Role of the first WHO mutation catalogue in the diagnosis of antibiotic resistance in Mycobacterium tuberculosis in the Valencia Region, Spain: a retrospective genomic analysis

BACKGROUND

In June, 2021, WHO published the most complete catalogue to date of resistance-conferring mutations in Mycobacterium tuberculosis. Here, we aimed to assess the performance of genome-based antimicrobial resistance prediction using the catalogue and its potential for improving diagnostics in a real low-burden setting.

METHODS

In this retrospective population-based genomic study M tuberculosis isolates were collected from 25 clinical laboratories in the low-burden setting of the Valencia Region, Spain. Culture-positive tuberculosis cases reported by regional public health authorities between Jan 1, 2014, and Dec 31, 2016, were included. The drug resistance profiles of these isolates were predicted by the genomic identification, via whole-genome sequencing (WGS), of the high-confidence resistance-causing variants included in the catalogue and compared with the phenotype. We determined the minimum inhibitory concentration (MIC) of the isolates with discordant resistance profiles using the resazurin microtitre assay.

FINDINGS

WGS was performed on 785 M tuberculosis complex culture-positive isolates, and the WGS resistance prediction sensitivities were: 85·4% (95% CI 70·8-94·4) for isoniazid, 73·3% (44·9-92·2) for rifampicin, 50·0% (21·1-78·9) for ethambutol, and 57·1% (34·0-78·2) for pyrazinamide; all specificities were more than 99·6%. Sensitivity values were lower than previously reported, but the overall pan-susceptibility accuracy was 96·4%. Genotypic analysis revealed that four phenotypically susceptible isolates carried mutations (rpoB Leu430Pro and rpoB Ile491Phe for rifampicin and fabG1 Leu203Leu for isoniazid) known to give borderline resistance in standard phenotypic tests. Additionally, we identified three putative resistance-associated mutations (inhA Ser94Ala, katG Leu48Pro, and katG Gly273Arg for isoniazid) in samples with substantially higher MICs than those of susceptible isolates. Combining both genomic and phenotypic data, in accordance with the WHO diagnostic guidelines, we could detect two new multidrug-resistant cases. Additionally, we detected 11 (1·6%) of 706 isolates to be monoresistant to fluoroquinolone, which had been previously undetected.

INTERPRETATION

We showed that the WHO catalogue enables the detection of resistant cases missed in phenotypic testing in a low-burden region, thus allowing for better patient-tailored treatment. We also identified mutations not included in the catalogue, relevant at the local level. Evidence from this study, together with future updates of the catalogue, will probably lead in the future to the partial replacement of culture testing with WGS-based drug susceptibility testing in our setting.

FUNDING

European Research Council and the Spanish Ministerio de Ciencia.

Population-based sequencing of Mycobacterium tuberculosis reveals how current population dynamics are shaped by past epidemics

Transmission is a driver of tuberculosis (TB) epidemics in high-burden regions, with assumed negligible impact in low-burden areas. However, we still lack a full characterization of transmission dynamics in settings with similar and different burdens. Genomic epidemiology can greatly help to quantify transmission, but the lack of whole genome sequencing population-based studies has hampered its application. Here, we generate a population-based dataset from Valencia region and compare it with available datasets from different TB-burden settings to reveal transmission dynamics heterogeneity and its public health implications. We sequenced the whole genome of 785 Mycobacterium tuberculosis strains and linked genomes to patient epidemiological data. We use a pairwise distance clustering approach and phylodynamic methods to characterize transmission events over the last 150 years, in different TB-burden regions. Our results underscore significant differences in transmission between low-burden TB settings, i.e., clustering in Valencia region is higher (47.4%) than in Oxfordshire (27%), and similar to a high-burden area as Malawi (49.8%). By modeling times of the transmission links, we observed that settings with high transmission rate are associated with decades of uninterrupted transmission, irrespective of burden. Together, our results reveal that burden and transmission are not necessarily linked due to the role of past epidemics in the ongoing TB incidence, and highlight the need for in-depth characterization of transmission dynamics and specifically tailored TB control strategies.

High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain

BACKGROUND

Whole genome sequencing provides better delineation of transmission clusters in Mycobacterium tuberculosis than traditional methods. However, its ability to reveal individual transmission links within clusters is limited. Here, we used a 2-step approach based on Bayesian transmission reconstruction to (1) identify likely index and missing cases, (2) determine risk factors associated with transmitters, and (3) estimate when transmission happened.

METHODS AND FINDINGS

We developed our transmission reconstruction method using genomic and epidemiological data from a population-based study from Valencia Region, Spain. Tuberculosis (TB) incidence during the study period was 8.4 cases per 100,000 people. While the study is ongoing, the sampling frame for this work includes notified TB cases between 1 January 2014 and 31 December 2016. We identified a total of 21 transmission clusters that fulfilled the criteria for analysis. These contained a total of 117 individuals diagnosed with active TB (109 with epidemiological data). Demographic characteristics of the study population were as follows: 80/109 (73%) individuals were Spanish-born, 76/109 (70%) individuals were men, and the mean age was 42.51 years (SD 18.46). We found that 66/109 (61%) TB patients were sputum positive at diagnosis, and 10/109 (9%) were HIV positive. We used the data to reveal individual transmission links, and to identify index cases, missing cases, likely transmitters, and associated transmission risk factors. Our Bayesian inference approach suggests that at least 60% of index cases are likely misidentified by local public health. Our data also suggest that factors associated with likely transmitters are different to those of simply being in a transmission cluster, highlighting the importance of differentiating between these 2 phenomena. Our data suggest that type 2 diabetes mellitus is a risk factor associated with being a transmitter (odds ratio 0.19 [95% CI 0.02-1.10], p < 0.003). Finally, we used the most likely timing for transmission events to study when TB transmission occurred; we identified that 5/14 (35.7%) cases likely transmitted TB well before symptom onset, and these were largely sputum negative at diagnosis. Limited within-cluster diversity does not allow us to extrapolate our findings to the whole TB population in Valencia Region.

CONCLUSIONS

In this study, we found that index cases are often misidentified, with downstream consequences for epidemiological investigations because likely transmitters can be missed. Our findings regarding inferred transmission timing suggest that TB transmission can occur before patient symptom onset, suggesting also that TB transmits during sub-clinical disease. This result has direct implications for diagnosing TB and reducing transmission. Overall, we show that a transition to individual-based genomic epidemiology will likely close some of the knowledge gaps in TB transmission and may redirect efforts towards cost-effective contact investigations for improved TB control.

Clinical factors associated with a Candida albicans Germ Tube Antibody positive test in Intensive Care Unit patients

BACKGROUND

Poor outcomes of invasive candidiasis (IC) are associated with the difficulty in establishing the microbiological diagnosis at an early stage. New scores and laboratory tests have been developed in order to make an early therapeutic intervention in an attempt to reduce the high mortality associated with invasive fungal infections. Candida albicans IFA IgG has been recently commercialized for germ tube antibody detection (CAGTA). This test provides a rapid and simple diagnosis of IC (84.4% sensitivity and 94.7% specificity). The aim of this study is to identify the patients who could be benefited by the use of CAGTA test in critical care setting.

METHODS

A prospective, cohort, observational multicentre study was carried out in six medical/surgical Intensive care units (ICU) of tertiary-care Spanish hospitals. Candida albicans Germ Tube Antibody test was performed twice a week if predetermined risk factors were present, and serologically demonstrated candidiasis was considered if the testing serum dilution was ≥ 1:160 in at least one sample and no other microbiological evidence of invasive candidiasis was found.

RESULTS

Fifty-three critically ill non-neutropenic patients (37.7% post surgery) were included. Twenty-two patients (41.5%) had CAGTA-positive results, none of them with positive blood culture for Candida. Neither corrected colonization index nor antifungal treatment had influence on CAGTA results. This finding could corroborate that the CAGTA may be an important biomarker to distinguish between colonization and infection in these patients. The presence of acute renal failure at the beginning of the study was more frequent in CAGTA-negative patients. Previous surgery was statistically more frequent in CAGTA-positive patients.

CONCLUSIONS

This study identified previous surgery as the principal clinical factor associated with CAGTA-positive results and emphasises the utility of this promising technique, which was not influenced by high Candida colonization or antifungal treatment. Our results suggest that detection of CAGTA may be important for the diagnosis of invasive candidiasis in surgical patients admitted in ICU.

Prognostic factors of mortality in patients with community-acquired bloodstream infection with severe sepsis and septic shock

PURPOSE

The purpose of the study was to determine the independent risk factors on mortality in patients with community-acquired severe sepsis and septic shock.

METHODS

A single-site prospective cohort study was carried out in a medical-surgical intensive care unit in an academic tertiary care center. One hundred twelve patients with community-acquired bloodstream infection with severe sepsis and septic shock were identified. Clinical, microbiologic, and laboratory parameters were compared between hospital survivors and hospital deaths.

RESULTS

One-hundred twelve patients were included. The global mortality rate was 41.9%, 44.5% in septic shock and 34.4% in severe sepsis. One or more comorbidities were present in 66% of patients. The most commonly identified bloodstream pathogens were Escherichia coli (25%) and Staphylococcus aureus (21.4%). The proportion of patients receiving inadequate antimicrobial treatment was 8.9%. By univariate analysis, age, Acute Physiology and Chronic Health Evaluation II score, at least 3 organ dysfunctions, and albumin, but neither microbiologic characteristics nor site of infection, differed significantly between survivors and nonsurvivors. Acute Physiology and Chronic Health Evaluation II (odds ratio, 1.13; 95% confidence interval, 1.06-1.21) and albumin (odds ratio, 0.34; 95% confidence interval, 0.15-0.76) were independent risk factors associated with global mortality in logistic regression analysis.

CONCLUSION

In addition to the severity of illness, hypoalbuminemia was identified as the most important prognostic factor in community-acquired bloodstream infection with severe sepsis and septic shock.

Clinical significance of the detection of Candida albicans germ tube-specific antibodies in critically ill patients

The present study, comprising a prospective multicentre study including 53 non-neutropenic patients from intensive care units (ICU) in six Spanish tertiary-care hospitals, was carried out to determine the clinical significance and influence on mortality of Candida albicans germ tube-specific antibodies (CAGTA). There were 22 patients (41.5%) for whom the CAGTA results were positive, although none of had a blood culture positive for Candida. The intra-ICU mortality rate was significantly lower (p = 0.004) in CAGTA-positive patients (61.2% vs. 22.7%). Multivariate analysis confirmed that a positive CAGTA result was the only protective factor to be independently associated with ICU mortality (beta coefficient = -0.3856; 95% confidence interval = -0.648 to -0.123).

The influence of inadequate empirical antimicrobial treatment on patients with bloodstream infections in an intensive care unit

OBJECTIVE

To determine the occurrence of inadequate antimicrobial therapy among critically ill patients with bacteremia and the factors associated with it, to identify the microorganisms that received inadequate antimicrobial treatment, and to determine the relationship between inadequate treatment and patients outcome.

METHODS

From June 1995 to January 1999 we collected data on all clinically significant ICU-bacteremias in our teaching hospital. Clinical and microbiological characteristics were recorded and the adequacy of empirical antimicrobial treatment in each case was determined. We defined inappropriate empirical antimicrobial treatment as applying to infection that was not being effectively treated at the time the causative microorganism and its antibiotic susceptibility were known. Multivariate analysis was used to determine the variables associated with inappropriate empirical antimicrobial treatment and to evaluate the influence of this on the related mortality to bacteremia, using the SPSS package (9.0).

RESULTS

Among 166 intensive care unit patients with bacteremia, 39 (23.5%) received inadequate antimicrobial treatment. In this last group the mean age of patients was 64.1 +/- 13.2 years, and 64% were men. Bacteremia was hospital-acquired in 92% of these cases. Eleven percent developed septic shock and 37.7% severe sepsis, and ultimately fatal underlying disease was present in 28.2% of patients given inadequate empirical antimicrobial treatment. The main sources of bacteremias in this group were: a vascular catheter (15.3%), respiratory (7.6%) or unknown (53.8%). The microorganisms most frequently isolated in the group with inadequate empirical antimicrobial treatment were: coagulase-negative staphylococci (29.5%), Acinetobacter baumannii (27.3%), Enterococcus faecalis, Pseudomonas aeruginosa, Enterobacter cloacae, Proteus mirabilis, Escherichia coli, and Candida species (4.5% each). The frequency of coagulase-negative staphylococci in the cases with inappropriate treatment was higher than in the group with appropriate treatment (OR 2.62; 95% CI: 1.10-6.21; P = 0.015). The global mortality rate was 56% and the related mortality was 30% in the group with inadequate empirical antimicrobial treatment. The only factor associated with inappropriate empirical antibiotic treatment was the absence of abdominal or respiratory focus (P = 0.04; OR = 0.35; 95% CI: 0.12-0.97). Septic shock was related to attributable mortality (P = 0.03; OR = 3.19; 95% CI: 1.08-9.40), but not inappropriate empirical antibiotic treatment (P = 0.24; OR = 1.71; 95% CI: 0.66-4.78).

CONCLUSION

Almost a quarter of critically ill patients with bloodstream infections were given inadequate empirical antibiotic treatment, but mortality was not higher in the group with inadequate treatment than in the group with adequate treatment. This fact was probably due to microbiological factors and clinical features, such as the type of microorganism most frequently isolated and the source of the bacteremia.

Comparison of PCR mediated amplification of DNA and the classical methods for detection of Mycobacterium leprae in different types of clinical samples in leprosy patients and contacts

Traditional staining and microscopic examination techniques for the detection of Mycobacterium leprae, DNA amplification by polymerase chain reaction (PCR) of a 531-bp fragment of the M. leprae specific gene encoding the 36-kDa antigen, and serodiagnosis with M. leprae specific antigens (PGL-1 and D-BSA) were compared on different clinical specimens (serum samples, slit-skin smears, biopsies and swabs) from 60 leprosy patients attending the Sanatorium of Fontilles. Patients were divided into groups; (i) 20 multibacillary patients (MB) with positive bacteriological index (BI) by conventional methods and on WHO multidrug therapy (MDT); (ii) 30 MB patients with negative BI and completed minimum 2 years treatment MDT; (iii) 10 paucibacillary (PB) patients who had completed 6 months MDT at least 8 years ago. Control groups included four non-leprosy patients for PCR methods and 40 health control patients and 10 tuberculosis patients for serological methods. In the multibacillary BI positive group, there was a good correlation between all methods. All tests were negative in the paucibacillary group, although only a few patients were tested and all had been treated many years ago. One must be cautious concerning the diagnostic potential of these techniques in this type of leprosy. We also studied different combinations of leprosy diagnosis methods to determine the potential risk in a leprosy contact individuals group. The prevalence of antibodies to M. leprae antigens in serum was measured, together with the presence of M. leprae DNA in the nose and lepromin status in a group of 43 contacts of leprosy patients (12 household and 31 occupational) to evaluate the maintenance of infection reservoirs and transmission of the disease. Only two individuals were found to form a potential high risk group.

Serological response (Western blot) to fractions of Mycobacterium tuberculosis sonicate antigen in tuberculosis patients and contacts

OBJECTIVE

To assess the serological response to fractions of Mycobacterium tuberculosis sonicate antigen by Western blot analysis in patients with tuberculosis and contacts.

METHODS

We studied 71 individuals including 43 patients with active tuberculosis, 16 contacts and 12 healthy blood donors. For Western blot analysis, M. tuberculosis (H37Rv strain) sonicate antigen extract was fractionated by electrophoresis on polyacrylamide gel (SDS-PAGE).

RESULTS

We obtained antibody responses directed against four antigenic fractions with molecular weights of 71, 65, 26-38 and 19 kDa. Sixty per cent of pleural tuberculosis and 52.4% of smear-positive pulmonary tuberculosis had whole responses against all four fractions; there were no partial responses in these groups. For patients with smear-negative pulmonary tuberculosis whole responses were 17.6% and partial responses 41.2%. All contacts whose tuberculin tests converted from negative to positive (three cases) reacted exclusively against the 19 kDa fraction.

CONCLUSIONS

Western blot-positive results in patients with pleural and smear-positive pulmonary tuberculosis were characterised by a whole pattern against all four antigenic fractions, whereas patients with smear-negative pulmonary tuberculosis showed heterogeneous results. The exclusive response against the 19 kDa fraction observed in contacts with tuberculin conversion could help to identify candidates for preventive therapy.

Pneumococcal pyomyositis

Pyomyositis is most commonly caused by Staphylococcus aureus. A 25-month-old child developed infection of the biceps brachialis muscle caused by Streptococcus pneumoniae. The child had no underlying immune or anatomic defect.

[Tuberculosis in AIDS patients: the contribution of an analysis of the restriction fragment length polymorphism of Mycobacterium tuberculosis isolates]

BACKGROUND

In this report we study tuberculosis transmission in HIV infected patients using molecular epidemiological methods.

PATIENTS AND METHODS

We have studied 60 M. tuberculosis isolates from 30 HIV infected cases, and their clinical-epidemiological data. Susceptibility to tuberculostatic agents and electrophoretic patterns using RFLPs (restriction fragment length polymorphisms) method were evaluated. Dice's coefficient was used for the similarity analysis.

RESULTS

Over 73% studied patients were included in clusters using RFLPs analysis. This data show that nearly 60% of the tuberculosis cases in our area have a recent transmission. Forty per cent of these cases were included in the main cluster. The frequency of tuberculostatic-resistant strains in HIV infected patients was similar to the that of observed in other patients. We did not find correlation between RFLPs clusters and clinical-epidemiological data.

CONCLUSIONS

Tuberculosis transmission in HIV-positive patients using RFLPs as molecular marker shows that 60% of the cases are caused by recently acquired strains. We did not find multi-drug resistant strains in our isolates. However due to the high transmissibility of these circulating clones, control disease measures in this group of risk population are required.

Application of an optimized and highly discriminatory method based on arbitrarily primed PCR for epidemiologic analysis of methicillin-resistant Staphylococcus aureus nosocomial infections

The optimization of an arbitrarily primed PCR method for typing 96 methicillin-resistant Staphylococcus aureus (MRSA) isolates was compared with pulsed-field gel electrophoresis. Identical results in the differentiation of MRSA clones and identification of the main cluster that included 82 strains (88% of patients) were obtained by both techniques.

DNA amplification fingerprinting for subtyping Neisseria gonorrhoeae strains

BACKGROUND AND OBJECTIVES

DNA amplification fingerprinting is used in most epidemiologic studies as a substitute for conventional typing methods. DNA amplification fingerprinting and conventional typing methods were compared in this epidemiologic study of Neisseria gonorrhoeae.

GOAL OF THIS STUDY

To differentiate 70 Neisseria gonorrhoeae isolates from untreated patients with urogenital gonococcal infection.

STUDY DESIGN

Gonococcal strains were characterized by auxotyping, serotyping, plasmid profile, antibiotic sensitivity, and DNA amplification fingerprinting. The method of unweighted pair-group average linkage was used for cluster analysis. Discriminatory power was calculated applying Simpson's index.

RESULTS

Amplification of Neisseria gonorrhoeae DNA with primers OPA-03 and OPA-13 produced well-resolved patterns of 15 and 22 DNA fragments, respectively, with a discriminatory power (0.978 with OPA-13 and 0.967 with OPA-03) comparable to that obtained with auxotyping/serotyping combination (D:0.968) or with auxotype/serotype/plasmid profile combination (D:0.983). Correlation between DNA amplification fingerprinting pattern and auxotype/serotype class was not always uniform. Some strains with the same auxotype/serotype/plasmid profile were subdivided by DNA amplification fingerprinting, and vice versa.

CONCLUSION

Although auxotype/serotype class and DNA amplification fingerprinting can be used in the epidemiologic characterization of strains, DNA amplification fingerprinting offers a better discriminatory index than the separate serotyping. It is especially useful for differentiating serologically identical strains and nontypable strains. A combination of serotyping and DNA amplification fingerprinting seems to be the best way to differentiate Neisseria gonorrhoeae strains in epidemiologic studies, bringing together the most simple techniques and the best discriminatory power among isolates.

Use of genomic fingerprinting in the characterization of Neisseria gonorrhoeae isolated in Valencia, Spain

Ninety-five Neisseria gonorrhoeae organisms isolated in Valencia, Spain, were characterized by antibiotic sensitivity testing, auxotyping, serotyping, plasmid analysis and restriction endonuclease fingerprinting (HindIII digestion). Cluster analysis of the restriction patterns revealed that 31 isolates (32.6%) formed 12 clearly defined clusters. Penicillinase-producing Neisseria gonorrhoeae strains formed four of these groups. Eight groups of gonococcal strains were identified by auxotyping, although 83% of isolates belonged to two auxotypes (Proto, Pro-). Twenty-three different serovars were identified by serotyping. The serovar pattern IB/rop was found in 38% of isolates. A 60% coincidence was found between gonococcal groupings obtained by combination of auxotyping, serotyping and plasmid analysis and those obtained with the restriction enzyme fingerprinting technique. The specificity of enzyme restriction patterns of Neisseria gonorrhoeae is confirmed to be of practical importance in the epidemiologic study of gonorrhoea.

Genomic fingerprinting of penicillinase-producing strains of Neisseria gonorrhoeae in Valencia, Spain

OBJECTIVE

To compare the value of different markers and their combinations with the restriction enzyme technique in the differentiations of penicillinase-producing N. gonorrhoeae (PPNG) strains.

MATERIALS AND METHODS

17 PPNG strains isolated from symptomatic, untreated male patients with urethritis were characterised by antibiotic sensitivity testing, auxotyping, serotyping, plasmid profile, and restriction endonuclease fingerprinting (Hind III digestion). Cluster analysis with the method of unweighted pair-group average (UPGMA) linkage was used to calculate similarity or dissimilarity for PPNG strains.

MAIN RESULTS

Either auxotyping or plasmid profile alone differentiated three groups of PPNG strains, whereas the combination auxotyping/serotyping identified 10. Although the combination auxotyping/serotyping/plasmid profile and the restriction enzyme technique showed a similar discrimination ability (differentiation of 11 PPNG strains), genomic fingerprinting gave highly specific restriction patterns on individual gonococcal isolates.

CONCLUSIONS

The combination of different markers gave more epidemiological information than the use of only one. The sequence of discriminating ability for PPNG strains was: auxotyping/serotyping less than auxotyping/serotyping/plasmid profile less than restriction patterns of genomic DNA.

[Membrane proteins electrophoretic profiles study applied to Neisseria gonorrhoeae epidemiology]

The analysis of electrophoretic profiles of membrane proteins is one of the epidemiological methods of bacterial typing. The profiles of membrane proteins of 95 isolates were studied for valuing their usefulness in the epidemiology of N. gonorrhoeae. The results were compared with the obtained using other characterization methods (auxotyping, serotyping and antimicrobial sensibility). The proteins I and II (PI and PII) showed clear differences between isolates. Only protein-I (PI) with constant molecular weight for each isolate was valid to discriminate between strains. It was observed correlation between serovariety IA and molecular weight of PI 33.6-36 kD, and the serovariety IB with molecular weight 35.5-37 kD. Though it wasn't possible discriminated between the different serovarieties. It was proved a sensibility decrease to penicillin, tetracycline and cloramfenicol in those strains with molecular weight of PI greater than 35.5 kD (serogroup WII/WIII). In the 80% of the isolates considered multiple antibiotic-resistant it was observed a significant increase of the membrane protein dough of 52 kD. All the strains with this protein increased were multiple antibiotic-resistant.

Effect of cutaneous and digestive colonization in the induction of anti-Candida albicans antibodies: experimental study

Candida albicans colonization induces antibodies, which must be taken into account in the serological diagnosis of candidiasis. In order to determine the degree of this effect, an experimental study in rabbits free of specific anti-Candida antibodies by cutaneous and digestive inoculation has been carried out. The evolution of humoral response was studied over 8 weeks by indirect immunofluorescence (IIF), direct agglutination (DA), counterimmunoelectrophoresis (CIE) and double diffusion (DD). The cutaneous colonization detectable by culture was maintained until the second week in 70% of the animals and the presence of antibodies detectable by IIF and DA was observed after the 2nd week. The highest antibody titre by IFF and DA was 1/64, and was reached in the 5th week, with a tendency to drop in the following weeks. Precipitins were only detected by CIE in 15% of the animals in the 7th week. Elimination of yeast in stools continued only in 20% of the animals in the 2nd week of the experiment. Antibodies were detected by IIF and DA after the 2nd week, with the highest titres detectable by IFF in the 5th week. Precipitant antibodies detectable by CIE appeared in 15% of the animals in the 8th week.