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Background: Opportunistic infections in the central nervous system (CNS) can be a serious threat to people living with HIV. Early aetiological diagnosis and targeted treatment are crucial but difficult. Metagenomic next-generation sequencing (mNGS) has significant advantages over traditional detection methods. However, differences in the cerebrospinal fluid (CSF) microbiome profiles of patients living with and without HIV with suspected CNS infections using mNGS and conventional testing methods have not yet been adequately evaluated., Methods: We conducted a retrospective cohort study in the first hospital of Changsha between January 2019 and June 2022 to investigate the microbiomes detected using mNGS of the CSF of patients living with and without HIV with suspected CNS infections. The pathogens causing CNS infections were concurrently identified using both mNGS and traditional detection methods. The spectrum of pathogens identified was compared between the two groups., Results: Overall, 173 patients (140 with and 33 without HIV) with suspected CNS infection were enrolled in our study. In total, 106 (75.7%) patients with and 16 (48.5%) patients without HIV tested positive with mNGS (p = 0.002). Among the enrolled patients, 71 (50.7%) with HIV and five (15.2%) without HIV tested positive for two or more pathogens (p < 0.001). Patients with HIV had significantly higher proportions of fungus (20.7% vs. 3.0%, p = 0.016) and DNA virus (59.3% vs. 21.2%, p < 0.001) than those without HIV. Epstein-Barr virus (33.6%) was the most commonly identified potential pathogen in the CSF of patients living with HIV using mNGS, followed by cytomegalovirus (20.7%) and torque teno virus (13.8%). The top three causative pathogens identified in patients without HIV were Streptococcus (18.2%), Epstein-Barr virus (12.1%), and Mycobacterium tuberculosis (9.1%). In total, 113 patients living with HIV were diagnosed as having CNS infections. The rate of pathogen detection in people living with HIV with a CNS infection was significantly higher with mNGS than with conventional methods (93.8% vs. 15.0%, p < 0.001)., Conclusion: CSF microbiome profiles differ between patients living with and without HIV with suspected CNS infection. mNGS is a powerful tool for the diagnosis of CNS infection among people living with HIV, especially in those with mixed infections., (© 2024 British HIV Association.)

Objectives: Incidence rates (IRs) of Staphylococcus aureus bacteraemia (SAB) are known to be higher in HIV-infected individuals than in the general population, but have not been assessed in the era of highly active antiretroviral therapy., Methods: From 1 January 1995 to 31 December 2007, all Danish HIV-infected individuals (n=4871) and population controls (n=92 116) matched on age and sex were enrolled in a cohort and all cases of SAB were registered. IRs and risk factors were estimated using time-updated Poisson regression analysis., Results: We identified 329 cases of SAB in 284 individuals, of whom 132 individuals were infected with HIV and 152 were not [crude IR ratio (IRR) 24.2; 95% confidence interval (CI) 19.5-30.0, for HIV-infected vs. non-HIV-infected individuals]. Over time, IR declined for HIV-infected individuals (IRR 0.40). Injecting drug users (IDUs) had the highest incidence and the smallest decline in IR, while men who have sex with men (MSM) had the largest decline over time. Among HIV-infected individuals, a latest CD4 count <100 cells/μL was the strongest independent predictor of SAB (IRR 10.2). Additionally, HIV transmission group was associated with risk of SAB. MSM were more likely to have hospital-acquired SAB, a low CD4 cell count and AIDS at the time of HIV acquisition compared with IDUs., Conclusions: We found that the incidence of SAB among HIV-infected individuals declined during the study period, but remained higher than that among HIV-uninfected individuals. There was an unevenly distributed burden of SAB among HIV transmission groups (IDU>MSM). Low CD4 cell count and IDU were strong predictors of SAB among HIV-infected individuals., (© 2011 British HIV Association.)

Background: Risks for methicillin-resistant Staphylococcus aureus (MRSA) among those with HIV infection have been found to vary, and the epidemiology of USA-300 community-acquired (CA) MRSA has not been adequately described., Methods: We conducted a retrospective review of HIV-infected out-patients from January 2002 to December 2007 and employed multivariate logistic regression (MLR) to identify risks for MRSA colonization or infection. Pulsed-field gel electrophoresis (PFGE) was used to identify USA-300 strains., Results: Seventy-two (8%) of 900 HIV-infected patients were colonized or infected with MRSA. MLR identified antibiotic exposure within the past year [odds ratio (OR) 3.4; 95% confidence interval (CI) 1.5-7.7] and nadir CD4 count <200 cells/microL (OR 2.5; 95% CI 1.2-5.3) as risks for MRSA colonization or infection. Receipt of antiretroviral therapy (ART) within the past year was associated with decreased risk (OR 0.16; 95% CI 0.07-0.4). Eighty-nine percent of available strains were USA-300. MLR identified skin or soft tissue infection (SSTI) as the only predictor for infection with USA-300 (OR 5.9; 95% CI 1.4-24.3)., Conclusion: Significant risks for MRSA among HIV-infected patients were CD4 count nadir <200 cells/microL and antibiotic exposure. Only the presence of an SSTI was associated with having USA-300, and thus the use of patient characteristics to predict those with USA-300 was limited. In addition, ART within the previous year significantly reduced the risk of MRSA colonization or infection.

Objectives: Despite a recent decrease, bacterial pneumonia (BP) is still the most common admission diagnosis in HIV patients. We analyse BP incidence, characteristics and prevention measures., Methods: Observational study of all patients hospitalized for BP in a tertiary hospital in Barcelona, Spain, from January 2000 to December 2005. Demographic and HIV-related data, BP risk factors, characteristics of BP and outcomes are analysed., Results: One hundred and eighty-six BP episodes in 161 patients were included; patients were mainly male (73.7%) and intravenous drug users (73.7%). A decrease in BP incidence was seen during the study period, especially in vaccinated patients. The most commonly isolated microorganism was Streptococcus pneumoniae (31.7%), followed by Legionella pneumophila (5.9%). Legionella pneumophila was more likely in patients with undetectable viral load, higher CD4 cell counts or prior vaccination. Highly active antiretroviral therapy, cotrimoxazole prophylaxis and pneumococcal vaccination did not have a significant influence on bacteraemia rate, in-hospital complications or BP mortality. High Pneumonia Severity Index (PSI) predicted mortality accurately [relative risk 15.2, 95% confidence interval 3.2-71.7; P=0.001]. Mortality was 9.1%, but was significantly higher in patients with CD4 counts under 200 cells/microL (P=0.022)., Conclusions: A decline in BP incidence was seen during the study period. Combining CD4 cell count and PSI score could become a good strategy in deciding which patients have to be hospitalized.

Objectives: HIV-infected patients responding to combination antiretroviral therapy (ART) after experiencing severe immunodeficiency may exhibit persistent immune defects and occasionally experience opportunistic infections (OIs) despite increased CD4 T-cell counts. The investigation of immune defects in such patients was examined in this study., Methods: CD4 effector memory T-cell (T(em)-cell) function [assessed by blood cytomegalovirus (CMV) interferon-gamma (IFN-gamma) enzyme-linked immunosorbent spot-forming cell assay (ELISPOT) counts] and B-cell dysregulation [assessed by serum immunoglobulin A (IgA) and IgE levels] were examined in 27 patients with increased CD4 T-cell counts after receiving ART for over 2 years. Two of these patients and one other had developed OIs on ART and are described in detail., Results: Serum levels of IgA and IgE were higher than reference intervals (P<0.001) and CMV IFN-gamma ELISPOT counts were lower than those in non-HIV-infected controls (P<0.001) in the HIV-infected patients. Low CMV IFN-gamma ELISPOT counts were associated with high IgA levels (r=-0.5, P=0.01, Spearman's correlation test) and segregated with high IgE levels (P=0.06, Fisher's test). CMV IFN-gamma ELISPOT counts and serum IgA and IgE levels did not change significantly over a median time of 35 (range 8-60) months after the first measurement, whereas CD4 T-cell counts increased. All three patients who experienced OIs had repeatedly low CMV IFN-gamma ELISPOT counts and increased serum levels of IgA and/or IgE., Conclusion: Low CD4 T(em)-cell function and B-cell dysregulation are immune defects that may persist independently of changes in the CD4 T-cell count in HIV-1-infected patients responding to ART and are associated with an increased risk of developing an OI.

Several studies from developed countries have documented the association between trimethoprim-sulfamethoxazole prophylaxis failure and mutations in the Pneumocystis jirovecii gene coding for dihydropteroate synthase (DHPS). DNA was extracted from Giemsa-stained smears of 70 patients with P. jirovecii pneumonia seen in Porto Alegre, Brazil, from 1997 to 2004. Successful PCR amplification of the DHPS locus was obtained in 57 of 70 cases (81.4%), including five cases (8.7%) that had used sulfa prophylaxis. No DHPS gene mutations were seen. These results suggest that DHPS mutations are currently as rare in Brazil as in other developing countries.

Objective: To describe the incidence and risk factors of bacterial pneumonia occurring in patients treated with antiretrovirals., Methods: In the ongoing APROCO (Anti-proteases) cohort, 1281 patients at the initiation of a protease inhibitor (PI)-containing antiretroviral regimen were enrolled from 1997-1999. All events requiring hospitalization during follow up are recorded. Of these, bacterial pneumonia was defined as the occurrence of a new pulmonary infiltrate with fever and either evidence of a bacteriological cause (definite cases) or favourable outcome with antimicrobial therapy (presumptive cases). Risk factors of bacterial pneumonia were studied using survival analyses., Results: During a median follow up of 43 months, 29 patients had at least one episode of bacterial pneumonia, giving an incidence of 0.8/100 patient years. The 11 definite cases were attributable to Streptococcus pneumoniae (n=9), Legionella pneumophila (n=1) and Haemophilus influenzae (n=1). In multivariate analysis, bacterial pneumonia was significantly more frequent in older patients, injecting drug users, patients having a CD4 cell count>500 cells/microL at baseline and patients who initiated PI therapy with nonboosted saquinavir. It was significantly less frequent in nonsmokers. The occurrence of bacterial pneumonia was also associated with lower self-reported adherence to antiretroviral therapy and to higher plasma HIV-1 RNA levels during follow-up., Conclusions: Bacterial pneumonia occurs rarely in patients treated with a PI-containing regimen and may be associated with virological failure.

Pneumocystis, an AIDS-associated opportunistic pathogen of the lung has some unusual features. This article focuses on work done by my group to understand the organism's distinct sterols. Although Pneumocystis is closely related to fungi, it lacks the major fungal sterol, ergosterol. Several delta(7) 24-alkysterols synthesized by P. carinii are the same as those reported in some basidiomycete rust fungi. The 24-alkylsterols are synthesized by the action of S-adenosyl-L-methionine:C-24 sterol methyl transferase (SAM:SMT). Fungal SAM:SMT enzymes normally transfer only one methyl group to the C-24 position of the sterol side chain and the cells accumulate C28 24-alkylsterols. In contrast, the P. carinii SAM:SMT and those of some plants catalyze one or two methyl transfer reactions producing both C28 and C29 24-alkylsterols. However, unlike most fungi, plants, and the kinetoplastid flagellates Leishmania and Trypanosoma cruzi, P. carinii does not appear to form double bonds at C-5 of the sterol nucleus and C-22 of the sterol side chain. Furthermore, the P. carinii SAM:SMT substrate preference for C30 lanosterol differs from that of homologous enzymes in any other organisms studied. C31 24-Methylenelanosterol and C32 pneumocysterol, products of SAM:SMT activity on lanosterol, can accumulate in high amounts in some, but not all, human-derived Pneumocystis jiroveci populations.

Background: Cellulitis and soft tissue infection are underestimated complications of HIV disease., Patients and Methods: Sixty-seven bacteriologically proven consecutive episodes were identified among 2221 HIV-infected patients hospitalized in a 10-year period, and assessed according to several epidemiological, microbiological and clinical variables., Results: Staphylococcus aureus was the most frequently cultured pathogen (50% of 92 isolates), followed by Pseudomonas spp., Escherichia coli and Streptococcus pyogenes; a polymicrobial infection was present in 38.1% of episodes. Drug addiction (p < 0.003) and male gender (p < 0.04) were significantly associated with the occurrence of these complications, which were community-acquired in 83.6% of cases. While a remarkable variation in the severity of underlying immunodeficiency was shown, hematogenous dissemination occurred in 25.4% of episodes, and proved significantly related to a low CD4+ lymphocyte count, and neutropenia. A 21.7% methicillin-resistance rate was shown among S. aureus isolates. All episodes were favorably treated in 5-16 days, in over 60% of cases with associated beta-lactam-aminglycoside antibiotics; a recurrence of staphylococcal cellulitis occurred in four patients only., Conclusion: Skin and soft tissue infections are continuing causes of morbidity in HIV-infected patients, even in the highly active antiretroviral therapy era.

Objectives: To determine whether systemic or deep fungal infections can be prevented, a double-blind, placebo-controlled, phase III trial of itraconazole prophylaxis was undertaken in HIV-infected patients., Methods: HIV-1 infected patients with CD4 counts < 300 cells/microL were treated with itraconazole (200 mg per day) or matching placebo and followed for 2 years. Development of deep fungal infections, episodes of mucocutaneous candidiasis, change in CD4 count, survival and safety data were collected at each study visit., Results: Three hundred and seventy-four patients received study medication, 187 were given itraconazole and 187 matching placebo. Time to development of deep fungal infection did not differ between groups, in an intention to treat analysis. Low CD4 cell count and prior use of Pneumocystis carinii pneumonia (PCP) prophylaxis were significantly associated with a more rapid development of deep fungal infection (P = 0.044 and 0.017, respectively). Itraconazole treatment significantly reduced the incidence of oral candidosis (25% vs. 48% P < 0.001) and time to development of oral candidosis (508 vs. 413 days, P < 0.001) but not the number of deep fungal infections (11 vs. 13). Survival did not differ significantly between groups (nine vs. 14 deaths). CD4 counts decreased significantly over time in both study arms. Adverse events did not differ between groups; 20% vs. 23% stopped study medication due to an adverse experience., Conclusions: Although itraconazole prophylaxis significantly reduced the number and time to development of oral candidosis, too few episodes of deep fungal infection were noted to determine whether itraconazole prophylaxis was effective for this condition. Chronic itraconazole treatment is well tolerated in HIV-infected patients with marked immunodeficiency.

To test the viability of Pneumocystis carinii f. sp. hominis, an RT-PCR assay that employs specific primers from the Heat Shock Protein 70 gene was developed. Using this method, the viability of P.c. hominis in bronchoalveolar lavage fluids from patients developing PCP and in the environment of PCP patients was established.

Objective: To investigate the role of Mycoplasma fermentans in lower respiratory tract disease of HIV-positive patients., Methods: A polymerase chain reaction (PCR) assay was used to detect M. fermentans in broncho-alveolar lavage (BAL) fluid and peripheral blood mononuclear cells (PBMCs) collected from 78 hospitalized HIV-positive patients with lower respiratory tract disease (the index group). BAL specimens were also assessed from two control groups; 25 HIV-positive patients without respiratory symptoms and 46 patients with a respiratory illness who did not have risk factors for HIV., Results: Seventy-one (91%) of the 78 patients who comprised the index group had AIDS. Sixty-one patients provided BAL and PBMC specimens; 16 provided a BAL specimen and one only a PBMC specimen; 15 (25%) of the 61 patients had M. fermentans positive BAL fluid, of whom 10 (67%) also had a positive PBMC specimen. In contrast, of the 46 patients who had a negative BAL fluid, only three (6.4%) had a positive PBMC sample (P < 0.00001 Fisher's exact test). Overall, 21 (27%) of 77 patients had M. fermentans positive BAL fluid. Of these positive patients, 16 also had another microorganism in the BAL fluid and for five patients M. fermentans was detected alone. Compared with patients in the index group, none of the 46 BAL fluid specimens from patients at low risk of HIV infection was M. fermentans positive (P < 0.001, chi2 15.13). Two (8%) of the 25 HIV-positive patients without respiratory symptoms had a M. fermentans positive BAL fluid, positivity that was also statistically different from the index group (P = 0.045, chi2 4.01)., Conclusions: M. fermentans frequently invades the lower respiratory tract of AIDS patients as an opportunist and may cause disease in some.

Multiple copies of a gene may lead to difficulty in the interpretation of typing results because polymorphism of the copies may wrongly lead to the conclusion that different types are present in a specimen. To determine the copy number per genome of the nuclear rDNA and beta-tubulin genes analyzed for the typing of Pneumocystis carinii f. sp. hominis, we developed a strategy based on the use of the same multicompetitor molecule in two different quantitative-competitive PCRs, one for the gene under study and the other for a reference single copy gene, allowing direct comparison of the results of both PCRs. Control experiments showed that the strategy was sensitive enough to detect duplication of a gene. The copy number of the nuclear rDNA operon was determined by amplification of the intron of the 26S rDNA gene and that of the beta-tubulin by amplification of the region surrounding the intron no. 6. The method was first tested on P. c. carinii, the special form commonly infecting rats. Pneumocystis c. carinii was found to contain a single copy of the rDNA operon. The method was then applied to P. c. hominis. The results confirmed that P. c. hominis genome contains a single copy of the nuclear rDNA and beta-tubulin genes.

In recent years the clinical face of the Acquired Immune Deficiency Syndrome has changed significantly as a consequence of use of prophylaxis against Pneumocystis carinii pneumonia and combination antiretroviral therapy. In this context several opportunistic pathogens have emerged as causes of clinically important disease. Many of these infective agents have previously been defined by specific geographical locations. Their clinical presentation frequently mimics other (non) opportunistic infections with which they may co-exist. The diagnosis is frequently delayed as the diagnostic possibility may not be in the clinician's differential diagnosis. Invasive procedures are frequently required in order to secure a diagnosis. Despite treatment, prognosis is often poor. Clinicians should be aware of these opportunistic pathogens in order that a timely diagnosis may be made and appropriate therapy given.

Most species of Penicillium are considered relatively benign with respect to causing human disease. However, one species, P. marneffei, has emerged as a significant pathogen particularly among individuals who live in Southeast Asia and are concurrently infected with the human immunodeficiency virus. While environmental and epidemiological studies have yet to resolve the reason for the heightened virulence of P. marneffi, one characteristic does distinguish this fungus from other Penicillium species. Whereas the latter grow as monomorphic moulds bearing typical asexual propagules (conidia), P. marneffei is thermally dimorphic. At room temperature, P. marneffei exhibits the morphology characteristic of the genus. In contrast to other Penicillia, though, P. marneffei grows as a yeast-like entity (arthroconidium) when found in diseased tissue or cultivated at 37 degrees C. Studies in our laboratory have focused on the differential gene expression between the mould and arthroconidial phases. Many of the genes whose expression differs during mould-to-arthrocondium transition are related to energy metabolism. A better understanding of gene expression during morphogenesis in P. marneffei may help detect unique target sites or cellular processes that can be exploited in the development of antifungal agents or immunomodulation therapies.

To understand the way of reinfection of Pneumocystis carinii we have analyzed the genetic variation at the internal transcribed spacer (ITS) in DNA samples from bronchoalveolar lavage fluid of Italian HIV patients who had multiple episodes of P.carinii pneumonia. The presence of the same and/or a new type in both episodes suggest the possible occurrence of both reactivation of a previously acquired infection and reinfection from an exogenous source. Furthermore the occurrence of two different types in the same episode indicate that a mixed infection is common.

Oropharyngeal washings (Ophs) from 27 HIV infected patients (18 with P. carinii pneumonia, PCP, and 9 without PCP) were examined for P. carinii using morphological staining and DNA amplification with PCR-SHELA and nested PCR methods. The comparison of these techniques shows that 1. the amplification of P. carinii DNA is more sensitive than (and as specific as) morphological staining; 2. PCR-SHELA is less sensitive than (and as specific as) nested PCR.

P.carinii molecular epidemiology appears a new interesting investigational field to understand distribution and incidence of isolates from different geographical locations. Recently a typing system, the Type Specific Oligoblotting (TSO) based on 6 different sequences of the Internal Transcribed Spacers (ITSs) of P.carinii rRNA has been developed [1]. By using P.carinii ITSs nested PCR followed by TSO hybridization we have typed 55 lung derived specimens collected in Italy, The Netherlands and sub-Saharian Africa from pts with microscopically detected P.carinii pneumonia.