Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome.

BACKGROUND: Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients. METHODS: Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method. RESULTS: Statistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods' data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly. CONCLUSIONS: It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.

Aetiological testing compared with syndromic management for sexually transmitted infections in HIV-infected pregnant women in South Africa: a non-randomised prospective cohort study.

OBJECTIVE: To measure the frequencies of sexually transmitted infections (STIs) and adverse pregnancy outcomes among women receiving either aetiological testing or syndromic management for STIs. DESIGN: Non-randomised prospective cohort study. SETTING: Primary healthcare facilities in Tshwane, South Africa. POPULATION: HIV-infected pregnant women attending antenatal care services. METHODS: Participants were enrolled to receive aetiological testing using Xpert® CT/NG and Xpert® TV assays or standard syndromic management. Outcome data were collected at the postnatal care visit (≤30 days from delivery) and from maternity records. Enrolment gestational age-adjusted relative risk (aRR) was calculated. MAIN OUTCOME MEASURES: STI prevalence at postnatal visit, and frequency of adverse pregnancy outcomes (preterm birth, low birthweight). RESULTS: We enrolled 841 women. The prevalence of any STI at baseline was 40%; Chlamydia trachomatis 30%, Neisseria gonorrhoeae 5.6%, Trichomonas vaginalis 20%. The prevalence of STIs at postnatal care was lower among those receiving aetiological testing compared with those receiving syndromic management (14% versus 23%; aRR 0.61; 95% CI 0.35-1.05). No difference was observed between study groups for frequency of preterm birth (23% versus 23%; aRR 1.2, 95% CI 0.81-1.8) and low birth weight (15% versus 13%; aRR 1.1, 95% CI 0.66-1.7). CONCLUSIONS: Aetiological testing provides an effective intervention to reduce the high burden of STIs in pregnant women in South Africa; however, the optimal implementation strategy remains to be determined. TWEETABLE ABSTRACT: Aetiological testing effectively reduces the burden of sexually transmitted infections in pregnancy.

Ocular disease in patients with TB and HIV presenting with fever in Malawi.

AIMS: To investigate ocular disease in Malawian patients with tuberculosis (TB) and HIV in presenting with fever, and to determine if indirect ophthalmoscopy is useful in the diagnosis of mycobacteraemia. METHODS: A prospective study of all adult patients admitted with fever to Queen Elizabeth Central Hospital, Blantyre. All recruited patients had an ophthalmic examination, HIV tests, chest x-ray, sputum examinations, bacterial and mycobacterial blood cultures and malaria slide. RESULTS: 307 patients were recruited; 109 (36%) had TB, including 53 (17%) with mycobacteraemia; 255 (83%) had HIV and 191 (62%) had AIDS. Of the patients with TB 102 (94%) had HIV. Choroidal granulomas were found in four patients, all of whom had AIDS; three had disseminated TB with mycobacteraemia, and one had persistent fever but no other evidence of TB. Among the patients with AIDS, 32 (17%) had retinal microangiopathy manifest by cotton wool spots; one (0.5%) had signs of active cytomegalovirus (CMV) retinitis. The presence of microangiopathy was not related to TB. CONCLUSIONS: In Malawian patients with TB presenting acutely with fever, choroidal granulomas were found in 2.8%, and were concurrent with mycobacteraemia and AIDS. Ophthalmoscopy was not a useful aid in the diagnosis of mycobacteraemia. CMV retinitis is rarely seen in African AIDS patients. This may be due to mortality early in the disease course, or differences in race, HIV sub-type or co-morbidity.

Clinical indicators of mycobacteraemia in adults admitted to hospital in Blantyre.

The aims of the study were to measure the prevalence and outcome of mycobacteraemia in febrile hospitalised adults; to determine what proportion could be identified using routine methods; to assess clinical indicators of mycobacteraemia and the usefulness of a diagnostic trial of anti-TB treatment. We prospectively examined adults with fever or a history of fever admitted to adult medical wards of QECH, Blantyre. All had blood cultured for bacteria and mycobacteria, chest x-ray and sputum smears. M. tuberculosis was the commonest blood isolate, affecting 57 of 344 patients (17%). In 44 (77%) patients with mycobacteraemia, TB was identified using routine investigations; in only 6 (11%) it was not suspected. Strong clinical indicators of mycobacteraemia were anaemia, HIV seropositivity, cough, chronic fever, and a clinical diagnosis of AIDS on the day of admission. Of nine patients selected for a therapeutic trial of TB treatment, six had mycobacteraemia, of whom five died during the trial. Mortality on short course chemotherapy on the TB ward after one month, was similar whether patients had mycobacteramia (21%) or not (32%). TB can be identified with routine methods in most patients with mycobacteraemia. If treated, mycobacteraemia has as good an early outcome as TB without mycobacteraemia. Strengthening of basic facilities is likely to improve detection and treatment of mycobacterial disease.