The virtual CF clinic: Implications for sputum microbiology.

The COVID19 pandemic has shifted the paradigm of how outpatient clinics are delivered within CF care, resulting in a significant reduction of patient visits to CF centres. One consequence of this has been a reduction in the number of sputa/cough swabs that patients submit for routine analysis. This report examines why it is important to maintain optimal sputum microbiology and explores (i). the microbiological efficiency of postal submission of sputum specimens from the community and (ii) the regulatory conditions that must be met through postal submission of respiratory specimens. Virtual clinics have now been established within CF care and it is incumbent on each speciality within the CF MDT to explore ways to nurture and support their individual contribution to the success of the virtual clinic. Within microbiology, adopting innovative approaches to sputum collection in the community and transportation via postal services will allow for continued microbiological vigilance thereby supporting patient safety.

Isolation of and risk factors for airway infection with Pseudomonas aeruginosa in patients with non-cystic fibrosis bronchiectasis / Isolamento de Pseudomonas aeruginosa e fatores de risco de infecção das vias aéreas pela bactéria em pacientes com bronquiectasias não fibrocísticas

ABSTRACT Objective: To identify microorganisms in sputum samples of patients with stable non-cystic fibrosis bronchiectasis and to determine risk factors related to the isolation of Pseudomonas aeruginosa (PA) in those patients. Methods: Consecutive patients were recruited from a tertiary hospital outpatient clinic in the city of Fortaleza, Brazil. The patients were submitted to spirometry, six-minute walk test, HRCT, and sputum collection. Data on serum fibrinogen levels, disease severity, sputum color, and history of azithromycin treatment were collected. Results: The study included 112 patients, and females predominated (68%). The mean age was 51.6 ± 17.4 years. Most patients presented with mild-to-moderate disease (83%). The mean six-minute walk distance was 468.8 ± 87.9 m. Mean FEV1 and FVC, in % of predicted values, were 60.4 ± 21.8% and 69.9 ± 18.5%, respectively. The mean serum fibrinogen level was 396.1 ± 76.3 mg/dL. PA was isolated in 47 patients, other potentially pathogenic microorganisms (PPMs) were isolated in 31 patients, and non-PPMs were isolated in 34 patients. Purulent sputum was identified in 77 patients (68%). The patients with PA, when compared with those without it, presented with more severe disease, higher serum fibrinogen levels, and lower FVC%. In addition, purulent sputum and long-term azithromycin treatment were more common in those with PA. The multivariate regression analysis showed that the independent factors associated with PA were serum fibrinogen level > 400 mg/dL (OR = 3.0; 95% CI: 1.1-7.7) and purulent sputum (OR = 4.3; 95% CI: 1.6-11.3). Conclusions: In our sample, the prevalence of PA in sputum was 42%. Sputum color and inflammatory markers were able to predict the isolation of PA, emphasizing the importance of routine sputum monitoring.

RESUMO Objetivo: Identificar microrganismos em amostras de escarro de pacientes com bronquiectasia não fibrocística estável e determinar os fatores de risco relacionados com o isolamento de Pseudomonas aeruginosa (PA) nesses pacientes. Métodos: Pacientes consecutivos foram recrutados em um ambulatório de um hospital terciário em Fortaleza (CE). Os pacientes foram submetidos a espirometria, teste de caminhada de seis minutos, TCAR e coleta de escarro. Foram coletados dados referentes ao fibrinogênio sérico, gravidade da doença, cor do escarro e histórico de tratamento com azitromicina. Resultados: O estudo incluiu 112 pacientes, com predomínio do sexo feminino (68%). A média de idade foi de 51,6 ± 17,4 anos. A maioria dos pacientes apresentou doença leve a moderada (83%). A média da distância percorrida no teste de caminhada de seis minutos foi de 468,8 ± 87,9 m. A média do VEF1 em % do previsto foi de 60,4 ± 21,8%, e a da CVF em % do previsto foi de 69,9 ± 18,5%. A média do fibrinogênio sérico foi de 396,1 ± 76,3 mg/dL. PA foi isolada em 47 pacientes; outros microrganismos potencialmente patogênicos (MPP) foram isolados em 31; não MPP foram isolados em 34. Escarro purulento foi identificado em 77 pacientes (68%). Os pacientes com PA, em comparação com aqueles sem, apresentaram doença mais grave, fibrinogênio sérico mais elevado e menor CVF%. Além disso, escarro purulento e tratamento prolongado com azitromicina foram mais comuns naqueles com PA. A análise de regressão multivariada mostrou que os fatores independentes relacionados com PA foram fibrinogênio sérico > 400 mg/dL (OR = 3,0; IC95%: 1,1-7,7) e escarro purulento (OR = 4,3; IC95%: 1,6-11,3). Conclusões: Em nossa amostra, a prevalência de PA no escarro foi de 42%. A cor do escarro e os marcadores inflamatórios foram capazes de prever o isolamento de PA, o que enfatiza a importância do monitoramento rotineiro do escarro.

Risk of infection and disease progression in children exposed to tuberculosis at home, Colombia / Riesgo de infección y progresión de la enfermedad en niños expuestos a tuberculosis en el hogar, Colombia

Abstract Aim: To assess the risk of tuberculosis (infection and disease) in children less than 15 years' old who are household contacts of pulmonary tuberculosis patients in three Colombian cities (Medellín, Cali, and Popayán). Methods: A cohort of 1,040 children household contacts of 380 adults with smear-positive pulmonary tuberculosis was followed up for 24 months. Study period 2005-2009. Results: Tuberculin skin test was positive (≥10 mm) in 43.7% (95% CI: 39.2-48.2). Tuberculin skin test positivity was associated with age 10-14 years (Prevalence Ratio -PR= 1.43, 95% CI: 1.1-1.9), having a BCG vaccine scar (PR= 1.52, 95% CI: 1.1-2.1), underweight, closer proximity to the index case and exposure time >3 months. The annual risk of infection (tuberculin skin test induration increase of 6 mm or more per year) was 17% (95% CI: 11.8-22.2) and was associated with a bacillary load of the adult index case (Relative Risk -RR= 2.12, 95% CI: 1.0-4.3). The incidence rate of active tuberculosis was 12.4 cases per 1,000 persons-year. Children <5 years without BCG vaccine scar had a greater risk of developing active disease (Hazard Ratio -HR= 6.00, 95% CI: 1.3-28.3) than those with scar (HR= 1.33, 95% CI: 0.5-3.4). The risk of developing active tuberculosis augmented along with the increase from initial tuberculin skin test (tuberculin skin test 5-9 mm HR= 8.55, 95% CI: 2.5-29.2; tuberculin skin test ≥10 mm HR= 8.16, 95% CI: 2.0-32.9). Conclusions: There is a need for prompt interruption of adult-to-children tuberculosis transmission within households. Conducting proper contact investigation and offering chemoprophylaxis to infected children could reduce tuberculosis transmission.

Resumen Objetivo: Evaluar el riesgo de tuberculosis (infección y enfermedad) en niños menores de 15 años de edad convivientes de pacientes con tuberculosis pulmonar en tres ciudades colombianas (Medellín, Cali y Popayán). Métodos: Se siguió durante 24 meses una cohorte de 1,040 niños convivientes de 380 adultos con tuberculosis pulmonar bacilífera. Periodo de estudio 2005-2009. Resultados: La prueba de tuberculina fue positiva (≥10 mm) en el 43.7% (IC 95%: 39.2-48.2), y estuvo asociada con la edad de 10-14 años (Razón de Prevalencia-RP= 1.43, IC 95%: 1.1-1.9), tener cicatriz de la vacuna BCG (RP= 1.52, IC 95%: 1.1-2.1). El riesgo anual de infección (aumento de la induración en la prueba de tuberculina de 6 mm o más al año) fue 17% (IC 95%: 11.8-22.2), y estuvo asociado con mayor carga bacilar en el adulto con tuberculosis pulmonar (Riesgo Relativo-RR= 2.12, IC 95%: 1.0-4.3). La tasa de incidencia de tuberculosis activa fue de 12.4 casos por 1,000 años-persona de seguimiento. Los niños menores de 5 años sin cicatriz de vacuna BCG tuvieron un mayor riesgo de desarrollar tuberculosis activa (Razón de Peligro -HR= 6.00, IC 95%: 1.3-28.3), que quienes tenían cicatriz (HR= 1.33, IC 95%: 0.5-3.4). El riesgo de desarrollar tuberculosis activa aumentó conforme el aumento de la prueba de tuberculina inicial (prueba de tuberculina 5-9 mm HR= 8.55, IC 95%: 2.5-29.2; prueba de tuberculina ≥10 mm HR= 8.16, IC 95%: 2.0-32.9). Conclusión: Es necesario interrumpir rápidamente la transmisión de tuberculosis de adultos a niños en los hogares. Realizar investigaciones de contacto apropiadas y ofrecer quimioprofilaxis a los niños infectados podría reducir la transmisión de la tuberculosis.

Risk of infection and disease progression in children exposed to tuberculosis at home, Colombia.

AIM: To assess the risk of tuberculosis (infection and disease) in children less than 15 years' old who are household contacts of pulmonary tuberculosis patients in three Colombian cities (Medellín, Cali, and Popayán). METHODS: A cohort of 1,040 children household contacts of 380 adults with smear-positive pulmonary tuberculosis was followed up for 24 months. Study period 2005-2009. RESULTS: Tuberculin skin test was positive (≥10 mm) in 43.7% (95% CI: 39.2-48.2). Tuberculin skin test positivity was associated with age 10-14 years (Prevalence Ratio -PR= 1.43, 95% CI: 1.1-1.9), having a BCG vaccine scar (PR= 1.52, 95% CI: 1.1-2.1), underweight, closer proximity to the index case and exposure time >3 months. The annual risk of infection (tuberculin skin test induration increase of 6 mm or more per year) was 17% (95% CI: 11.8-22.2) and was associated with a bacillary load of the adult index case (Relative Risk -RR= 2.12, 95% CI: 1.0-4.3). The incidence rate of active tuberculosis was 12.4 cases per 1,000 persons-year. Children <5 years without BCG vaccine scar had a greater risk of developing active disease (Hazard Ratio -HR= 6.00, 95% CI: 1.3-28.3) than those with scar (HR= 1.33, 95% CI: 0.5-3.4). The risk of developing active tuberculosis augmented along with the increase from initial tuberculin skin test (tuberculin skin test 5-9 mm HR= 8.55, 95% CI: 2.5-29.2; tuberculin skin test ≥10 mm HR= 8.16, 95% CI: 2.0-32.9). CONCLUSIONS: There is a need for prompt interruption of adult-to-children tuberculosis transmission within households. Conducting proper contact investigation and offering chemoprophylaxis to infected children could reduce tuberculosis transmission.

OBJETIVO: Evaluar el riesgo de tuberculosis (infección y enfermedad) en niños menores de 15 años de edad convivientes de pacientes con tuberculosis pulmonar en tres ciudades colombianas (Medellín, Cali y Popayán). MÉTODOS: Se siguió durante 24 meses una cohorte de 1,040 niños convivientes de 380 adultos con tuberculosis pulmonar bacilífera. Periodo de estudio 2005-2009. Resultados: La prueba de tuberculina fue positiva (≥10 mm) en el 43.7% (IC 95%: 39.2-48.2), y estuvo asociada con la edad de 10-14 años (Razón de Prevalencia-RP= 1.43, IC 95%: 1.1-1.9), tener cicatriz de la vacuna BCG (RP= 1.52, IC 95%: 1.1-2.1). El riesgo anual de infección (aumento de la induración en la prueba de tuberculina de 6 mm o más al año) fue 17% (IC 95%: 11.8-22.2), y estuvo asociado con mayor carga bacilar en el adulto con tuberculosis pulmonar (Riesgo Relativo-RR= 2.12, IC 95%: 1.0-4.3). La tasa de incidencia de tuberculosis activa fue de 12.4 casos por 1,000 años-persona de seguimiento. Los niños menores de 5 años sin cicatriz de vacuna BCG tuvieron un mayor riesgo de desarrollar tuberculosis activa (Razón de Peligro -HR= 6.00, IC 95%: 1.3-28.3), que quienes tenían cicatriz (HR= 1.33, IC 95%: 0.5-3.4). El riesgo de desarrollar tuberculosis activa aumentó conforme el aumento de la prueba de tuberculina inicial (prueba de tuberculina 5-9 mm HR= 8.55, IC 95%: 2.5-29.2; prueba de tuberculina ≥10 mm HR= 8.16, IC 95%: 2.0-32.9). CONCLUSIÓN: Es necesario interrumpir rápidamente la transmisión de tuberculosis de adultos a niños en los hogares. Realizar investigaciones de contacto apropiadas y ofrecer quimioprofilaxis a los niños infectados podría reducir la transmisión de la tuberculosis.

Sputum is a surrogate for bronchoalveolar lavage for monitoring Mycobacterium tuberculosis transcriptional profiles in TB patients.

Pathogen-targeted transcriptional profiling in human sputum may elucidate the physiologic state of Mycobacterium tuberculosis (M. tuberculosis) during infection and treatment. However, whether M. tuberculosis transcription in sputum recapitulates transcription in the lung is uncertain. We therefore compared M. tuberculosis transcription in human sputum and bronchoalveolar lavage (BAL) samples from 11 HIV-negative South African patients with pulmonary tuberculosis. We additionally compared these clinical samples with in vitro log phase aerobic growth and hypoxic non-replicating persistence (NRP-2). Of 2179 M. tuberculosis transcripts assayed in sputum and BAL via multiplex RT-PCR, 194 (8.9%) had a p-value <0.05, but none were significant after correction for multiple testing. Categorical enrichment analysis indicated that expression of the hypoxia-responsive DosR regulon was higher in BAL than in sputum. M. tuberculosis transcription in BAL and sputum was distinct from both aerobic growth and NRP-2, with a range of 396-1020 transcripts significantly differentially expressed after multiple testing correction. Collectively, our results indicate that M. tuberculosis transcription in sputum approximates M. tuberculosis transcription in the lung. Minor differences between M. tuberculosis transcription in BAL and sputum suggested lower oxygen concentrations or higher nitric oxide concentrations in BAL. M. tuberculosis-targeted transcriptional profiling of sputa may be a powerful tool for understanding M. tuberculosis pathogenesis and monitoring treatment responses in vivo.

Adaptation of Mycobacterium tuberculosis to Impaired Host Immunity in HIV-Infected Patients.

BACKGROUND: It is unknown whether immunosuppression influences the physiologic state of Mycobacterium tuberculosis in vivo. We evaluated the impact of host immunity by comparing M. tuberculosis and human gene transcription in sputum between human immunodeficiency virus (HIV)-infected and uninfected patients with tuberculosis. METHODS: We collected sputum specimens before treatment from Gambians and Ugandans with pulmonary tuberculosis, revealed by positive results of acid-fast bacillus smears. We quantified expression of 2179 M. tuberculosis genes and 234 human immune genes via quantitative reverse transcription-polymerase chain reaction. We summarized genes from key functional categories with significantly increased or decreased expression. RESULTS: A total of 24 of 65 patients with tuberculosis were HIV infected. M. tuberculosis DosR regulon genes were less highly expressed among HIV-infected patients with tuberculosis than among HIV-uninfected patients with tuberculosis (Gambia, P < .0001; Uganda, P = .037). In profiling of human genes from the same sputa, HIV-infected patients had 3.4-fold lower expression of IFNG (P = .005), 4.9-fold higher expression of ARG1 (P = .0006), and 3.4-fold higher expression of IL10 (P = .0002) than in HIV-uninfected patients with tuberculosis. CONCLUSIONS: M. tuberculosis in HIV-infected patients had lower expression of the DosR regulon, a critical metabolic and immunomodulatory switch induced by NO, carbon monoxide, and hypoxia. Our human data suggest that decreased DosR expression may result from alternative pathway activation of macrophages, with consequent decreased NO expression and/or by poor granuloma formation with consequent decreased hypoxic stress.

Association of chronic Candida albicans respiratory infection with a more severe lung disease in patients with cystic fibrosis.

BACKGROUND: Despite the increase in fungal isolates, the significance of chronic Candida albicans airway colonization in CF is unclear. AIM: To investigate the impact of C. albicans airway colonization on CF disease severity. METHODS: Longitudinal analysis of clinical data from CF patients followed during 2003-2009 at our CF center. Patients were stratified based on their C. albicans colonization status--chronic, intermittent, and none. RESULTS: A total of 4,244 cultures were obtained from 91 patients (mean age 19.7 years, range 5-68). The three colonization groups were similar in age, gender,and body mass index (BMI). Compared to the non-colonized group (n = 27, 30%), the chronic C. albicans colonization group (n = 34, 37%), had a significantly lower FEV1 percent predicted (74.3 ± 23.1% vs. 93.9% ± 22.2) with a higher annual rate of FEV1 decline (-1.9 ± 4.2% vs. 0.7 ± 4.5%). The patients who were intermittently colonized with C. albicans had intermediate values. CONCLUSIONS: Chronic respiratory colonization of C. albicans is associated with worsening of FEV1 in CF. Prospective studies are needed to confirm this finding and to corroborate whether indeed C. albicans drives a deleterious lung phenotype.

Transcriptional Adaptation of Drug-tolerant Mycobacterium tuberculosis During Treatment of Human Tuberculosis.

BACKGROUND: Treatment initiation rapidly kills most drug-susceptible Mycobacterium tuberculosis, but a bacterial subpopulation tolerates prolonged drug exposure. We evaluated drug-tolerant bacilli in human sputum by comparing messenger RNA (mRNA) expression of drug-tolerant bacilli that survive the early bactericidal phase with treatment-naive bacilli. METHODS: M. tuberculosis gene expression was quantified via reverse-transcription polymerase chain reaction in serial sputa from 17 Ugandans treated for drug-susceptible pulmonary tuberculosis. RESULTS: Within 4 days, bacterial mRNA abundance declined >98%, indicating rapid killing. Thereafter, the rate of decline slowed >94%, indicating drug tolerance. After 14 days, 16S ribosomal RNA transcripts/genome declined 96%, indicating slow growth. Drug-tolerant bacilli displayed marked downregulation of genes associated with growth, metabolism, and lipid synthesis and upregulation in stress responses and key regulatory categories-including stress-associated sigma factors, transcription factors, and toxin-antitoxin genes. Drug efflux pumps were upregulated. The isoniazid stress signature was induced by initial drug exposure, then disappeared after 4 days. CONCLUSIONS: Transcriptional patterns suggest that drug-tolerant bacilli in sputum are in a slow-growing, metabolically and synthetically downregulated state. Absence of the isoniazid stress signature in drug-tolerant bacilli indicates that physiological state influences drug responsiveness in vivo. These results identify novel drug targets that should aid in development of novel shorter tuberculosis treatment regimens.

Analysis of the distribution of age and sex and the resistance of penicillin and levofloxacin among 672 Streptococcus pneumoniae that were isolated from sputum / 中国医师杂志

Objective To investigate the distribution of age and sex and the resistance of penicillin (p) and levofloxacin (LEV) among Streptococcus pneumoniae that were isolated from sputum.Methods The sputum specimens of our hospital from 2011 to 2013 were collected with the requirements of the third edition of National Clinical Laboratory Procedures,and 672 Streptococcus pneumoniae bacteria were isolated.Gram-Positive (GP) identification card was used to identify any doubt bacteria.LEV sensitivity was tested with Kirby-Bauer (KB) assay,and minimum inhibitory concentration (MIC) of P was tested with reagent strips (P-E test).Results A total of 672 Streptococcus pneumoniae bacteria was isolated in sputum.The number of age 0 to 6 years was 267 (39.73％),＞6 to 14 years was 62 (9.23％),＞ 14 to 60 years was 85 (12.65％),and ＞60 years was 258(38.39％) ; and isolating rates of age 0 to 6 years and ＞60 years were higher than other groups with statistically significant difference (P ＜0.01).The isolating rate of male (59.23％) was higher than female (40.77％) with a statistically significant difference (P ＜0.01).The sensitive rate of penicillin (p) to isolated strain was 73.78％ in 2011,71.32％ in 2012,and 53.50％ in 2013,respectively.MIC of isolated strain penicillin was increased year by year; however,LEV treated the isolated strain remain had a high sensitivity in first three years,the sensitivity of Streptococcus pneumoniae had no significant correlation between penicillin and LEV.Conclusions The resistance of penicillin was increased to streptococcus pneumoniae,patients who were infected by streptococcus pneumoniae and were allergic or resistant to penicillin can be considered to use an alternative therapy with LEV.

The role of the third acid-fast bacillus smear in tuberculosis screening for infection control purposes: A controversial topic revisited.

INTRODUCTION: Recent studies have suggested that two negative acid-fast bacillus (AFB) smears may be as effective as three when screening patients with suspected Mycobacterium tuberculosis for respiratory isolation purposes. However, current recommendations in Canada, the United States and Europe still support a three-smear approach. METHODS: The microbiology database of a tertiary care hospital was searched for sputum, tracheal aspirates and bronchoalveolar lavage samples from 2003 to 2007 that had been sent for mycobacterial testing. The first patient specimen to become AFB smear positive was noted. As well, the time required to collect the third specimen in hospitalized patients who remained smear negative was used to estimate the savings in isolation costs associated with a two-smear approach. RESULTS: There were 8347 respiratory specimens from 5168 patients in the five-year period. Of these patients, 2.2% (116 of 5168) were AFB smear positive, of whom 55.2% (64 of 116) were culture positive for Mycobacterium tuberculosis. Overall 89% (57 of 64) of patients were identified as being AFB smear positive by the first smear, 7.8% (five of 64) were identified by the second smear and 3.2% (two of 64) were identified by further smears. Smear-negative patients spent a combined 710 days in isolation awaiting collection of the third sample at a cost of approximately $142,000 over five years. CONCLUSION: A two-smear approach for discontinuation of respiratory isolation precautions is safe and has the potential to reduce hospital expenditures.