Multi-drug resistant tuberculosis in Finland; treatment outcome and the role of whole genome sequencing

Treatment of multi-drug resistant tuberculosis (MDR-TB) is a global challenge requiring long treatment with costly drugs. We assessed treatment combinations, outcome and the utility of whole genome sequencing (WGS) in MDR-TB cases.

Clinical, demographic, and microbiological data were obtained of all patients with MDR-TB who started treatment in Finland in 2007–2016. Definitions of MDR, pre-extensively drug-resistant TB (pre-XDR) and XDR-TB were those applicable at the study period. Treatment outcome was defined according to WHO guidelines.M. tuberculosisisolates were analysed by WGS in addition to routinely performed phenotypic drug susceptibility testing and genotyping.

Among the 47 cases, 35 (74%) had a successful treatment outcome. Risk factors for non-successful outcome were Finnish origin and XDR. Almost ninety percent of our cases had an adverse event for at least one drug. Phenotypic and WGS drug resistance results were fully concordant for isoniazid, fluoroquinolones, and amikacin, and >90% concordant for rifampicin, pyrazinamide, kanamycin and capreomycin. More than 60% of phenotypically ethambutol susceptible isolates were genotypically resistant. The results of the rifampicin and isoniazid NAA tests performed for the isolates were identical to the WGS results except for three isolates having uncommon resistance mutations not included in the NAATs. WGS did not reveal unexpected clustering.

More training is needed for physicians treating MDR-TB, and especially XDR-TB, to improve treatment outcome. Phenotypical drug susceptibility testing was shown to be unreliable for ethambutol. WGS can aid in the selection of optimal treatment regimen in the future.

Transmission of tuberculosis between foreign-born and Finnish-born populations in Finland, 2014-2017

We describe the epidemiology of tuberculosis (TB) and characterized Mycobacterium tuberculosis (M. tuberculosis) isolates to evaluate transmission between foreign-born and Finnish-born populations. Data on TB cases were obtained from the National Infectious Disease Register and denominator data on legal residents and their country of birth from the Population Information System. M. tuberculosis isolates were genotyped by spoligotyping and Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR). We characterized clusters by age, sex, origin and region of living which included both foreign-born cases and those born in Finland. During 2014-2017, 1015 TB cases were notified; 814 were confirmed by culture. The proportion of foreign-born cases increased from 33.3% to 39.0%. Foreign-born TB cases were younger (median age, 28 vs. 75 years), and had extrapulmonary TB or multidrug-TB more often than Finnish-born cases (P<0.01 for all comparisons). Foreign-born cases were born in 60 different countries; most commonly in Somalia (25.5%). Altogether 795 isolates were genotyped; 31.2% belonged to 80 different clusters (range, 2-13 cases/cluster). Fourteen (17.5%) clusters included isolates from both Finnish-born and foreign-born cases. An epidemiological link between cases was identified by (epidemiological) background information in two clusters. Although the proportion of foreign-born TB cases was considerable, our data suggests that transmission of TB between foreign and Finnish born population is uncommon.

Emerging source of infection - Mycobacterium tuberculosis in rescue dogs: a case report

Rescue dog activity is a heavily increasing form of dog charity. Imported homeless dogs represent a reservoir of zoonotic diseases putting owners, veterinarians and pathologists repeatedly at risk. The clinical signs of tuberculosis in a dog are non-specific and diagnosis is often delayed or dismissed. We present a case of 9 months of possible exposure at home and definite exposure at laparotomy and autopsy to intestinal tuberculosis in a family dog imported from Romania to Finland. Persistent gastrointestinal symptoms started 2 years after the import. Abdominal pain, diarrhoea and vomiting proceeded and led to spontaneous death. Mycobacterium tuberculosis was identified in the liver, lymph nodes and intestine at autopsy. Exposed persons were notified and follow-up was provided, and no further infections were identified within 12 months of follow-up. The heavily increasing import of companion animals presents unexpected public health risks, such as prolonged exposure to tuberculosis, of which the general public is not aware. The dramatic consequences and high costs of tuberculosis could be reduced through accessible information of the risks of imported animals to both the general public and veterinarians, in addition to availability of rapid diagnostics and proper personal protection.

Trends and differences in tuberculosis incidences and clustering among natives in Denmark, Sweden and Finland: comparison of native incidences and molecular epidemiology among three low-incidence countries

OBJECTIVES

To compare the epidemiology of tuberculosis (TB) in Denmark, Sweden and Finland, by focusing on the native population in order to identify epidemiologic differences and thus indirectly possible differences in TB control.

METHODS

TB incidence trends from 1990 through 2015 were compared among the countries. In addition, for the periods 2012-2013 and 2014-2015, genotyping data were compared. Genotyping was performed using the 24-locus mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) method in Denmark and Sweden. For Finland, spoligotyping in conjunction with the 15-locus MIRU-VNTR method was used for 2012-2013 and translated into the 24-locus MIRU-VNTR when feasible, and for 2014-2015 only MIRU-VNTR was used. Both incidence trends and molecular epidemiology were assessed for native cases.

RESULTS

The average annual rate of change in TB incidence for native Danes was -2.4% vs. -6.1% and -6.9% for native Swedes and Finns respectively. In 2012-2013 Denmark had 52 native cases in the largest transmission chain vs. three cases in Sweden and ten in Finland, and during the same period the clustering rate for native Danes was 48.8% vs. 6.5% and 18.2% for native Swedes and Finns respectively. For 2014-2015, a similar pattern was seen.

CONCLUSIONS

The decline of TB among natives in Denmark is slower than for Sweden and Finland, and it seems Denmark has more active transmission among natives. The focused assessment on basic native TB epidemiology reveals striking differences in TB transmission among otherwise similar low-TB-incidence countries.

Whole genome analysis of Mycobacterium tuberculosis isolates from recurrent episodes of tuberculosis, Finland, 1995-2013

Recurrent tuberculosis (TB) is caused by an endogenous re-activation of the same strain of Mycobacterium tuberculosis (relapse) or exogenous infection with a new strain (re-infection). Recurrence of TB in Finland was analysed in a population-based, 19-year study, and genotyping was used to define relapse and re-infection. The M. tuberculosis isolates from patients with suspected relapse were further analysed by whole genome sequencing (WGS) to determine the number and type of mutations occurring in the bacterial genome between the first and second disease episodes. In addition, publicly available tools (PhyResSE and SpolPred) were used to predict drug resistance and spoligotype profile from the WGS data. Of the 8299 notified TB cases, 48 (0.6%) patients had episodes classified as recurrent. Forty-two patients had more than one culture-confirmed TB episode, and isolates from two episodes in 21 patients were available for genotyping. In 18 patients, the M. tuberculosis isolates obtained from the first and second TB episodes had identical spoligotypes. The WGS analysis of the 36 M. tuberculosis isolates from the 18 suspected relapse patients (average time between isolates 2.8 years) revealed 0 to 38 single nucleotide polymorphisms (median 1, mean 3.78) between the first and second isolate. There seemed to be no direct relation between the number of years between the two isolates, or treatment outcome, and the number of single nucleotide polymorphisms. The results suggest that the mutation rate may depend on multiple host-, strain- and treatment-related factors.

Genotypic characterization and historical perspective of Mycobacterium tuberculosis among older and younger Finns, 2008-2011

The Mycobacterium tuberculosis genotypes obtained from elderly Finns were assessed and compared with those obtained from younger Finns to comprehend the epidemiology of tuberculosis (TB) in Finland. From 2008 to 2011, a total of 1021 M. tuberculosis isolates were characterized by spoligotyping and 15-locus mycobacterial interspersed repetitive units-variable number tandem repeat typing. In total, 733 Finnish-born cases were included in the study, of which 466 (64%) were born before 1945 (older Finns). Of these, 63 (14%) shared an M. tuberculosis genotype with foreign-born or younger Finnish cases (born after 1945), and 59 (13%) shared a genotype with older Finnish cases. Eighty-five per cent had a unique genotypic profile while 70% belonged to T or Haarlem families, suggesting that ongoing transmission is infrequent among young and elderly Finns. Simultaneous reactivation of TB among older Finns was the most likely cause for clustering. As most isolates belonged to Haarlem or T, Finland was most likely affected by a similar TB epidemic at the beginning of the twentieth century as that seen in Sweden and Norway. Younger Finns were significantly more likely to be clustered (56% versus 27%, p<0.001), have pulmonary TB (87% versus 71%, p<0.001) and to be sputum smear positive (57% versus 48%, p<0.05) indicating that the risk of TB transmission from younger Finns is likely to be larger than from older Finns. The M. tuberculosis isolates from elderly Finns were associated with dominant lineages of the early twentieth century and differed from the heterogeneous lineages found among younger TB patients. Additionally, younger TB patients were more likely to transmit TB than elderly Finns.

Molecular epidemiology of tuberculosis in Finland, 2008-2011

In industrialized countries the majority of tuberculosis (TB) cases are linked to immigration. In Finland, most cases are still Finnish born but the number of foreign born cases is steadily increasing. In this 4-year population based study, the TB situation in Finland was characterized by a genotypic analysis of Mycobacterium tuberculosis isolates. A total of 1048 M. tuberculosis isolates (representing 99.4% of all culture positive cases) were analyzed by spoligotyping and MIRU. Spoligotype lineages belonging to the Euro-American family were predominant among the Finnish isolates, particularly T (n=346, 33.0%) and Haarlem (n=237, 22.6%) strains. The lineage signature was unknown for 130 (12.4%) isolates. Out of the 17 multi-drug resistant TB strains, 10 (58.8%) belonged to the Beijing lineage. In total, 23 new SIT designations were given and 51 orphan strains were found, of which 58 patterns were unique to Finland. Phylogeographical TB mapping as compared to neighboring countries showed that the population structure in Finland most closely resembled that observed in Sweden. By combining spoligotyping and MIRU results, 98 clusters comprising 355 isolates (33.9%) were found. Only 10 clusters contained both Finnish and foreign born cases. In conclusion, a large proportion of the M. tuberculosis isolates were from Finnish born elderly patients. Moreover, many previously unidentified spoligotype profiles and isolates belonging to unknown lineages were encountered.

Interactions between Bordetella pertussis and the complement inhibitor factor H

Bordetella pertussis causes whooping cough in humans, a highly contagious disease of the upper respiratory tract. An increase in cases of whooping cough in adolescents and adults in many countries has been reported, despite high immunization rates in children. To efficiently colonize the host the bacteria have to resist complement, the first defence line of innate immunity. B. pertussis has previously been shown to bind the classical pathway inhibitors C4b-binding protein and C1-inhibitor being thereby able to escape the classical pathway of complement. In this study recent clinical isolates of B. pertussis and B. parapertussis were found to survive alternative pathway attack in fresh non-immune serum better than the reference B. pertussis strain, Tohama I. By using adsorption assays, flow cytometry and a radioligand binding assay we observed that both B. pertussis and B. parapertussis bound the alternative pathway inhibitor factor H (FH) from normal human serum. The surface attached FH maintained its complement regulatory activity and promoted factor I-mediated cleavage of C3b. The main binding region was located to the C-terminal part of FH, into short consensus repeat domains 19-20. In contrast, the avian pathogen B. avium did not bind FH and was sensitive to the alternative pathway of human complement. In conclusion, the human pathogens B. pertussis and B. parapertussis are able to evade the alternative complement pathway by surface acquisition of the host complement regulator FH.

Immunity to pertussis 5 years after booster immunization during adolescence

BACKGROUND

We conducted a 5-year follow-up study on the persistence of pertussis-specific antibody and cell-mediated immunity after booster immunization of adolescents aged 11-13 years with a tricomponent acellular pertussis vaccine (Boostrix; trials diphtheria-tetanus-acellular pertussis [Tdap]-004/030).

METHODS

Cellular and humoral immunity to pertussis toxin (PT), filamentous hemagglutinin, and pertactin were measured in adolescents (age, 16 years) 5 years after booster immunization. Similar investigations were performed for control adolescents who had received only diphtheria and tetanus booster vaccination.

RESULTS

Five years after pertussis booster vaccination, the geometric mean concentrations of immunoglobulin G (IgG) elicited by each of the 3 pertussis vaccine antigens decreased from 1-month and 3-year postvaccination levels, but with the exception of PT IgG, were still higher than the prevaccination levels. PT IgG levels were undetectable in 28% of the subjects, but 44% of those subjects still tested positive for cell-mediated immunity to PT. Filamentous hemagglutinin IgG and pertactin IgG levels were significantly higher in Tdap-boosted adolescents than in the control subjects. Antibody concentrations at 1 month after vaccination strongly predicted antibody persistence. Cell-mediated immunity levels to PT, filamentous hemagglutinin, and pertactin persisted above the prebooster levels measured 5 years earlier.

CONCLUSIONS

The results of the present study of adolescents indicate that the interval between acellular pertussis booster immunizations might be extended beyond 5 years.

Identification of alpha-hemolytic streptococci by pyrosequencing the 16S rRNA gene and by use of VITEK 2

Alpha-hemolytic streptococci are very difficult to identify by phenotypic methods. In this study, a pyrosequencing method for the identification of streptococcal species based on two variable regions of the 16S rRNA gene is described. Almost all studied streptococcal species (n = 51) represented by their type strains could be differentiated except for some closely related species of the Streptococcus bovis or S. salivarius group. The pyrosequencing results of alpha-hemolytic streptococci isolated from blood (n = 99) or from the normal pharyngeal microbiota (n = 25) were compared to the results obtained by the VITEK 2 with GP card (bioMérieux, Marcy l'Etoile, France). As expected, the results of the two methods did not completely agree, but 93 (75.0%) of the isolates assigned to the same streptococcal group by both methods and 57 (46.0%) reached consistent results at the species level. However, 10 strains remained unidentified by VITEK 2, and 4 isolates could not be assigned to any streptococcal group by pyrosequencing. Identification of members of the S. mitis and S. sanguinis groups proved difficult for both methods. Furthermore, the pyrosequencing analysis revealed great sequence variation, since only 43 (32.3%) of the 133 isolates analyzed by pyrosequencing had sequences identical to a type strain. The variation was greatest in the pharyngeal isolates, slightly lower in the blood culture isolates, and nonexistent in invasive pneumococcal isolates (n = 17) that all had the S. pneumoniae type strain sequence. The resolution of the results obtained by the two methods is impeded by the lack of a proper gold standard.

Bordetella holmesii DNA is not detected in nasopharyngeal swabs from Finnish and Dutch patients with suspected pertussis

Bordetella holmesii is a Gram-negative bacterium first identified in 1995. It can cause pertussis-like symptoms in humans. B. holmesii contains insertion sequences IS481 and IS1001, two frequently used targets in the PCR diagnosis of Bordetella pertussis and Bordetella parapertussis infections. To investigate the prevalence of B. holmesii in Finnish and Dutch patients with pertussis-like symptoms and whether B. holmesii has caused any false-positive results in diagnostic PCRs, B. holmesii-specific real-time PCRs were developed. The Finnish methods were conventional IS481 PCR and B. holmesii-specific real-time PCR (LightCycler, Roche) targeting the B. holmesii recA gene. The Dutch methods were IS481 and IS1001 PCRs with conventional or real-time formats and B. holmesii-specific real-time PCR targeting the homologue of IS1001. Of 11,319 nasopharyngeal swabs, 2804 were collected from Finnish patients from 2000 to 2003, and 8515 from Dutch patients from 1992 to 2003. B. holmesii DNA was not found in the samples analysed. The results suggest that B. holmesii is not among the causative agents of pertussis-like symptoms in Finnish and Dutch patients and thus does not in practice confound IS481 and IS1001 PCRs.

Detection and quantification of macrolide resistance mutations at positions 2058 and 2059 of the 23S rRNA gene by pyrosequencing

A pyrosequencing method for detection and quantification of macrolide resistance mutations at positions 2058 and 2059 (Escherichia coli numbering) of the 23S rRNA gene is described. The method was developed and tested for Streptococcus pneumoniae, Streptococcus pyogenes, Mycobacterium avium, Campylobacter jejuni, and Haemophilus influenzae.

Antimicrobial susceptibility patterns and macrolide resistance genes of viridans group streptococci from normal flora

OBJECTIVES

Our aim was to study the antimicrobial susceptibilities and macrolide resistance mechanisms of viridans group streptococci isolated from the normal flora.

METHODS

In vitro susceptibilities of 16 antimicrobials were studied for 161 viridans streptococci (on average 5.8 isolates per person) from the normal flora of 28 elderly persons. Resistance mechanisms of erythromycin-resistant isolates were studied by the double disc test and PCR.

RESULTS

In all, 16.8% of the isolates were non-susceptible (MIC > or =0.25 mg/L) to penicillin, but none showed high-level resistance (MIC > or =4 mg/L). Resistance to erythromycin, tetracycline, quinupristin/dalfopristin, levofloxacin and moxifloxacin was found in 22.4, 27.3, 13.0, 1.9 and 1.9% of the isolates, respectively. Combined resistance to erythromycin and tetracycline was found in 13.0% of the isolates. Erythromycin-resistant isolates were isolated from 57% of the study persons. Of the erythromycin-resistant isolates 80.6% were of the M phenotype and 19.4% were of the macrolide-lincosamide-streptogramin B (MLSB) phenotype (one isolate with constitutive and six with inducible expression). Isolates with the M phenotype were the least susceptible to telithromycin, a new ketolide. The mef(A) gene was found in the isolates with the M phenotype and the erm(B) gene in the isolates with the MLSB phenotype.

CONCLUSIONS

The distribution of phenotypes among the viridans streptococci resembles that found in Streptococcus pyogenes, with predominance of the M phenotype. However, the coding gene for the MLSB phenotype, erm(B), is the same in viridans streptococci as in Streptococcus pneumoniae. Viridans group streptococci carrying different resistance traits provide a pool of resistant bacteria that may transfer resistance determinants to more pathogenic organisms.