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      Pneumocystis jirovecii Pneumonia in Tropical and Low and Middle Income Countries: A Systematic Review and Meta-Regression

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          Abstract

          Objective

          Pneumocystis jirovecii pneumonia (PCP), the commonest opportunistic infection in HIV-infected patients in the developed world, is less commonly described in tropical and low and middle income countries (LMIC). We sought to investigate predictors of PCP in these settings.

          Design

          Systematic review and meta-regression.

          Methods

          Meta-regression of predictors of PCP diagnosis (33 studies). Qualitative and quantitative assessment of recorded CD4 counts, receipt of prophylaxis and antiretrovirals, sensitivity and specificity of clinical signs and symptoms for PCP, co-infection with other pathogens, and case fatality (117 studies).

          Results

          The most significant predictor of PCP was per capita Gross Domestic Product, which showed strong linear association with odds of PCP diagnosis (p<0.0001). This was not explained by study design or diagnostic quality. Geographical area, population age, study setting and year of study also contributed to risk of PCP. Co-infection was common (444 episodes/1425 PCP cases), frequently with virulent organisms. The predictive value of symptoms, signs or simple tests in LMIC settings for diagnosis of PCP was poor. Case fatality was >30%; treatment was largely appropriate. Prophylaxis appeared to reduce the risk for development of PCP, however 24% of children with PCP were receiving prophylaxis. CD4 counts at presentation with PCP were usually <200×10 3/ml.

          Conclusions

          There is a positive relationship between GDP and risk of PCP diagnosis. Although failure to diagnose infection in poorer countries may contribute to this, we also hypothesise that poverty exposes at-risk patients to a wide range of infections and that the relatively non-pathogenic P. jirovecii is therefore under-represented. As LMIC develop economically they eliminate the conditions underlying transmission of virulent infection: P. jirovecii, ubiquitous in all settings, then becomes a greater relative threat.

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          Most cited references120

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          Pneumocystis pneumonia.

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            Current Epidemiology of Pneumocystis Pneumonia

            Pneumocystis pneumonia (PCP), which is caused by Pneumocystis jirovecii (formerly P. carinii f. sp. hominis), is frequently the first serious illness encountered by HIV-infected persons. During the early years of the AIDS epidemic, PCP was the AIDS-defining illness for as many as two thirds of patients in the United States. Although a decline in incidence of PCP occurred during the era of highly active antiretroviral therapy (HAART), PCP remains the most common serious opportunistic illness in HIV-infected persons ( 1 ). Patients in the developing world without access to PCP prophylaxis or antiretroviral drugs remain at high risk, and PCP continues to develop in certain groups in industrialized countries. The drug of choice for treatment and chemoprophylaxis of PCP is trimethoprim-sulfamethoxazole (TMP-SMX). In recent years, antimicrobial drug resistance has emerged as a possible cause of failure of patients to respond to TMP-SMX. Investigators have demonstrated an association between exposure to sulfa drugs and mutations in the dihydropteroate synthase (DHPS) gene of P. jirovecii, but the relationship between these mutations and treatment (or prophylaxis) failure is unclear. Understanding whether DHPS mutations cause antimicrobial drug resistance is important in guiding clinicians who care for patients with PCP. A series of articles in this issue of Emerging Infectious Diseases highlights the continuing importance of PCP, the potential for drug resistance, and laboratory techniques that can be used to study the problem. We hope that these articles will stimulate interest in exploring the relationship between DHPS mutations and resistance of P. jirovecii to sulfa-containing drugs and in assessing DHPS mutations as possible causes of treatment failure in patients with PCP. In this introductory article, we summarize the changes in incidence of PCP since the introduction of HAART, discuss groups at risk for PCP in developing and industrialized nations, and examine possible future trends in the disease. A data collection form has been included online with this series of articles to assist in the collection of appropriate and standardized data from patients with PCP and to facilitate comparing and pooling data from different centers (Appendix). PCP before HAART The first clinical cases of PCP were reported during World War II in orphanages in Europe. These cases of "plasma cell pneumonia" were common among malnourished children and were later reported in children in Iranian orphanages. The disease was then recognized in patients who were immunocompromised because of malignancies, immunosuppressive therapy, or congenital immunodeficiencies. Solid organ transplantation increased the number of patients at risk for PCP, although rates diminished after chemoprophylaxis was introduced. Without chemoprophylaxis, rates of PCP are 5%–25% in transplant patients, 2%–6% in patients with collagen vascular disease, and 1%–25% in patients with cancer. Defects in CD4+ lymphocytes are a primary risk factor for developing PCP, but the immune response to Pneumocystis is complex. CD8+ lymphocytes seem to be important in Pneumocystis clearance, and defects in B-cells and antibody production may also predispose to PCP. The beginning of the AIDS epidemic in the early 1980s shifted the incidence of PCP from a rare disease to a more common pneumonia. Clusters of PCP cases in homosexual men and intravenous drug users were one of the first indications of the HIV epidemic ( 2 ). PCP rapidly became the leading AIDS-defining diagnosis in HIV-infected patients. In the initial stages of the epidemic, PCP rates were as high as 20 per 100 person-years for those with CD4+ cell counts 5,000 homosexual men since 1984 ( 6 ). Of these, 2,195 were either HIV-infected at time of enrollment or seroconverted to HIV during the study. Opportunistic infection rates were compared for the HAART era (1996–1998) and the era of antiretroviral monotherapy (1990–1992) ( 7 ). For persons who seroconverted during the study period, the relative hazard for development of PCP from seroconversion to initial AIDS-defining opportunistic infection was 0.06 during the HAART era compared to the time of monotherapy. For those already diagnosed with AIDS, the study found a hazard of 0.16, which demonstrated a dramatically lower risk for PCP during the HAART era. In Europe, the EuroSIDA study has followed a cohort of >8,500 HIV-infected patients. The investigators examined changes in incidence of AIDS-defining illnesses before and after HAART was introduced and found results similar to those in North America ( 8 ). PCP cases decreased over time (1994–1998). Incidence of PCP fell from 4.9 cases per 100 person-years before March 1995 to 0.3 cases per 100 person-years after March 1998 ( 9 ). Occurrence in Relation to PCP Prophylaxis PCP still occurs in industrialized nations despite the availability of HAART and anti-Pneumocystis prophylaxis. ASD investigated the history of prescriptions for PCP prophylaxis in HIV-infected adults in whom developed PCP from 1999 through 2001 (Figure 2). Almost 44% of PCP cases occurred in patients not receiving medical care, most of whom were probably not known to be HIV-infected. Forty-one percent of patients were prescribed prophylaxis but did not adhere to treatment, or PCP developed despite their taking medications appropriately. Possible explanations for PCP in the "breakthrough" group include the development of drug-resistant Pneumocystis or decreased efficacy of prophylaxis in those with low CD4+ cell counts. An additional 9.6% of patients were under medical care and should have received prophylaxis based on current recommendations, but had not been prescribed prophylaxis by their providers. Five percent of patients were under care but did not meet criteria for prophylaxis. Figure 2 Classification of Pneumocystis pneumonia cases from 1999–2001, CDC Adult and Adolescent Spectrum of HIV Disease Project, n = 1,073. Risk Factors A CD4+ cell count 200 cells/µL, the risk for PCP decreases sufficiently to safely discontinue both primary and secondary prophylaxis ( 9 , 11 ). Those in whom PCP develops while on HAART typically have low CD4+ cell levels. ASD found that the median CD4+ cell count in persons with PCP while on HAART was extremely low (29 cells/µL), although the count was somewhat higher than for those not on HAART (13 cells/µL) ( 1 ). The EuroSIDA study reported that persons on HAART in whom PCP developed had a median CD4+ cell count of 30 cells/µL, identical to those with PCP who were not receiving HAART ( 8 ). Patients without improvement in their CD4+ cell count despite use of HAART remain at risk for PCP, and PCP still rarely occurs in persons with CD4+ cell counts >200 cells/µL. Other clinical factors such as sex, race or ethnicity, and HIV transmission category have been examined as risk factors for PCP. Men and women appear to have an equivalent risk for PCP ( 12 ). One study demonstrated that African Americans have approximately one third the risk for PCP as white persons ( 10 ), but this finding has not been replicated ( 12 ). PCP risk according to HIV transmission category is also debated. One autopsy study found that PCP was less common in intravenous drug users than in other risk groups ( 13 ). Kaplan et al. found a slightly increased risk for those men who had sex with men and were intravenous drug users, but risk was equivalent in other transmission categories ( 12 ). Risk for Pneumocystis Colonization Although PCP cases have declined, polymerase chain reaction (PCR) has led to the discovery of Pneumocystis DNA in asymptomatic persons. Pneumocystis in respiratory specimens from persons who do not have signs or symptoms of clinical infection and who do not progress to infection has been defined as colonization or subclinical carriage. Often, Pneumocystis DNA is detected only by PCR, and the organism is not seen on routine histochemical staining. The clinical significance of Pneumocystis in respiratory specimens and the viability of organisms detected only by PCR are unknown. However, colonization may be important for several reasons. Pneumocystis colonization may increase the risk for progression to PCP, carriers of the organism may transmit infection to others, and latent infection may lead to inflammation that is detrimental to the lung. Most healthy persons do not have detectable Pneumocystis in respiratory specimens, but rates of colonization may be as high as 69% in HIV-infected persons ( 14 ). Recent evidence suggests that non–HIV-infected persons may also be colonized with Pneumocystis, thus increasing the potential number of persons affected ( 15 ). PCP in Children in Industrialized Countries Incidence Early in the HIV epidemic, PCP occurred in HIV-infected children at a rate of 1.3 cases per 100 child-years from infancy to adolescence and was as high as 9.5 cases per 100 child-years in the first year of life ( 16 , 17 ). In the 1990s, pediatric HIV infection decreased, primarily as a result of improved prenatal HIV testing and use of HIV treatment to prevent vertical transmission of the virus. The Pediatric Spectrum of Disease (PSD) study found significant decreases in the rates of most opportunistic infections in HIV-infected children during the HAART era (Figure 3). PCP cases declined significantly from 1992 to 1997, with an increase in the rate of decline after 1995, presumably from HAART ( 1 ). Because widespread use of HAART for children has occurred more recently than for adults, the full effect of HAART on pediatric PCP likely has not yet been realized. Figure 3 Yearly opportunistic infection rates per 1,000 HIV-infected children, CDC Pediatric Spectrum of Disease Project, 1994–2001. Bacterial, bacterial infections; CMV, cytomegalovirus; HAART, highly active antiretroviral therapy; LIP, lymphocytic interstitial pneumonia; MAC, Mycobacterium avium complex; PCP, Pneumocystis pneumonia. Incidence rates were calculated per 1,000 children at risk each year. All trends were significant at p 10 years) except for the 15 months ( 41 ). The largest autopsy series examined 180 HIV-infected children in Zambia ( 38 ). Twenty-nine percent of the children died of PCP, making PCP the third leading cause of death overall. Among children 40% among HIV-infected children hospitalized with pneumonia ( 42 , 43 ). Ruffini studied children from 2 to 24 months of age with pneumonia and found that 48.6% had PCP ( 43 ). Madhi found that in 231 episodes of pneumonia in HIV-infected children, 101 (43.7%) were due to PCP ( 39 ). PCP was most common in infants 10,000 copies/mL after 48 weeks of treatment ( 45 ). In the EuroSIDA cohort, an increasing proportion of HIV-infected patients have been exposed to all classes of antiretrovirals, with 47% of their cohort exposed to nucleoside reverse transcriptase inhibitors, protease inhibitors, and non-nucleoside reverse transcriptase inhibitors by 2001 ( 45 ). Of those patients in the cohort with multidrug-resistant HIV who received salvage regimens, a new AIDS-defining opportunistic infection developed in 11%. Growing transmission of resistant HIV is also likely. If new drugs do not become available, the number of patients with resistant virus and opportunistic infections, including PCP, will continue to climb. Not only is HIV developing resistance, but Pneumocystis may also develop resistance to standard prophylaxis and treatment regimens. Many researchers have reported mutations of Pneumocystis in response to use of sulfa- or sulfone-containing anti-Pneumocystis regimens. Whether these mutations increase the likelihood of prophylaxis or treatment failure is unclear and is reviewed in other papers in this series. Conclusion Despite the declines in death and disease from HIV in the United States and western Europe, PCP remains an important disease and is unlikely to be eradicated. In industrialized nations, PCP still occurs in those not yet diagnosed with HIV or not in medical care, those not receiving PCP prophylaxis, and those not taking or not responding to HAART. Resistance in HIV and Pneumocystis may contribute to future increases in PCP incidence. In most developing nations, AIDS patients are at high risk for PCP. In sub-Saharan Africa, the effect of disease from PCP in infants and children is high and is probably greater in adults than previously recognized. Colonization rates among both HIV-infected and non–HIV-infected populations may also be substantial. Better understanding of the epidemiology and transmission of PCP, and improved efforts in prevention and treatment, are needed. Supplementary Material Appendix PNEUMOCYSTIS CARINII: SURVEILLANCE FOR DRUG-RESISTANCE PCP CHART ABSTRACTION FORM.
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              Epidemiology of human pulmonary infection with nontuberculous mycobacteria.

              A great deal of study has gone into the assessment of the epidemiology of NTM infection and disease in many different parts of the world. Review of the available studies provides insight into the frequency of this clinical problem as well as important limitations in current data. Study methods have varied greatly, undoubtedly leading to differing biases. In general, reported rates of infection and disease are likely underestimates, with the former probably less accurate than the latter, given that people without significant symptoms are not likely to have intensive investigations to detect infection. Pulmonary NTM is a problem with differing rates in various parts of the world. North American rates of infection and disease have been reported to range from approximately 1-15 per 100,000 and 0.1-2 per 100,000, respectively (see Table 1). Rates have been observed to increase with coincident decreases in TB. MAC has been reported most commonly, followed by rapid growers and M kansasii. Generally similar rates have been reported in European studies, with the exception of extremely high rates in an area of the Czech Republic where mining is the dominant industry (see Table 2). These studies have also shown marked geographic variability in prevalence. The only available population-based studies have been in South Africa and report extremely high rates of infection, three orders of magnitude greater than studies from other parts of the world (see Table 3). This undoubtedly reflects the select population with an extremely high rate of TB and resultant bronchiectasis leading to NTM infection. Rates in Japan and Australia were similar to those reported in Europe and North America and also show significant increases over time (see Table 3). Specific risk factors have been identified in several studies. CF and HIV, mentioned above, are two important high-risk groups. Other important factors include underlying chronic lung disease, work in the mining industry, warm climate, advancing age, and male sex. Aside from HIV and CF, mining with associated high rates of pneumoconiosis and previous TB may be the most important historically, reported in studies worldwide [63]. A recurring observation is the increase in rates of infection and disease. The reason for this is unclear but may be caused by any of several contributing factors. The possibility exists that the apparent increase is either spurious or less significant than studies would suggest. Changes in clinician awareness leading to increased investigations, or laboratory methods leading to isolation and identification of previously unnoticed organisms, could play a role in this trend, and studies have been published that support [67] and refute [31] this argument. We believe such factors may contribute to but do not explain the significant increases that have been observed. A true increase could be related to the host, the pathogen, or some interaction between the two. Host changes leading to increased susceptibility could play an important role, with increased numbers of patients with inadequate defenses from diseases such as HIV infection, malignancy, or simply advanced age [31]. An increase in susceptibility could also relate to the decrease in infection with two other mycobacteria. It has been speculated that infection with TB [29,38] and Bacillus Calmette-Guerin (BCG) [19,68] may provide cross-immunity protecting against NTM infection. Many investigations have observed decreasing rates of TB concomitant with the increases in NTM. In addition, studies from Sweden [68] and the Czech Republic [19] have found that children who were not vaccinated with BCG had a far higher rate of extrapulmonary NTM infection. Potential changes in the pathogens include increases in NTM virulence, and it has been argued that this should be considered as a possible contributing factor [69]. Finally, an interaction between the host and pathogen could involve a major increase in pathogen exposure or potential inoculum size. This may be occurring secondary to the increase in popularity of showering as a form of bathing [66], a habit that greatly increases respiratory exposure to water contaminants. Several limitations of our review should be noted. We reviewed English-language reports and abstracts, probably leading to fewer data from non-English speaking regions, which may explain the paucity of studies from Africa, Eastern Europe, and most Asian nations. The heterogeneity of study methods in identifying cases and the lack of a uniformly applied definition of disease makes it difficult to compare rates between studies. Finally, the lack of systematic reporting of NTM infection in most nations limits the ability to derive accurate estimates of infection and disease. Regardless, there are more than adequate data to conclude that NTM disease rates vary widely depending on population and geographic location. NTM disease is clearly a major problem in certain groups, including patients with underlying lung disease and also in individuals with impaired immunity. The rates of NTM infection and disease are increasing, so the problem will likely continue to grow and become a far more important issue than current rates suggest.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2013
                2 August 2013
                : 8
                : 8
                : e69969
                Affiliations
                [1 ]Wellcome Trust Centre for Research in Clinical Tropical Medicine, Department of Medicine, Imperial College London, London, United Kingdom
                [2 ]Clinical Infectious Disease Research Initiative, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
                [3 ]Statistical Advisory Service, Imperial College London, London, United Kingdom
                [4 ]World Health Organisation Western Pacific Regional Office, Manila, Philippines
                [5 ]Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
                [6 ]Research Department of Infection and Population Health, Institute of Epidemiology and Healthcare, University College London, London, United Kingdom
                Vanderbilt University, United States of America
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: DML MXR CDJ RFM. Performed the experiments: DML RFM. Analyzed the data: DML FG. Wrote the paper: DML MXR CDJ RFM.

                [¤]

                Current address: Oxford Policy Management, Oxford, United Kingdom

                Article
                PONE-D-13-11290
                10.1371/journal.pone.0069969
                3732248
                23936365
                aa9202c0-9b99-48f3-b9d5-0f18daa9dc8d
                Copyright @ 2013

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 16 March 2013
                : 12 June 2013
                Page count
                Pages: 16
                Funding
                Wellcome Trust (Grant WT087754 to Dr DML). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology
                Population Biology
                Epidemiology
                Economic Epidemiology
                Infectious Disease Epidemiology
                Medicine
                Clinical Research Design
                Meta-Analyses
                Systematic Reviews
                Epidemiology
                Economic Epidemiology
                Infectious Disease Epidemiology
                Infectious Diseases
                Fungal Diseases
                Pneumocystis
                Viral Diseases
                HIV
                HIV opportunistic infections
                Non-Clinical Medicine
                Socioeconomic Aspects of Health
                Public Health
                Socioeconomic Aspects of Health

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                Uncategorized

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