nonclustered

M. tuberculosis isolates, 459 (81%) had isolates of the Euro-American lineages, of which

the majority were of the Haarlem (36%), T-specific (33%), and LAM (13%) lineages (Table 1).

2

Figure 1. Identification of clonal complexes in the total study population in a minimum-spanning

tree

Patient factors significantly associated with VNTR clustering in the whole study population, using identical profiles as a cluster definition, were analyzed. As observed in previous studies (17, 18), we found male sex, young age, urban residence, having pulmonary tuberculosis, and no previous treatment for tuberculosis as significant risk factors for clustering. All risk factors became less strongly associated when analyses was restricted to cases caused by non-Euro-American lineages (Table 2). Only age (<30 and 55 to 70 years) and having pulmonary tuberculosis remained significantly associated with clustering.

Table 1. Distribution of non-Euro-American and Euro-American lineages over clustered and

nonclustered immigrant and native Dutch tuberculosis cases

No. of isolates

Nonclustered cases Clustered cases Immigrants

Lineage Resident <3 yr Resident ≥3 yr Natives Immigrants Natives Total study population Non-Euro-American

EAI 108 135 19 96 26 384

CAS 63 108 15 117 25 328

Beijing 42 69 37 98 28 274

Bovis 5 10 26 10 11 62

West African (I,II) 16 21 2 18 2 59

With <10 isolates 5 10 6 2 0 23 Total 239 353 105 341 92 1,130 Euro-American Haarlem 55 133 166 278 182 814 T specific 64 126 151 152 134 627 LAM 68 148 61 236 102 615 S 13 44 30 23 22 132 Uganda (I,II) 9 28 4 36 4 81 New-1 15 47 8 8 7 85 TUR 9 16 5 32 20 82 X 8 16 16 19 21 80 Cameroon 13 15 10 30 6 74 Ural 7 11 6 5 2 31 With <15 isolates 4 14 2 5 0 25 Total 265 598 459 824 500 2,646

Allowing SLVs to be clustered increased the clustering proportion by 24% and 57% among cases with Euro-American isolates and non-Euro-American isolates, respectively (Table 2). This resulted in a decreased magnitude of association between the risk factors and clustering, in particular for the cases caused by non-Euro-American lineages (Table 2). Similarly, the association between RFLP and VNTR clustering in cases caused by non-Euro-American lineages was reduced compared to that in cases caused by Euro-American lineages. Discrepancy between VNTR and RFLP typing (i.e., clustered by either VNTR or RFLP) was in most cases caused by VNTR clustered and RFLP nonclustered isolates (Table 2). Among 1,130 non-Euro-American isolates, 177

2

Euro-American isolates, 263 (10%) were clustered by VNTR and nonclustered by RFLP (Table 2).

This study shows the lineage-dependent degree of reliability of the inference on transmission. Classification of lineage type was based on the geographical association between patient origin and strain lineage, defined as Euro-American and non-Euro-American. Among nonclustered native Dutch TB cases, Euro-American lineages were most frequently isolated. Domination of these lineages among native TB cases has also been shown in other European populations (19, 20), suggesting that these lineages have been circulating in Europe for centuries (21). In contrast, recent-immigrant cases caused by nonclustered non-Euro-American strains originated from distant geographical areas.

Risk factors for recent transmission, as determined by VNTR clustering, were reduced in the non-Euro-American lineages compared to the Euro-American lineages, indicating the lineage dependence. This was further visible when testing the effect of tolerating single-locus variants in the cluster definition, as the increase in clustered non-Euro-American strains was twice as high as that among Euro-American strains, reflecting the clonality of the former strains in the study population. Furthermore, the magnitude of association between risk factors and clustering decreased after allowing single-locus variants, especially among cases with non-Euro-American isolates, thus increasing overestimation of recent transmission for cases caused by non-Euro-American lineages.

In conclusion, to remain useful in TB control practice, the definition of a cluster on the basis of VNTR typing should be a fully identical 24-locus VNTR typing result. This study further indicated limits in the interpretation of recent transmission based on clustering by VNTR typing in the recent-immigrant population. Our findings are in particular relevant for other European low-incidence countries having similar forms of immigration.

Table 2. Risk f act ors f or c lust ering,

with and without allo

wing single-locus v ariants t o be c lust er ed, ac cor ding t o lineag e a   N on-Eur o-Americ an lineag es Eur o-Americ an lineag es N o locus v ariation Allo wing SL Vs t o be clust er ed N o locus v ariation Allo wing SL Vs t o be clust er ed Par amet er N o. (%) of VNTR clust er ed isolat es OR (95% CI) N o. (%) of VNTR clust er ed isolat es OR (95% CI) Total no. of _isolat es N o. (%) of VNTR clust er ed isolat es OR (95% CI) N o. (%) of VNTR clust er ed isolat es OR (95% CI) Total no. of _isolat es Total no . of isolat es in stud y population Se x M ale 243 (39) 1.1 (0.9-1.4) 373 (60) 1.0 (0.8-1.3) 619 855 (54) 1.5 (1.3-1.8) 1,023 (65) 1.3 (1.1-1.6) 1,579 2,198 Female 190 (37) 1 306 (60) 1 511 469 (44) 1 616 (58) 1 1,067 1,578 Ag e, y ears <30 157 (40) 1.7 (1.0-2.8) 240 (61) 1.7 (1.1-2.7) 392 429 (58) 5.1 (3.9-6.7) 501 (68) 3.5 (2.7-4.6) 734 1,126 30-55 202 (38) 1.6 (0.9-2.6) 323 (61) 1.6 (1.0-2.6) 534 645 (56) 4.6 (3.5-5.9) 771 (67) 3.3 (2.6-4.2) 1,153 1,687 55-70 49 (43) 1.9 (1.1-3.4) 73 (64) 1.9 (1.1-3.3) 115 162 (46) 3.1 (2.3-4.2) 213 (61) 2.5 (1.9-3.4) 352 467 >70 25 (28) 1 43 (48) 1 89 88 (22) 1 154 (38) 1 407 496 Residenc e _Urban 165 (42) 1.3 (0.9-1.6) 237 (60) 1.0 (0.8-1.3) 393 601 (58) 1.7 (1.4-1.9) 721 (69) 1.7 (1.4-2) 1,040 1,433 Rur al 268 (36) 1 442 (60) 1 737 723 (45) 1 918 (57) 1 1,606 2,343 H ad TB bef or e Ye s 12 (26) 0.5 (0.3-1.1) 25 (53) 0.7 (0.4-1.3) 47 72 (38) 0.6 (0.4-0.8) 89 (47) 0.5 (0.4-0.7) 190 237 N o/unkno wn 421 (39) 1 654 (60) 1 1,083 1,252 (51) 1 1,550 (63) 1 2,456 3,539 Loc alization o f TB PT B 228 (44) 1.8 (1.4-2.4) 332 (65) 1.5 (1.2-2.0) 514 844 (53) 1.6 (1.3-1.9) 1,026 (65) 1.5 (1.3-1.8) 1,589 2,103 EP TB 141 (31) 1 251 (54) 1 463 303 (41) 1 396 (54) 1 732 1,195 PTB+EP TB 64 (42) 1.6 (1.1-2.4) 96 (63) 1.4 (0.9-2.1) 153 177 (55) 1.7 (1.3-2.2) 217 (67) 1.7 (1.3-2.2) 325 478

2

with and without allo

wing single-locus v ariants t o be c lust er ed, ac cor ding t o lineag e a N on-Eur o-Americ an lineag es Eur o-Americ an lineag es N o locus v ariation Allo wing SL Vs t o be clust er ed N o locus v ariation Allo wing SL Vs t o be clust er ed amet er N o. (%) of VNTR clust er ed isolat es OR (95% CI) N o. (%) of VNTR clust er ed isolat es OR (95% CI) Total no. of _isolat es N o. (%) of VNTR clust er ed isolat es OR (95% CI) N o. (%) of VNTR clust er ed isolat es OR (95% CI) Total no. of _isolat es Total no . of isolat es in stud y population Clust er ed 256 (74) 9.9 (7.4-13.3) 306 (89) 8.7 (6.0-12.4) 345 1,061 (84) 21.9 (17.9-26.7) 1,145 (90) 16.8 (13.5-20.8) 1,267 1,612 onc lust er ed 177 (23) 1 373 (48) 1 785 263 (19) 1 494 (36) 1 1,379 2,164 433   679   1,130 1,324   1,639   2,646 3,776 V, single-locus v ariant (maximum thr eshold o f one MIR U locus v ariation fr om a c entr al str ain or an y other str

ain within the same lineag

e [E ur o-Americ an v ersus non-Eur o-Americ an es]) atio; CI=c on fidenc e int er val; P TB=pulmonar y tuber culosis; EP TB=extr apulmonar y tuber culosis

Acknowledgements

We thank all the Municipal Health Services that reported their cluster investigations to the national surveillance unit and the microbiological laboratories in the Netherlands for their efforts to send Mycobacterium tuberculosis isolates to the RIVM.

P.S. is a consultant for GenoScreen, Lille, France. All other authors have declared that no competing interests exist.

2

References

1. Small PM, Hopewell PC, Singh SP, Paz A, Parsonnet J, Ruston DC, Schecter GF, Daley CL, Schoolnik GK. 1994. The epidemiology of tuberculosis in San Francisco. A population-based study using conventional and molecular methods. N. Engl. J. Med. 330:1703–1709.

2. Jasmer RM, Hahn JA, Small PM, Daley CL, Behr MA, Moss AR, Creasman JM, Schecter GF, Paz EA, Hopewell PC. 1999. A molecular epidemiologic analysis of tuberculosis trends in San Francisco, 1991-1997. Ann. Intern. Med. 130:971–978.

3. Glynn JR, Bauer J, de Boer AS, Borgdorff MW, Fine PE, Godfrey-Faussett P, Vynnycky E. 1999. Interpreting DNA fingerprint clusters of Mycobacterium tuberculosis. Int. J. Tuberc. Lung Dis. 3:1055–1060.

4. Ellis BA, Crawford JT, Braden CR, McNabb SJ, Moore M, Kammerer S. 2002. Molecular epidemiology of tuberculosis in a sentinel surveillance population. Emerg. Infect. Dis. 8:1197–1209.

5. Braden CR, Templeton GL, Cave MD, Valway S, Onorato IM, Castro KG, Moers D, Yang Z, Stead WW, Bates JH. 1997. Interpretation of restriction fragment length polymorphism analysis of Mycobacterium tuberculosis isolates from a state with a large rural population. J. Infect. Dis. 175:1446 –1452.

6. Schürch AC, Kremer K, Daviena O, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D. 2010. High resolution typing

by integration of genome sequencing data in a large tuberculosis cluster. J. Clin. Microbiol. 48:3403–3406. 7. Diel R, Rüsch-Gerdes S, Niemann S. 2004. Molecular epidemiology of tuberculosis among immigrants in

Hamburg, Germany. J. Clin. Microbiol. 42:2952–2960.

8. Iñigo J, García de Viedma D, Arce A, Palenque E, Alonso Rodríguez N, Rodríguez E, Ruiz Serrano MJ, Andrés S, Bouza E, Chaves F. 2007. Analysis of changes in recent tuberculosis transmission patterns after a sharp increase in immigration. J. Clin. Microbiol. 45:63– 69.

9. van Soolingen D, Qian L, de Haas PE, Douglas JT, Traore H, Portaels F, Qing HZ, Enkhsaikan D, Nymadawa P, van Embden JD. 1995. Predominance of a single genotype of Mycobacterium tuberculosis in countries of east Asia. J. Clin. Microbiol. 33:3234 –3238.

10. Hirsh AE, Tsolaki AG, DeRiemer K, Feldman MW, Small PM. 2004. Stable association between strains of

Mycobacterium tuberculosis and their human host populations. Proc. Natl. Acad. Sci. U. S. A. 101:4871–4876.

11. Cardoso Oelemann M, Gomes HM, Willery E, Possuelo L, Batista Lima KV, Allix-Béguec C, Locht C, Goguet de la Salmonière YO, Gutierrez MC, Suffys P, Supply P. 2011. The forest behind the tree: phylogenetic exploration of a dominant Mycobacterium tuberculosis strain lineage from a high tuberculosis burden country. PLoS One 6:e18256. doi:10.1371/journal.pone.0018256.

12. Lillebaek T, Andersen AB, Bauer J, Dirksen A, Glismann S, de Haas P, Kok-Jensen A. 2001. Risk of

Mycobacterium tuberculosis transmission in a low-incidence country due to immigration from high-incidence

areas. J.Clin. Microbiol. 39:855– 861.

13. Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, Savine E, de Haas P, van Deutekom H, Roring S, Bifani P, Kurepina N, Kreiswirth B, Sola C, Rastogi N, Vatin V, Gutierrez MC, Fauville M, Niemann S, Skuce R, Kremer K, Locht C, van Soolingen D. 2006. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium

tuberculosis. J. Clin. Microbiol. 44:4498–4510.

14. van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, Hermans P, Martin C, McAdam R, Shinnick TM, Small PM. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31:406–409.

15. Weniger T, Krawczyk J, Supply P, Niemann S, Harmsen D. 2010. MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria. Nucleic Acids Res. 38:W326–W331.

16. Allix-Béguec C, Fauville-Dufaux M, Supply P. 2008. Three-year population- based evaluation of standardized mycobacterial interspersed repetitive- unit-variable-number tandem-repeat typing of Mycobacterium

tuberculosis. J. Clin. Microbiol. 46:1398 –1406.

17. Bauer J, Yang Z, Poulsen S, Andersen AB. 1998. Results from 5 years of nationwide DNA fingerprinting of

Mycobacterium tuberculosis complex isolates in a country with a low incidence of M. tuberculosis infection. J.

Clin. Microbiol. 36:305–308.

18. van Soolingen D, Borgdorff MW, de Haas PE, Sebek MM, Veen J, Dessens M, Kremer K, van Embden JD. 1999. Molecular epidemiology of tuberculosis in the Netherlands: a nationwide study from 1993 through 1997. J. Infect. Dis. 180:726 –736.

19. Garzelli C, Lari N, Cuccu B, Tortoli E, Rindi L. 2010. Impact of immigration on tuberculosis in a low-incidence area of Italy: a molecular epidemiological approach. Clin. Microbiol. Infect. 16:1691–1697.

20. Kinander W, Bruvik T, Dahle UR. 2009. Dominant Mycobacterium tuberculosis lineages in elderly patients born in Norway. PLoS One. 4:e8373. doi:10.1371/journal.pone.0008373.

21. Lillebaek T, Dirksen A, Vynnycky E, Baess I, Thomsen VØ, Andersen AB. 2003. Stability of DNA patterns and evidence of Mycobacterium tuberculosis reactivation occurring decades after the initial infection. J. Infect. Dis. 188:1032–1039.

Chapter

3

Yield of tuberculosis

contact investigations in

Amsterdam: opportunities

for improvement

Abstract

We aimed to determine the coverage and yield of tuberculosis contact investigation, and compliance with guidelines, and to identify opportunities for improvement. Data were extracted from records on contacts of pulmonary tuberculosis patients at the Public Health Service (Amsterdam, the Netherlands) from 2008 to 2011. Additional data were obtained from the national tuberculosis register.

Among 3,743 contacts of 235 pulmonary tuberculosis index patients, 2,337 (62%) were screened for latent tuberculosis infection (LTBI). Those less likely to be screened for LTBI included contacts of sputum smear-negative index patients (adjusted odds ratio (aOR) 0.6, 95% CI 0.4–0.9) and bacille Calmette-Guérin (BCG)-vaccinated contacts (aOR 0.06, 95% CI 0.04–0.09). Among BCG-vaccinated contacts, the proportion screened increased from 9% in 2008 to 43% in 2011 (p-value for trend <0.001). LTBI diagnosis among contacts screened was associated with non-Dutch nationality (aOR 2.8, 95% CI 1.9–4.1) and being a close contact (aOR 4.0, 95% CI 1.9–8.3). Of the 254 contacts with LTBI diagnosis, 142 (56%) started preventive treatment. Starting treatment was associated with Dutch nationality (aOR 2.6, 95% CI 1.2–5.4) and being a close contact (aOR 10.5, 95% CI 1.5–70.7). Treatment completion was achieved by 129 (91%) of the 142 contacts who started treatment.

Two areas for improvement were identified: further expanding LTBI screening, particularly among BCG vaccinated contacts and contacts of sputum smear-negative index patients, and expanding preventive treatment among contacts with LTBI.

3

Introduction

The objective of screening for latent tuberculosis infection (LTBI) during contact investigations in low-incidence countries is to prevent the occurrence of secondary patients through the identification and treatment of contacts after their recent exposure to an index patient with active tuberculosis [1]. Contacts of pulmonary tuberculosis (PTB) patients are identified and graded according to the duration and intensity of exposure [2]. Preventive therapy is indicated if a contact has an increased risk of developing disease and if the benefit of treatment outweighs the risk of side-effects. Thus, the success of contact investigation depends on adequate identification and diagnosis of recently infected contacts at risk of progression to active tuberculosis, provision of preventive treatment and treatment completion. With the introduction of interferon-γ release assays (IGRAs), screening for LTBI has become more specific, especially among bacille Calmette–Guérin (BCG)-vaccinated individuals [3].

The goals of our study were to determine the coverage and yield of contact investigation, to assess compliance with guidelines, and to identify opportunities for improvement.

Methods

Index patients

In the city of Amsterdam, the Netherlands, the diagnosing physician notifies the Public Health Service (PHS) of patients in whom tuberculosis is diagnosed. Demographic information including sex, year of birth, country of origin and being part of a risk group (the homeless and drug users) is recorded by the PHS staff. In addition, clinical and laboratory information is collected, including details on HIV infection, type of tuberculosis (PTB or extrapulmonary tuberculosis), results of sputum smears and sputum culture, results of tuberculin skin tests (TSTs), and chest radiography findings. In order to assess the risk of transmission, a nurse at the tuberculosis control department of the PHS interviews the patient and enquires about persons with whom the patient has had recent contact. The PHS then starts a source and contact investigation.

Contact investigations

The PHS staff investigates recent contacts of PTB index patients, and evaluates duration and frequency of exposure to the index patient during the infectious period. Accordingly, contacts are listed as first-, second-, or third-circle contacts based on national guidelines for contact investigation [4]. Screening for LTBI and tuberculosis starts among first-circle contacts (categorised as close contacts) of PTB patients and, depending on the infection and disease prevalence among first-circle contacts of smear-positive PTB index patients, second-circle and eventually possibly third-circle contacts are also invited for screening (second- and third-circle categorised as casual contacts).

According to national guidelines for LTBI screening, all contacts born after 1945 of sputum positive PTB patients and first-circle contacts born after 1945 of smear-negative PTB patients should be screened for LTBI [5]. LTBI screening starts with a TST and contacts are concurrently screened for tuberculosis by chest radiography. The TST is performed by intradermal injection of 2 U purified protein derivative RT23 on the volar side of the forearm. After 72–96 h, the diameter of the induration at the site of injection is measured in millimetres. If the TST induration is ≥5 mm, the TST is followed by an IGRA. At the PHS in Amsterdam, QuantiFERON-TB (QFT) (Cellestis, Carnegie, Australia) is used. This assay measures the production of interferon-γ (IFN-γ) after T-cells are exposed in vitro to a Mycobacterium tuberculosis-specific antigen mix; a QFT is considered positive if the IFN-γ concentration is ≥0.35 IU·mL-1 _[6].

Contacts with a high risk of progression to active tuberculosis after recent infection, in particular those younger than 5 years of age or HIV-infected contacts, are screened for active tuberculosis irrespective of the duration and frequency of contact with their index case. If a tuberculosis diagnosis is made, the tuberculosis control physician gives the patient antituberculosis treatment. Contacts with an LTBI diagnosis are offered preventive treatment (either 3 months of isoniazid and rifampicin, 6 months of isoniazid or 4 months of rifampicin) or, if contraindicated, follow-up of contacts at risk of progression to tuberculosis is proposed.

3

Study population

Index patients

Data for our study were obtained from the Netherlands Tuberculosis Register (NTR). This database combines mandatory tuberculosis notification data with voluntary input of other relevant information by PHSs. It contains information on virtually all tuberculosis patients in the Netherlands, including: HIV status; whether the patient belongs to a risk group; and drug sensitivity of the infecting M. tuberculosis strain. All sputum smear-positive and sputum smear-negative PTB index patients reported to the PHS in Amsterdam from 2008 through 2011 were eligible for study inclusion. Subsequently, index patients were excluded if no contact could be linked to the index patient, if all contacts of a sputum smear-negative index patient were casual contacts, if all contacts had coprevalent tuberculosis or if contacts were born before 1945. Contacts of index patients

The Tuberculosis Information System, an electronic tuberculosis patient and client registration system at the PHS in Amsterdam, was used to identify all contacts who were traced and examined in the course of contact investigations around PTB index patients during the study period. Some individuals were a contact in more than one contact investigation during the study period and these individuals were included multiple times. Data on treatment initiation and treatment completion from contacts who started with preventive therapy were extracted from the section of the NTR in which records of newly diagnosed LTBI patients are notified to the register by the PHSs.

Definitions

Contacts eligible for analysis were classified according to their TST and IGRA results based on the guidelines for LTBI screening and LTBI diagnosis (table 1). TST and IGRA results of contacts were included if the date of the result was ≤180 days after the first contact of the PHS with an index patient, which constitutes the actual start of any source and contact investigation. If active TB was diagnosed ≤180 days after tuberculosis diagnosis of the index patient, contacts were considered coprevalent tuberculosis cases.

Table 1. Indication for screening, diagnosis and preventive treatment of latent tuberculosis infection

(LTBI) of contacts of patients with tuberculosis, according to guidelines [4, 5]

Criteria for LTBI screening

• First-circle contacts and contacts with high risk of active tuberculosis, born after 1945, of PTB patients, are investigated for LTBI and tuberculosis by the combination of a TST and CXR, irrespective of BCG status

• If the TST induration is 5–<15 mm and active tuberculosis is excluded by CXR, the TST is followed by an IGRA; if the TST induration is ≥15 mm, an IGRA is not indicated • In contacts where the TST result might be less reliable, an IGRA may be used instead

of a TST

• Depending on the infection prevalence among first-circle contacts, second- and eventually possibly third-circle contacts of sputum smear-positive PTB patients are investigated for LTBI similar to that described for first-circle contacts

Criteria for LTBI diagnosis

• Contacts are diagnosed with LTBI if the IGRA is positive or if TST induration is ≥15 mm • Contacts have indeterminate outcome for LTBI if neither IGRA nor TST are performed,

or if the TST induration is 5–<15 mm is not followed by the IGRA

• In contacts below the age of 5 years, who were not BCG-vaccinated and who have a TST induration ≥10 mm, LTBI is diagnosed irrespective of the IGRA result

• HIV-positive contacts with an induration of TST ≥5 mm are diagnosed with LTBI irrespective of the IGRA result

Criteria for starting preventive LTBI treatment and treatment completion

• All contacts diagnosed with LTBI are eligible for preventive treatment except for contacts of index patients with MDR-TB

• Contacts are regarded as having completed treatment if the prescribed amount of medication has been taken or if, in case of treatment interruption, 80% of the prescribed medication has been taken

PTB=pulmonary tuberculosis; TST=tuberculin skin test; CXR=chest radiography; BCG=bacille Calmette–Guérin; IGRA=interferon-γ release assay; MDR-TB=multidrug-resistant tuberculosis

Screening for LTBI

A contact was considered to have been screened for LTBI if an IGRA result was available or if the TST was performed and an intermediate TST induration of 5–<15 mm was followed by an IGRA. As the national guideline for the use of the IGRA is ambivalent regarding the additional value of the IGRA with a TST induration of ≥15 mm, contacts were considered screened if the TST induration was ≥15 mm, irrespective of an IGRA result. Children without BCG vaccination below the age of 5 years with a TST

3

also considered screened if the TST was not followed by an IGRA. Other contacts were considered not screened if neither a TST nor IGRA were done, or when a TST induration of 5–<15 mm was not followed by an IGRA.

LTBI diagnosis

Contacts were regarded as having LTBI if the IGRA was positive or if their TST induration was ≥15 mm. For contacts below the age of 5 years, who were not BCG-vaccinated and had a TST induration ≥10 mm, an IGRA was considered redundant; these contacts were diagnosed with LTBI. HIV-infected contacts with a TST induration of ≥5 mm were diagnosed with LTBI irrespective of an IGRA result.

Treatment initiation and completion

All contacts diagnosed with LTBI were considered eligible for treatment, except for contacts of multidrug-resistant tuberculosis index patients. For these contacts, treatment regimen and initiation was dependent on the susceptibility pattern of

M. tuberculosis cultured from the index patient. Contacts were regarded as having

completed treatment if the prescribed amount of medication had been taken or if, in case of treatment interruption, 80% of medication prescribed had been taken.

Analysis

This study had four outcomes of interest: 1) the coverage of LTBI screening among listed contacts; 2) the proportion of contacts screened with an LTBI diagnosis; 3) the proportion of LTBI cases starting LTBI treatment; and 4) the proportion of contacts who completed treatment. Demographic, laboratory and clinical determinants (both index patient and contact related) were identified using logistic regression. In order to adjust for correlated data (multiple contacts belonging to the same contact investigation), generalised estimating equations were used. Variables that were associated with the outcome in univariate analysis at p<0.2 were included in a model, and variables were subsequently eliminated from the model if they did not have an independent association with the outcome and their exclusion did not substantially affect the estimates of the other variables. Sex and age, of both index and contact, were kept in the models a priori and the level of significance in all analyses was p<0.05.

Results

Study population

Index patients

From 2008 to 2011, 292 PTB index patients were reported to the PHS in Amsterdam and registered in the NTR. 57 (20%) patients were excluded from further analysis for the following reasons: no contact investigation was performed (n=17); it was not possible to link any contact to the index patient (n=27); or all contacts of a sputum smear-negative index patient were casual contacts, all contacts had coprevalent tuberculosis or contacts were born before 1945 (n=13). Excluded index patients did not differ significantly from the 235 included index patients, except for country of birth (p=0.044) and smear status (p<0.001) (table 2). Culture status was known for 227 out of 235 included index patients and of these, 211 (93%) were culture positive.

Contacts listed among index patients

The 235 PTB index patients had 4,295 listed contacts. Casual contacts of sputum smear-negative PTB index patients (n=364, 9%), contacts with coprevalent tuberculosis (n=30, 1%) and contacts born before 1945 (n=158, 4%) were excluded from further analysis (fig. 1).

Of 30 contacts with coprevalent tuberculosis, 17 (57%) were female, 19 (63%) were first-circle contacts, 14 (47%) had evidence of BCG vaccination and their median age was 23 years (interquartile range (IQR) 6–43 years).

Of the 3,743 contacts eligible for analysis, 2,337 (62%) were screened for LTBI and included: contacts with a TST induration of <5 mm (n=1,982) and of ≥15 mm (n=226), contacts with an intermediate TST followed by an IGRA (n=120), contacts without TST but with an IGRA result (n=6), and three other contacts (two HIV-infected and one below the age of 5 years without BCG vaccination) (fig. 1). The remaining 1,406 (38%) contacts were not screened for LTBI: for 196 contacts, an intermediate TST result was not followed by IGRA and for 1,210 contacts neither TST nor IGRA were done. Among 2,337 contacts screened for LTBI, 254 (11%) were diagnosed with LTBI.

Among the 226 contacts with an induration ≥15 mm, 82 (36%) were also investigated by IGRA; 38 (46%) of these had a negative IGRA.

3

Service (Amsterdam, the Netherlands) from 2008 to 2011

Included Excluded p-value #

All 235 (80) 57 (20)

Sex

Male 146 (80) 37 (20) 0.697

Female 89 (82) 20 (18)

Age

Years, median (IQR) 42 (28-58) 39 (27-53) 0.573 +

0-14 2 (100) 0 0.403 15-34 91 (78) 26 (22) 35-54 73 (78) 20 (22) ≥55 69 (86) 11 (14) Country of birth The Netherlands 63 (89) 8 (11) 0.044

Outside the Netherlands 172 (78) 49 (22)

At risk ¶

No 220 (81) 51 (19) 0.263

Yes 15 (71) 6 (29)

Sputum smear status

Positive 154 (94) 9 (6) <0.001 Negative 81 (63) 48 (37) MDR-TB No/ unknown 233 (81) 55 (19) 0.172 Yes 2 (50) 2 (50) HIV status Negative 98 (75) 33 (25) 0.076 Positive 18 (90) 2 (10) Unknown 119 (84) 22 (16)  

Data are presented as n (%) unless otherwise stated

IQR=interquartile range; MDR-TB=multidrug-resistant tuberculosis; #= Chi-squared test or Fisher’s exact test,

Figure 1. Flow chart of study inclusion of contacts of 235 patients with pulmonary tuberculosis

reported to the Public Health Service in Amsterdam, the Netherlands, from 2008 to 2011

TST= tuberculin skin test; IGRA= interferon-γ release assay; BCG= bacille Calmette–Guérin. #_{= 4,242 individuals}

LTBI screening among eligible contacts

In the multivariable analysis, contacts of younger index patients were more likely to be screened for LTBI and contacts of sputum smear-negative index patients were less likely to be screened for LTBI (adjusted odds ratio (aOR) 0.6, 95% CI 0.4–0.9) (table 3). LTBI screening was associated with contact age groups 0–4 years (aOR 7.0, 95% CI 3.6–13.7) and 5–14 years (aOR 3.2, 95% CI 1.8–5.6) as compared with age ≥55 years. BCG-vaccinated contacts were less likely to be screened for LTBI (aOR 0.06, 95% CI 0.04–0.09) (table 3).

Figure 2 shows coverage of LTBI screening among contacts by year of contact investigation and BCG status. The proportion of BCG-vaccinated contacts screened for LTBI increased over time from 9% in 2008 to 43% in 2011 (Chi-squared test for trend, p<0.001). The proportion of contacts screened for LTBI among non-BCG-vaccinated contacts remained relatively constant over the 4-year study period at an average of 79% (Chi-squared test for trend, p=0.225) (fi g. 2).

3

screened for latent tuberculosis infection (LTBI) at the Public Health Service in Amsterdam (the Netherlands) from 2008 to 2011

Factor Screened Not screened Crude OR Adjusted OR

All 2,337 (62) 1,406 (38) Index factors Sex Male 1,323 (60) 886 (40) 1 1 Female 1,014 (66) 520 (34) 1.1 (0.8-1.5) 1.3 (0.9-1.9) Age, years 0-14 105 (81) 25 (19) 4.9 (3.4-7.0) 10.6 (4.9-23.1) 15-34 963 (67) 479 (33) 1.7 (1.2-2.3) 1.4 (1.0-2.1) 35-54 871 (64) 499 (36) 1.3 (0.9-1.9) 1.0 (0.7-1.6) ≥55 398 (50) 403 (50) 1 1 Country of birth The Netherlands 923 (68) 434 (32) 1

Outside the Netherlands 1,414 (59) 972 (41) 0.4 (0.3-0.6)

At risk #

No 2,231 (64) 1,272 (36) 1

Yes 106 (44) 134 (56) 0.8 (0.4-1.3)

Sputum smear status

Positive 2,096 (64) 1,203 (36) 1 1 Negative 241 (54) 203 (46) 0.5 (0.3-0.7) 0.6 (0.4-0.9) Contact factors Sex Male 1,206 (63) 717 (37) 1 1 Female 1,078 (61) 676 (39) 1.0 (0.9-1.2) 1.1 (0.9-1.4) Age, years 0-4 184 (80) 45 (20) 4.0 (2.5-6.2) 7.0 (3.6-13.7) 5-14 152 (66) 77 (34) 2.1 (1.4-3.1) 3.2 (1.8-5.6) 15-34 854 (64) 484 (36) 1.3 (1.0-1.9) 1.3 (0.9-1.9) 35-54 868 (59) 600 (41) 1.0 (0.8-1.3) 1.0 (0.7-1.4) ≥55 275 (58) 198 (42) 1 1 Nationality Dutch 1,507 (65) 827 (35) 1 Other 213 (35) 388 (65) 0.3 (0.2-0.4) Unknown 617 (76) 191 (24) 1.2 (0.8-1.7) Type of contact First circle 1,067 (66) 557 (34) 1.0 (0.7-1.4) Second circle 934 (60) 636 (41) 1.0 (0.7-1.5) Third circle 276 (61) 175 (39) 1 Unknown 60 (61) 38 (39) 1.7 (0.9-3.4) Year of contact investigation 2008 396 (52) 370 (48) 1 2009 915 (66) 480 (34) 1.1 (0.7-1.6) 2010 471 (61) 300 (39) 1.1 (0.7-1.7) 2011 555 (68) 256 (32) 1.4 (0.9-2.1) BCG No evidence of vaccination/ unknown 2,069 (80) 530 (20) 1 1 Evidence of vaccination 268 (23) 876 (77) 0.08 (0.05-0.1) 0.06 (0.04-0.09)