1
|
Tsvetkova N, Harizanov R, Rainova I, Ivanova A, Yancheva-Petrova N. Molecular Analysis of Dihydropteroate Synthase Gene Mutations in Pneumocystis jirovecii Isolates among Bulgarian Patients with Pneumocystis Pneumonia. Int J Mol Sci 2023; 24:16927. [PMID: 38069248 PMCID: PMC10707730 DOI: 10.3390/ijms242316927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Pneumocystis jirovecii pneumonia (PCP) is a significant cause of morbidity and mortality in immunocompromised people. The widespread use of trimethoprim-sulfamethoxazole (TMP-SMZ) for the treatment and prophylaxis of opportunistic infections (including PCP) has led to an increased selection of TMP-SMZ-resistant microorganisms. Sulfa/sulfone resistance has been demonstrated to result from specific point mutations in the DHPS gene. This study aims to investigate the presence of DHPS gene mutations among P. jirovecii isolates from Bulgarian patients with PCP. A total of 326 patients were examined via real-time PCR targeting the P. jirovecii mitochondrial large subunit rRNA gene and further at the DHPS locus. P. jirovecii DNA was detected in 50 (15.34%) specimens. A 370 bp DHPS locus fragment was successfully amplified in 21 samples from 19 PCP-positive patients, which was then purified, sequenced, and used for phylogenetic analysis. Based on the sequencing analysis, all (n = 21) P. jirovecii isolates showed DHPS genotype 1 (the wild type, with the nucleotide sequence ACA CGG CCT at codons 55, 56, and 57, respectively). In conclusion, infections caused by P. jirovecii mutants potentially resistant to sulfonamides are still rare events in Bulgaria. DHPS genotype 1 at codons 55 and 57 is the predominant P. jirovecii strain in the country.
Collapse
Affiliation(s)
- Nina Tsvetkova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Rumen Harizanov
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Iskra Rainova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Aleksandra Ivanova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Nina Yancheva-Petrova
- Department for AIDS, Specialized Hospital for Active Treatment of Infectious and Parasitic Diseases, Ivan Geshev Blvd. 17, 1431 Sofia, Bulgaria
| |
Collapse
|
2
|
Duysak T, Jeong JH, Kim K, Kim JS, Choy HE. Analysis of random mutations in Salmonella Gallinarum dihydropteroate synthase conferring sulfonamide resistance. Arch Microbiol 2023; 205:363. [PMID: 37906281 DOI: 10.1007/s00203-023-03696-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 11/02/2023]
Abstract
In bacteria and primitive eukaryotes, sulfonamide antibiotics block the folate pathway by inhibiting dihydropteroate synthase (FolP) that combines para-aminobenzoic acid (pABA) and dihydropterin pyrophosphate (DHPP) to form dihydropteroic acid (DHP), a precursor for tetrahydrofolate synthesis. However, the emergence of resistant strains has severely compromised the use of pABA mimetics as sulfonamide drugs. Salmonella enterica serovar Gallinarum (S. Gallinarum) is a significant source of antibiotic-resistant infections in poultry. Here, a sulfonamide-resistant FolP mutant library of S. Gallinarum was generated through random mutagenesis. Among resistant strains, substitution of amino acid Arginine 171 with Proline (R171P) in the FolP protein conferred the highest resistance against sulfonamide. Substitution of Phe28 with Leu or Ile (F28L/I) led to modest sulfonamide resistance. Structural modeling indicates that R171P and Phenylalanine 28 with leucine or isoleucine (F28L/I) substitution mutations are located far from the substrate-binding site and cause insignificant conformational changes in the FolP protein. Rather, in silico studies suggest that the mutations altered the stability of the protein, potentially resulting in sulfonamide resistance. Identification of specific mutations in FolP that confer resistance to sulfonamide would contribute to our understanding of the molecular mechanisms of antibiotic resistance.
Collapse
Affiliation(s)
- Taner Duysak
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 61468, Korea
- Basic Medical Research Building, Odysseus Bio, Chonnam National University Medical College, 322 Seoyang-ro, Hwasun, 58128, Jeonnam, Korea
| | - Jae-Ho Jeong
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 61468, Korea
| | - Kwangsoo Kim
- Basic Medical Research Building, Odysseus Bio, Chonnam National University Medical College, 322 Seoyang-ro, Hwasun, 58128, Jeonnam, Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Korea.
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 61468, Korea.
- Basic Medical Research Building, Odysseus Bio, Chonnam National University Medical College, 322 Seoyang-ro, Hwasun, 58128, Jeonnam, Korea.
| |
Collapse
|
3
|
Bonnet PL, Hoffmann CV, Le Nan N, Bellamy L, Hoarau G, Flori P, Demar M, Argy N, Morio F, Le Gal S, Nevez G. Atovaquone exposure and Pneumocystis jirovecii cytochrome b mutations: French data and review of the literature. Med Mycol 2023; 61:myad095. [PMID: 37656874 DOI: 10.1093/mmy/myad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023] Open
Abstract
Pneumocystis jirovecii is a transmissible fungus responsible for severe pneumonia (Pneumocystis pneumonia [PCP]) in immunocompromised patients. Missense mutations due to atovaquone selective pressure have been identified on cytochrome b (CYB) gene of P. jirovecii. It was recently shown that atovaquone prophylaxis can lead to the selection of specific P. jirovecii CYB mutants potentially resistant to atovaquone among organ transplant recipients. In this context, our objectives were to provide data on P. jirovecii CYB mutants and the putative selective pressure exerted by atovaquone on P. jirovecii organisms in France. A total of 123 patients (124 P. jirovecii specimens) from four metropolitan hospitals and two overseas hospitals were retrospectively enrolled. Fourteen patients had prior exposure to atovaquone, whereas 109 patients did not at the time of P. jirovecii detection. A 638 base-pair fragment of the CYB gene of P. jirovecii was amplified and sequenced. A total of 10 single nucleotide polymorphisms (SNPs) were identified. Both missense mutations C431T (Ala144Val) and C823T (Leu275Phe), located at the Qo active site of the enzyme, were significantly associated with prior atovaquone exposure, these mutations being conversely incidental in the absence of prior atovaquone exposure (P < 0.001). Considering that the aforementioned hospitals may be representative of the national territory, these findings suggest that the overall presence of P. jirovecii CYB mutants remains low in France.
Collapse
Affiliation(s)
- Pierre L Bonnet
- Laboratory of Parasitology and Mycology, Brest University Hospital, 29609 Brest, France
- Fungal Respiratory Infections Research Unit (FRI), University of Angers, University of Western Brittany, 29238 Brest, France
| | - Claire V Hoffmann
- Fungal Respiratory Infections Research Unit (FRI), University of Angers, University of Western Brittany, 29238 Brest, France
| | - Nathan Le Nan
- Fungal Respiratory Infections Research Unit (FRI), University of Angers, University of Western Brittany, 29238 Brest, France
| | - Lorenn Bellamy
- Clinical Data Center, Brest University Hospital, 29609 Brest, France
| | - Gautier Hoarau
- Ophthalmology Department, OPHTARA Network, Bicêtre Paris Saclay University Hospital, AP-HP, 94276 Le Kremlin-Bicêtre, France
| | - Pierre Flori
- Laboratory of Infectious Agents, Parasitology Section, GIMAP, Faculty of Medicine, 42055 Saint-Etienne, France
| | - Magalie Demar
- University Hospital Laboratory of Parasitology-Mycology, Cayenne Hospital Center, 97306 Cayenne, French Guiana
| | - Nicolas Argy
- IRD, MERIT, University of Paris Cité, 75006 Paris, France
| | - Florent Morio
- Laboratory of Parasitology and Medical Mycology, Nantes University Hospital, 44000 Nantes, France
| | - Solène Le Gal
- Laboratory of Parasitology and Mycology, Brest University Hospital, 29609 Brest, France
- Fungal Respiratory Infections Research Unit (FRI), University of Angers, University of Western Brittany, 29238 Brest, France
| | - Gilles Nevez
- Laboratory of Parasitology and Mycology, Brest University Hospital, 29609 Brest, France
- Fungal Respiratory Infections Research Unit (FRI), University of Angers, University of Western Brittany, 29238 Brest, France
| |
Collapse
|
4
|
Nisa I, Driessen A, Nijland J, Rahman H, Mattner J, Qasim M. Novel plasmids in multidrug-resistant Shigella flexneri serotypes from Pakistan. Arch Microbiol 2023; 205:175. [PMID: 37027063 DOI: 10.1007/s00203-023-03523-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 02/25/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023]
Abstract
Shigellosis is the main cause of food and waterborne diarrhea and is an emerging threat to human health. The current study characterized the indigenous multidrug-resistant Shigella flexneri serotypes for their plasmid profiles and genetic diversity, to characterize the plasmid evolutionary patterns and distribution. In total, 199 identified S. flexneri isolates belonging to six different serotypes were analyzed for plasmid profiling, followed by an analysis of whole genome sequencing. All isolates of S. flexneri resistant to antibiotics harbored multiple copies of plasmids with sizes ranging from 1.25 kbp to 9.4 kbp. These isolates were clustered into 22 distinct plasmid patterns, labeled as p1-p22. Among these, p1 (24%) and p10 (13%) were the predominant plasmid profiles. All S. flexneri strains were grouped into 12 clades with a 75% similarity level. Also, a significant association was observed among the plasmid patterns, p23 and p17 with the drug-resistant patterns AMC, SXT, C (19.5%) and OFX, AMC, NA, CIP (13.5%), respectively. Moreover, the most widespread plasmid patterns p4, p10, and p1 showed a significant association with the serotypes 1b (29.16%), 2b (36%), and 7a (100%), respectively. After plasmid sequence assembly and annotation analysis, a variety of small plasmids that vary in size from 973 to 6200 bp were discovered. Many of these plasmids displayed high homology and coverage with plasmids from non-S. flexneri. Several novel plasmids of small size were discovered in multidrug-resistant S. flexneri. The data also showed that plasmid profile analysis is more consistent than antibiotic susceptibility pattern analysis for identifying epidemic strains of S. flexneri isolated in Pakistan.
Collapse
Affiliation(s)
- Iqbal Nisa
- Department of Microbiology, Kohat University of Science and Technology, Kohat, 26000, Pakistan
- Department of Microbiology, Women University Swabi, Swabi, Pakistan
| | - Arnold Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Jeroen Nijland
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Hazir Rahman
- Department of Microbiology, Abdul Wali Khan University, Mardan, Pakistan
| | - Jochen Mattner
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie Und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Muhammad Qasim
- Department of Microbiology, Kohat University of Science and Technology, Kohat, 26000, Pakistan.
| |
Collapse
|
5
|
Apparent Absence of Selective Pressure on Pneumocystis jirovecii Organisms in Patients with Prior Methotrexate Exposure. Antimicrob Agents Chemother 2022; 66:e0099022. [PMID: 36317930 PMCID: PMC9765006 DOI: 10.1128/aac.00990-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Pneumocystis jirovecii infections occur in patients treated with methotrexate (MTX) because of immunosuppressive effects of this highly potent dihydrofolate reductase (DHFR) inhibitor. Conversely, MTX may act as an anti-P. jirovecii drug and consequently may exert a selective pressure on this fungus. In this context, we compared the sequences of the dhfr gene of P. jirovecii isolates obtained from two groups of patients with P. jirovecii infections. The first group, with systemic diseases or malignancies, had prior exposure to MTX (21 patients), whereas the second group (22 patients), the control group, did not. Three single nucleotide polymorphisms (SNPs) were observed at positions 278, 312, and 381. The first one was located in the intronic region and the two others were synonymous. Based on these SNPs, three P. jirovecii dhfr alleles, named A, B, and C, were specified. Allele A was the most frequent, as it was observed in 18 patients (85.7%) and in 16 patients (72.7%) of the first and second groups, respectively. No significant difference in P. jirovecii dhfr gene diversity in the two patient groups was observed. In conclusion, these original results suggest that MTX does not exert an overt selective pressure on P. jirovecii organisms.
Collapse
|
6
|
Gu ZY, Liu WJ, Huang DL, Liu YJ, He HY, Yang C, Liu YM, Xu M, Rong RM, Zhu DM, Luo Z, Ju MJ. Preliminary Study on the Combination Effect of Clindamycin and Low Dose Trimethoprim-Sulfamethoxazole on Severe Pneumocystis Pneumonia After Renal Transplantation. Front Med (Lausanne) 2022; 9:827850. [PMID: 35602475 PMCID: PMC9120531 DOI: 10.3389/fmed.2022.827850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/11/2022] [Indexed: 11/15/2022] Open
Abstract
Objective Evaluate the effect of the combination of clindamycin with low-dose trimethoprim-sulfamethoxazole (TMP/SMX) regimen on sever Pneumocystis pneumonia (PCP) after renal transplantation. Method 20 severe PCP patients after renal transplantation were included in this historical-control, retrospective study. A 10 patients were treated with the standard dose of TMP/SMX (T group), the other 10 patients were treated with the combination of clindamycin and low dose TMP/SMX (CT group). Results Although there was no significant difference in the hospital survival between the two groups, the CT protocol improved the PaO2/FiO2 ratio more significantly and rapidly after the 6th ICU day (1.51 vs. 0.38, P = 0.014). CT protocol also ameliorated the pulmonary infiltration and the lactate dehydrogenase level more effectively. Moreover, the CT protocol reduced the incidence of pneumomediastinum (0 vs. 50%, P = 0.008), the length of hospital staying (26.5 vs. 39.0 days, P = 0.011) and ICU staying (12.5 vs. 22.5 days, P = 0.008). Furthermore, more thrombocytopenia (9/10 vs. 3/10, P = 0.020) was emerged in the T group than in the CT group. The total adverse reaction rate was much lower in the CT group than in the T group (8/80 vs. 27/80, P < 0.001). Consequently, the dosage of TMP/SMX was reduced in 8 patients, while only 2 patients in the CT group received TMP/SMX decrement (P = 0.023). Conclusion The current study proposed that clindamycin combined with low-dose TMP/SMX was more effective and safer the than single use of TMP/SMX for severe PCP patients after renal transplantation (NCT04328688).
Collapse
Affiliation(s)
- Zhun-Yong Gu
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wen-Jun Liu
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dan-Lei Huang
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yu-Jing Liu
- Department of Nursing, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hong-Yu He
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Yang
- Department of Urology Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yi-Mei Liu
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ming Xu
- Department of Urology Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rui-Ming Rong
- Department of Urology Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Du-Ming Zhu
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhe Luo
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Min-Jie Ju
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
7
|
Xue T, Du WQ, Dai WJ, Li YS, Wang SF, Wang JL, Zhang XR. Genetic Polymorphisms of Pneumocystis jirovecii in HIV-Positive and HIV-Negative Patients in Northern China. Pol J Microbiol 2022; 71:27-34. [PMID: 35635165 PMCID: PMC9152919 DOI: 10.33073/pjm-2022-002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
Pneumocystis jirovecii is an opportunistic fungus that can cause severe and potentially fatal Pneumocystis pneumonia (PCP) in immunodeficient patients. In this study, we investigated the genetic polymorphisms of P. jirovecii at eight different loci, including six nuclear genes (ITS, 26S rRNA, sod, dhps, dhfr and β-Tub) and two mitochondrial genes (mtLSU-rRNA and cyb) in three PCP cases, including two patients with HIV infection and one without HIV infection in Shanxi Province, P.R. China. The gene targets were amplified by PCR followed by sequencing of plasmid clones. The HIV-negative patient showed a coinfection with two genotypes of P. jirovecii at six of the eight loci sequenced. Of the two HIV-positive patients, one showed a coinfection with two genotypes of P. jirovecii at the same two of the six loci as in the HIV-negative patient, while the other showed a single infection at all eight loci sequenced. None of the three drug target genes (dhfr, dhps and cyb) showed mutations known to be potentially associated with drug resistance. This is the first report of genetic polymorphisms of P. jirovecii in PCP patients in Shanxi Province, China. Our findings expand our understanding of the genetic diversity of P. jirovecii in China. ![]()
Collapse
Affiliation(s)
- Ting Xue
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province , Department of Respiratory and Critical Care Medicine , First Affiliated Hospital of Shanxi Medical University , Taiyuan , P.R. China
| | - Wei-Qin Du
- Department of clinical inspection , Eleventh Affiliated Hospital of Shanxi Medical University , Lvliang , P.R. China
| | - Wen-Juan Dai
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province , Department of Respiratory and Critical Care Medicine , First Affiliated Hospital of Shanxi Medical University , Taiyuan , P.R. China
| | - Yi-Shan Li
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province , Department of Respiratory and Critical Care Medicine , First Affiliated Hospital of Shanxi Medical University , Taiyuan , P.R. China
| | - Shu-Feng Wang
- Department of Clinical Inspection , First Affiliated Hospital of Shanxi Medical University , Taiyuan , P.R. China
| | - Jun-Ling Wang
- Department of Translation Medicine , Jinzhou Medical University , Jinzhou , P.R. China
| | - Xin-Ri Zhang
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province , Department of Respiratory and Critical Care Medicine , First Affiliated Hospital of Shanxi Medical University , Taiyuan , P.R. China
| |
Collapse
|
8
|
de la Horra C, Friaza V, Morilla R, Delgado J, Medrano FJ, Miller RF, de Armas Y, Calderón EJ. Update on Dihydropteroate Synthase (DHPS) Mutations in Pneumocystis jirovecii. J Fungi (Basel) 2021; 7:jof7100856. [PMID: 34682277 PMCID: PMC8540849 DOI: 10.3390/jof7100856] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/28/2021] [Accepted: 10/10/2021] [Indexed: 12/21/2022] Open
Abstract
A Pneumocystis jirovecii is one of the most important microorganisms that cause pneumonia in immunosupressed individuals. The guideline for treatment and prophylaxis of Pneumocystis pneumonia (PcP) is the use of a combination of sulfa drug-containing trimethroprim and sulfamethoxazole. In the absence of a reliable method to culture Pneumocystis, molecular techniques have been developed to detect mutations in the dihydropteroate synthase gene, the target of sulfa drugs, where mutations are related to sulfa resistance in other microorganisms. The presence of dihydropteroate synthase (DHPS) mutations has been described at codon 55 and 57 and found almost around the world. In the current work, we analyzed the most common methods to identify these mutations, their geographical distribution around the world, and their clinical implications. In addition, we describe new emerging DHPS mutations. Other aspects, such as the possibility of transmitting Pneumocystis mutated organisms between susceptible patients is also described, as well as a brief summary of approaches to study these mutations in a heterologous expression system.
Collapse
Affiliation(s)
- Carmen de la Horra
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
| | - Vicente Friaza
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
- Correspondence: (V.F.); (E.J.C.); Tel.: +34-955923096 (E.J.C.)
| | - Rubén Morilla
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
- Departamento de Enfermería, Universidad de Sevilla, 41009 Seville, Spain
| | - Juan Delgado
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
| | - Francisco J. Medrano
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
- Departamento de Medicina, Universidad de Sevilla, 41009 Seville, Spain
| | - Robert F. Miller
- Institute for Global Health, University College London, London WC1E 6JB, UK;
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Yaxsier de Armas
- Department of Clinical Microbiology Diagnostic, Hospital Center of Institute of Tropical Medicine “Pedro Kourí”, Havana 11400, Cuba;
- Pathology Department, Hospital Center of Institute of Tropical Medicine “Pedro Kourí,” Havana 11400, Cuba
| | - Enrique J. Calderón
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Seville, Spain; (C.d.l.H.); (R.M.); (J.D.); (F.J.M.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
- Departamento de Medicina, Universidad de Sevilla, 41009 Seville, Spain
- Correspondence: (V.F.); (E.J.C.); Tel.: +34-955923096 (E.J.C.)
| |
Collapse
|
9
|
Latinne A, Chen HW, Kuo CC, Lorica R, Singleton G, Stuart A, Malbas FF, Demanche C, Chabé M, Michaux J, Morand S. Revisiting the Pneumocystis host specificity paradigm and transmission ecology in wild Southeast Asian rodents. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 93:104978. [PMID: 34175480 DOI: 10.1016/j.meegid.2021.104978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/04/2021] [Accepted: 06/21/2021] [Indexed: 01/16/2023]
Abstract
Pneumocystis fungi are opportunistic parasites of mammalian lungs whose evolution, ecology and host specificity in natural host populations remain poorly understood and controversial. Using an extensive collection of 731 lung samples from 27 rodent species sampled in five Southeast Asian countries, and nested PCR amplification of mitochondrial and nuclear genes, we investigated the host specificity and genetic structure of Pneumocystis lineages infecting wild rodents. We also identified the rodent species playing a central role in the transmission of these parasites using network analysis and centrality measurement and we characterized the environmental conditions allowing Pneumocystis infection in Southeast Asia using generalized linear mixed models. Building upon an unprecedented Pneumocystis sampling from numerous rodent species belonging to closely related genera, our findings provide compelling evidence that the host specificity of Pneumocystis lineages infecting rodents is not restricted to a single host species or genus as often presented in the literature but it encompasses much higher taxonomic levels and more distantly related rodent host species. The phylogenetic species status at both mitochondrial and nuclear genetic markers of at least three new Pneumocystis lineages, highly divergent from Pneumocystis species currently described, is also suggested by our data. Our models show that the probability of Pneumocystis infection in rodent hosts is positively correlated to environmental variables reflecting habitat fragmentation and landscape patchiness. Synanthropic and habitat-generalist rodents belonging to the Rattus, Sundamys and Bandicota genera played a role of bridge host species for Pneumocystis spreading in these heterogeneous habitats, where they can reach high population densities. These are critical findings improving our understanding of the ecology of these enigmatic parasites and the role played by cospeciation and host switches in their evolution. Our results also confirmed the role of land-use change and habitat fragmentation in parasite amplification and spillover in rodents.
Collapse
Affiliation(s)
- Alice Latinne
- Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam; Wildlife Conservation Society, Health Program, Bronx, NY, USA; Université de Liège, Laboratoire de Génétique de la Conservation, GeCoLAB, 4000 Liège, Belgium.
| | - Hsuan-Wien Chen
- Department of Biological Resources, National Chiayi University, Chiayi, Taiwan
| | - Chi-Chien Kuo
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Renee Lorica
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Grant Singleton
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines; Natural Resource Institute, University of Greenwich, Chatham Maritime, Kent, UK
| | - Alex Stuart
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Fedelino F Malbas
- Research Institute for Tropical Medicine, Department of Health, Muntinlupa, Metro Manila, Philippines
| | - Christine Demanche
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Magali Chabé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Johan Michaux
- Université de Liège, Laboratoire de Génétique de la Conservation, GeCoLAB, 4000 Liège, Belgium; Animal Santé Territoire Risque Environnement- Unité Mixe de Recherche 117 (ASTRE) Univ. Montpellier, Centre International de Recherche Agronomique pour le Développement (CIRAD), Institut National de la Recherche Agronomique, 34398 Montpellier, France
| | - Serge Morand
- University of Montpellier, Institut des Sciences de l'Evolution, CNRS-IRD, Montpellier, France; University of Kasetsart, Faculty of Veterinary Technology, ASTRE-CIRAD, Bangkok, Thailand
| |
Collapse
|
10
|
Gurbuz CE, Delibas SB, Alpaydin AO, Sayiner AA, Ozkoc S. Genetic diversity of Pneumocystis jirovecii isolates among Turkish population based on mitochondrial large subunit ribosomal RNA and dihydropteroate synthase gene typing. Med Mycol 2021; 59:813-820. [PMID: 33709136 DOI: 10.1093/mmy/myab004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/05/2021] [Accepted: 01/18/2021] [Indexed: 12/18/2022] Open
Abstract
Pneumocystis jirovecii (P. jirovecii) is an atypical fungus that can cause severe interstitial pneumonia in immunocompromised patients. In this study, mitochondrial large subunit ribosomal RNA (mtLSU-rRNA) and dihydropteroate synthase (DHPS) gene polymorphism in P. jirovecii isolates were investigated in Western Turkey's Izmir province and its surroundings. For this purpose, a total of 157 P. jirovecii isolates obtained from bronchoalveolar lavage samples of hospitalized cases and lung tissue samples of autopsy cases who died outside hospital were examined. Genotypes were identified by direct sequencing of mtLSU-rRNA restriction fragment length polymorphism analysis of the DHPS gene amplicons. The mtLSU-rRNA analysis revealed that genotype 2 was the most common genotype with 58%. The following genotypes were genotype 3 (13%), genotype 1 (11.6%) and genotype 4 (5.1%), while genotype 5 (0.7%) was detected in only one autopsy case. In addition, 16 (11.6%) cases had dual or triple different genotypes (mixed infection). It was observed that the genotype distribution was not affected by characteristics such as age, gender and immune status. However, the predominance of genotype 2 in solid organ tumors and the predominance of mixed infection in patients with chronic pulmonary disease were statistically significant. On the other hand, DHPS gene amplification was positive in 137 (87.3%) of 157 samples. While no mutation was observed in 135 samples, the association of wild-type and 57th codon mutation was detected in two hospitalized cases (1.5%). In this study, important epidemiological data on the distribution of mtLSU-rRNA genotypes were obtained. Also the existence of DHPS gene mutations associated with potential drug resistance in our community was shown for the first time. Further studies are needed to evaluate the possible effects of genotypes on the prognosis of the disease to help with the clinician's treatment decisions. LAY ABSTRACT Pneumocystis jirovecii (P. jirovecii) is an atypical fungus that can cause life-threatening pneumonia in immunocompromised patients. In this study, we investigated the mtLSU-rRNA and DHPS gene polymorphisms in P. jirovecii isolates from both hospital and autopsy cases.
Collapse
Affiliation(s)
- Ceren Erguden Gurbuz
- Department of Medical Parasitology, Dokuz Eylul University Faculty of Medicine, 35340 Izmir, Turkey
| | - Songul Bayram Delibas
- Department of Medical Parasitology, Dokuz Eylul University Faculty of Medicine, 35340 Izmir, Turkey
| | - Aylin Ozgen Alpaydin
- Department of Pulmonary Diseases, Dokuz Eylul University Faculty of Medicine, 35340 Izmir, Turkey
| | - Ayca Arzu Sayiner
- Department of Medical Microbiology, Dokuz Eylul University Faculty of Medicine, 35340 Izmir, Turkey
| | - Soykan Ozkoc
- Department of Medical Parasitology, Dokuz Eylul University Faculty of Medicine, 35340 Izmir, Turkey
| |
Collapse
|
11
|
Wang M, Xu X, Guo Y, Tao R, Hu C, Dong X, Huang Y, Zhu B. Polymorphisms involving the Pneumocystis jirovecii-related genes in AIDS patients in eastern China. INFECTION GENETICS AND EVOLUTION 2019; 75:103955. [PMID: 31284044 DOI: 10.1016/j.meegid.2019.103955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/25/2019] [Accepted: 07/05/2019] [Indexed: 11/18/2022]
Abstract
OBJECTIVE To investigate the genetic polymorphisms of mitochondrial large ribosomal subunit (mtLSU)-rRNA, dihydrofolate reductase (DHFR), dihydropteroate synthase (DHPS), cytochrome b (CYB), and superoxide dismutase (SOD) genes and its correlation with clinical outcomes of Pneumocystis jirovecii pneumonia in acquired immune deficiency(AIDS) patients. METHODS Eighty AIDS patients with P. jirovecii pneumonia that were admitted to our hospital from 2016 to 2018 were included in this study. Their demographic information and clinical data were collected, as well as corresponding saliva specimens for PCR and sequencing of mtLSU-rRNA, DHFR, DHPS, CYB, and SOD genes to analyze genetic polymorphisms, different polymorphic combinations, and clinical outcomes. RESULTS Of the 80 saliva specimens, mtLSU-rRNA was successfully amplified and sequenced in 30 cases; CYB was successfully amplified and sequenced in 26 cases; and SOD, DHFR, and DHPS were successfully amplified and sequenced in 18 cases. These results indicate that The mtLSU-rRNA, CYB, and SOD genes were highly polymorphic. mt85T and CYB1 were the variants dominantly detected at the mtLSU-rRNA and CYB loci, respectively. The SOD1 and SOD2 variants (each in 50% of the cases) were detected at the SOD locus. Among the 18 cases that were successfully amplified and sequenced for DHFR and DHPS, three DHFR nonsense mutations and no DHPS mutation were observed. The mt85C, CYB1, SOD1, and DHFR312T genes harbored common polymorphisms (n = 4; 22.22%) and the mt85T, CYB1, SOD1, DHFR312T genes were associated with poor clinical outcomes. CONCLUSION The types of genetic polymorphisms and polymorphic combinations of mtLSU-rRNA, DHFR, DHPS, CYB, and SOD in P. jirovecii were related to the clinical outcomes of patients with P. jirovecii pneumonia in Zhejiang Province, China.
Collapse
Affiliation(s)
- Mengyan Wang
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Xiaoke Xu
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Yongzheng Guo
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Ran Tao
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Caiqin Hu
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Xiaotian Dong
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Ying Huang
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Biao Zhu
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| |
Collapse
|
12
|
Singh Y, Mirdha BR, Guleria R, Kabra SK, Mohan A, Chaudhry R, Kumar L, Dwivedi SN, Agarwal SK. Genetic polymorphisms associated with treatment failure and mortality in pediatric Pneumocystosis. Sci Rep 2019; 9:1192. [PMID: 30718779 PMCID: PMC6361943 DOI: 10.1038/s41598-018-38052-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/19/2018] [Indexed: 12/15/2022] Open
Abstract
Data on the genetic diversity of Pneumocystis jirovecii causing Pneumocystis pneumonia (PCP) among children are still limited, and there are no available data from the Indian subcontinent, particularly associations between genotypes and clinical characteristics. A total of 37 children (62 days-12 years [median 5.5 years]) were included in this study. Pneumocystis was diagnosed by microscopy using Grocott-Gomori methenamine silver stain in 12 cases and by nested PCR using mtLSUrRNA in 25 cases. Genotyping was performed using three different genes, mitochondrial large subunit ribosomal RNA (mtLSUrRNA), dihydropteroate synthase (DHPS) and dihydrofolate reductase (DHFR). mtLSUrRNA genotype 3 and novel mutations at the gene target DHFR (401 T > C) and DHPS 96/98 were frequently observed and clinically associated with severe PCP and treatment failure. Phylogenetic analyses revealed 13 unique sequence types (STs). Two STs (i) 3-DHFR 401 T > C-DHPS 96/98 – PJ1 and (ii) 3-DHFR 401 T > C-DHPS 96- PJ3 were significantly associated with treatment failure and high mortality among PCP-positive patients. In conclusion, the present study strongly suggests the emergence of virulent P. jirovecii strains or genetic polymorphisms, leading to treatment failure and high mortality. Our study is the first of its kind from the Indian subcontinent and has highlighted the genetic diversity of Pneumocystis jirovecii among children and their clinical outcomes. These findings emphasize the need to focus more on genotypes to better understand the epidemiology of Pneumocystis pneumonia.
Collapse
Affiliation(s)
- Yogita Singh
- All India Institute of Medical Sciences, Department of Microbiology, New Delhi, 110029, India
| | - Bijay Ranjan Mirdha
- All India Institute of Medical Sciences, Department of Microbiology, New Delhi, 110029, India.
| | - Randeep Guleria
- All India Institute of Medical Sciences, Department of Pulmonary Medicine and Sleep Disorders, New Delhi, 110029, India
| | - Sushil K Kabra
- All India Institute of Medical Sciences, Department of Pediatrics, New Delhi, 110029, India
| | - Anant Mohan
- All India Institute of Medical Sciences, Department of Pulmonary Medicine and Sleep Disorders, New Delhi, 110029, India
| | - Rama Chaudhry
- All India Institute of Medical Sciences, Department of Microbiology, New Delhi, 110029, India
| | - Lalit Kumar
- All India Institute of Medical Sciences, Department of Medical Oncology, New Delhi, 110029, India
| | - Sada Nand Dwivedi
- All India Institute of Medical Sciences, Department of Biostatistics, New Delhi, 110029, India
| | - Sanjay K Agarwal
- All India Institute of Medical Sciences, Department of Nephrology, New Delhi, 110029, India
| |
Collapse
|
13
|
Singh Y, Mirdha BR, Guleria R, Kabra SK, Mohan A, Chaudhry R, Kumar L, Dwivedi SN, Agarwal SK. Novel dihydropteroate synthase gene mutation in Pneumocystis jirovecii among HIV-infected patients in India: Putative association with drug resistance and mortality. J Glob Antimicrob Resist 2019; 17:236-239. [PMID: 30658203 DOI: 10.1016/j.jgar.2019.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/14/2018] [Accepted: 01/09/2019] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES Pneumocystis pneumonia (PCP) remains a debilitating cause of death among HIV-infected patients. The combination trimethoprim/sulfamethoxazole (SXT) is the most effective anti-Pneumocystis treatment and prophylaxis. However, long-term use of this combination has raised alarms about the emergence of resistant organisms. This study was performed to investigate mutations in the dihydropteroate synthase (DHPS) gene and their clinical consequences in HIV-infected patients with PCP. METHODS A total of 76 clinically suspected cases of PCP among HIV-seropositive adult patients from March 2014 to March 2017 were included. Clinical samples (bronchoalveolar lavage fluid and sputum) were investigated for the detection of Pneumocystis jirovecii using both microscopy and nested PCR. DHPS genotyping and mutational analyses were performed and the data were correlated with clinical characteristics. RESULTS Among the 76 enrolled HIV-positive patients, only 17 (22.4%) were positive for P. jirovecii. DHPS gene sequencing showed a novel nucleotide substitution at position 288 (Val96Ile) in three patients (3/12; 25.0%). Patients infected with the mutant P. jirovecii genotype had severe episodes of PCP, did not respond to SXT and had a fatal outcome (P=0.005). All three patients had a CD4+ T-cell count <100 cells/μL, and two also had co-infections. CONCLUSION This study suggests that the emergence of a mutant P. jirovecii genotype is probably associated with drug resistance and mortality. The data also suggest that DHPS mutational analyses should be performed in HIV-seropositive patients to avoid treatment failure and death due to PCP. However, the role of underlying disease severity and co-morbidities should not be underestimated.
Collapse
Affiliation(s)
- Yogita Singh
- All India Institute of Medical Sciences, Department of Microbiology, New Delhi 110029, India
| | - Bijay Ranjan Mirdha
- All India Institute of Medical Sciences, Department of Microbiology, New Delhi 110029, India.
| | - Randeep Guleria
- All India Institute of Medical Sciences, Department of Pulmonary Medicine and Sleep Disorders, New Delhi 110029, India
| | - Sushil K Kabra
- All India Institute of Medical Sciences, Department of Pediatrics, New Delhi 110029, India
| | - Anant Mohan
- All India Institute of Medical Sciences, Department of Pulmonary Medicine and Sleep Disorders, New Delhi 110029, India
| | - Rama Chaudhry
- All India Institute of Medical Sciences, Department of Microbiology, New Delhi 110029, India
| | - Lalit Kumar
- All India Institute of Medical Sciences, Department of Medical Oncology, New Delhi 110029, India
| | - Sada Nand Dwivedi
- All India Institute of Medical Sciences, Department of Biostatistics, New Delhi 110029, India
| | - Sanjay K Agarwal
- All India Institute of Medical Sciences, Department of Nephrology, New Delhi 110029, India
| |
Collapse
|
14
|
Site-Directed Mutagenesis of the 1,3-β-Glucan Synthase Catalytic Subunit of Pneumocystis jirovecii and Susceptibility Assays Suggest Its Sensitivity to Caspofungin. Antimicrob Agents Chemother 2018; 62:AAC.01159-18. [PMID: 30249686 DOI: 10.1128/aac.01159-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/11/2018] [Indexed: 12/26/2022] Open
Abstract
The echinocandin caspofungin inhibits the catalytic subunit Gsc1 of the enzymatic complex synthesizing 1,3-β-glucan, an essential compound of the fungal wall. Studies with rodents showed that caspofungin is effective against Pneumocystis asci. However, its efficacy against asci of Pneumocystis jirovecii, the species infecting exclusively humans, remains controversial. The aim of this study was to assess the sensitivity to caspofungin of the P. jirovecii Gsc1 subunit, as well as of those of Pneumocystis carinii and Pneumocystis murina infecting, respectively, rats and mice. In the absence of an established in vitro culture method for Pneumocystis species, we used functional complementation of the Saccharomyces cerevisiae gsc1 deletant. In the fungal pathogen Candida albicans, mutations leading to amino acid substitutions in Gsc1 confer resistance to caspofungin. We introduced the corresponding mutations into the Pneumocystis gsc1 genes using site-directed mutagenesis. In spot dilution tests, the sensitivity to caspofungin of the complemented strains decreased with the number of mutations introduced, suggesting that the wild-type enzymes are sensitive. The MICs of caspofungin determined by Etest and YeastOne for strains complemented with Pneumocystis enzymes (respectively, 0.125 and 0.12 μg/ml) were identical to those upon complementation with the enzyme of C. albicans, for which caspofungin presents low MICs. However, they were lower than the MICs upon complementation with the enzyme of the resistant species Candida parapsilosis (0.19 and 0.25 μg/ml). Sensitivity levels of Gsc1 enzymes of the three Pneumocystis species were similar. Our results suggest that P. jirovecii is sensitive to caspofungin during infections, as are P. carinii and P. murina.
Collapse
|
15
|
Szydłowicz M, Jakuszko K, Szymczak A, Piesiak P, Kowal A, Kopacz Ż, Wesołowska M, Lobo ML, Matos O, Hendrich AB, Kicia M. Prevalence and genotyping of Pneumocystis jirovecii in renal transplant recipients-preliminary report. Parasitol Res 2018; 118:181-189. [PMID: 30392033 PMCID: PMC6329730 DOI: 10.1007/s00436-018-6131-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/23/2018] [Indexed: 12/24/2022]
Abstract
Pneumocystis jirovecii is an opportunistic fungus occurring in human lungs. The group at highest risk consists of HIV-infected and non-HIV-infected immunosuppressed individuals. In these patients, P. jirovecii infection may lead to Pneumocystis pneumonia; it may, however, persist also in an asymptomatic form. This study aimed to determine the prevalence of P. jirovecii and potential risk factors for infection in a group of renal transplant recipients and to characterize the genetic diversity of this fungus in the studied population. Sputum specimens from 72 patients were tested for presence of P. jirovecii using immunofluorescence microscopy, as well as nested PCR targeting the mtLSU rRNA gene. Genotyping involving analysis of four loci—mtLSU rRNA, CYB, DHPS, and SOD—was used to characterize the diversity of the detected organisms. Pneumocystis DNA was detected in eight (11.11%) patients. It has been shown that low eosinophil count and dual immunosuppressive treatment combining prednisone and calcineurin inhibitors are potential risk factors for colonization. Analysis of genotype distribution showed an association of the wild-type genotype of mtLSU rRNA with lower average age of patients and shorter time after kidney transplantation. Furthermore, CYB 2 genotype was detected only in patients with the ongoing prophylaxis regimen. In conclusion, renal transplant recipients are at risk of Pneumocystis colonization even a long time after transplantation. The present preliminary study identifies specific polymorphisms that appear to be correlated with certain patient characteristics and highlights the need for deeper investigation of these associations in renal transplant recipients.
Collapse
Affiliation(s)
- Magdalena Szydłowicz
- Department of Biology and Medical Parasitology, Wroclaw Medical University, ul. J. Mikulicza-Radeckiego 9, 50-345, Wroclaw, Poland.
| | - Katarzyna Jakuszko
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Anna Szymczak
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Paweł Piesiak
- Department of Pulmonology and Lung Cancer, Wroclaw Medical University, Wroclaw, Poland
| | - Aneta Kowal
- Department of Pulmonology and Lung Cancer, Wroclaw Medical University, Wroclaw, Poland
| | - Żaneta Kopacz
- Department of Biology and Medical Parasitology, Wroclaw Medical University, ul. J. Mikulicza-Radeckiego 9, 50-345, Wroclaw, Poland
| | - Maria Wesołowska
- Department of Biology and Medical Parasitology, Wroclaw Medical University, ul. J. Mikulicza-Radeckiego 9, 50-345, Wroclaw, Poland
| | - Maria Luísa Lobo
- Global Health and Tropical Medicine, Unit of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Olga Matos
- Global Health and Tropical Medicine, Unit of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Andrzej B Hendrich
- Department of Biology and Medical Parasitology, Wroclaw Medical University, ul. J. Mikulicza-Radeckiego 9, 50-345, Wroclaw, Poland
| | - Marta Kicia
- Department of Biology and Medical Parasitology, Wroclaw Medical University, ul. J. Mikulicza-Radeckiego 9, 50-345, Wroclaw, Poland
| |
Collapse
|
16
|
Griffith EC, Wallace MJ, Wu Y, Kumar G, Gajewski S, Jackson P, Phelps GA, Zheng Z, Rock CO, Lee RE, White SW. The Structural and Functional Basis for Recurring Sulfa Drug Resistance Mutations in Staphylococcus aureus Dihydropteroate Synthase. Front Microbiol 2018; 9:1369. [PMID: 30065703 PMCID: PMC6057106 DOI: 10.3389/fmicb.2018.01369] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/06/2018] [Indexed: 11/13/2022] Open
Abstract
Staphylococcal species are a leading cause of bacterial drug-resistant infections and associated mortality. One strategy to combat bacterial drug resistance is to revisit compromised targets, and to circumvent resistance mechanisms using structure-assisted drug discovery. The folate pathway is an ideal candidate for this approach. Antifolates target an essential metabolic pathway, and the necessary detailed structural information is now available for most enzymes in this pathway. Dihydropteroate synthase (DHPS) is the target of the sulfonamide class of drugs, and its well characterized mechanism facilitates detailed analyses of how drug resistance has evolved. Here, we surveyed clinical genetic sequencing data in S. aureus to distinguish natural amino acid variations in DHPS from those that are associated with sulfonamide resistance. Five mutations were identified, F17L, S18L, T51M, E208K, and KE257_dup. Their contribution to resistance and their cost to the catalytic properties of DHPS were evaluated using a combination of biochemical, biophysical and microbiological susceptibility studies. These studies show that F17L, S18L, and T51M directly lead to sulfonamide resistance while unexpectedly increasing susceptibility to trimethoprim, which targets the downstream enzyme dihydrofolate reductase. The secondary mutations E208K and KE257_dup restore trimethoprim susceptibility closer to wild-type levels while further increasing sulfonamide resistance. Structural studies reveal that these mutations appear to selectively disfavor the binding of the sulfonamides by sterically blocking an outer ring moiety that is not present in the substrate. This emphasizes that new inhibitors must be designed that strictly stay within the substrate volume in the context of the transition state.
Collapse
Affiliation(s)
- Elizabeth C. Griffith
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Miranda J. Wallace
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Yinan Wu
- Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Gyanendra Kumar
- Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Stefan Gajewski
- Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Pamela Jackson
- Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Gregory A. Phelps
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
- Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Zhong Zheng
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Charles O. Rock
- Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Richard E. Lee
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Stephen W. White
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
- Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| |
Collapse
|
17
|
Ma L, Cissé OH, Kovacs JA. A Molecular Window into the Biology and Epidemiology of Pneumocystis spp. Clin Microbiol Rev 2018; 31:e00009-18. [PMID: 29899010 PMCID: PMC6056843 DOI: 10.1128/cmr.00009-18] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Pneumocystis, a unique atypical fungus with an elusive lifestyle, has had an important medical history. It came to prominence as an opportunistic pathogen that not only can cause life-threatening pneumonia in patients with HIV infection and other immunodeficiencies but also can colonize the lungs of healthy individuals from a very early age. The genus Pneumocystis includes a group of closely related but heterogeneous organisms that have a worldwide distribution, have been detected in multiple mammalian species, are highly host species specific, inhabit the lungs almost exclusively, and have never convincingly been cultured in vitro, making Pneumocystis a fascinating but difficult-to-study organism. Improved molecular biologic methodologies have opened a new window into the biology and epidemiology of Pneumocystis. Advances include an improved taxonomic classification, identification of an extremely reduced genome and concomitant inability to metabolize and grow independent of the host lungs, insights into its transmission mode, recognition of its widespread colonization in both immunocompetent and immunodeficient hosts, and utilization of strain variation to study drug resistance, epidemiology, and outbreaks of infection among transplant patients. This review summarizes these advances and also identifies some major questions and challenges that need to be addressed to better understand Pneumocystis biology and its relevance to clinical care.
Collapse
Affiliation(s)
- Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA
| | - Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA
| |
Collapse
|
18
|
Singh Y, Mirdha BR, Guleria R, Khalil S, Panda A, Chaudhry R, Mohan A, Kabra SK, Kumar L, Agarwal SK. Circulating genotypes of Pneumocystis jirovecii and its clinical correlation in patients from a single tertiary center in India. Eur J Clin Microbiol Infect Dis 2017; 36:1635-1641. [PMID: 28401321 DOI: 10.1007/s10096-017-2977-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/27/2017] [Indexed: 10/19/2022]
Abstract
The present study was carried out with the objectives of genotyping Pneumocystis jirovecii at three distinct loci, to identify the single nucleotide polymorphisms (SNPs), and to study its clinical implications in patients with Pneumocystis pneumonia (PCP). Analysis of genetic diversity in P. jirovecii from immunocompromised patients was carried out by genotyping at three distinct loci encoding mitochondrial large subunit rRNA (mtLSU rRNA), cytochrome b (CYB), and superoxide dismutase (SOD) using polymerase chain reaction (PCR) assays followed by direct DNA sequencing. Of the 300 patients enrolled in the present study, 31 (10.33%) were positive for PCP by a specific mtLSU rRNA nested PCR assay, whereas only 15 P. jirovecii could be amplified at the other two loci (SOD and CYB). These positives were further subjected to sequence typing. Important genotypic combinations between four SNPs (mt85, SOD110, SOD215, and CYB838) and clinical outcomes could be observed in the present study, and mt85A, mt85T, and SOD110C/SOD215T were frequently associated with "negative follow-up". These SNPs were also noted to be relatively more prevalent amongst circulating genotypes in our study population. The present study is the first of its kind from the Indian subcontinent and demonstrated that potential SNPs of P. jirovecii may possibly be attributed to the clinical outcome of PCP episodes in terms of severity or fatality in different susceptible populations likely to develop PCP during their course of illness.
Collapse
Affiliation(s)
- Y Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - B R Mirdha
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
| | - R Guleria
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
| | - S Khalil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - A Panda
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - R Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - A Mohan
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
| | - S K Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - L Kumar
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - S K Agarwal
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
19
|
Low prevalence of DHFR and DHPS mutations in Pneumocystis jirovecii strains obtained from a German cohort. Infection 2017; 45:341-347. [PMID: 28303545 DOI: 10.1007/s15010-017-1005-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 03/07/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Pneumocystis pneumonia (PCP) is an opportunistic and potentially life-threatening infection of immunocompromised individuals. A combination of trimethoprim-sulfamethoxazole is widely used for prophylaxis and treatment of PCP. Polymorphisms in the drug targets, the dihydropteroate synthase (DHPS) or the dihydrofolate reductase (DHFR) are presumably a reason for treatment failure. METHODS We retrospectively examined the prevalence of DHPS and DHFR mutations in Pneumocystis jirovecii isolates obtained from HIV-infected and non-HIV-infected PCP patients. DHFR and DHPS genes were amplified using semi-nested PCR followed by sequencing. Obtained data were correlated with clinical findings. RESULTS Sequencing of the DHPS gene was achieved in 81 out of 128 isolates (63%), the DHFR-gene was successfully sequenced in 96 isolates (75%). The vast majority of DHFR and DHPS sequences were either wild-type or showed synonymous single nucleotide polymorphisms. Only one sample contained a double mutation at DHPS codon 55 and codon 57 which was associated with treatment failure in some studies. No linkage of treatment failure to a DHFR or DHPS genotype was observed. In our cohort, 35 of 95 Patients (37%) were HIV-positive and 60 (63%) were HIV-negative. The overall mortality rate was 24% with a much higher rate among non-HIV patients. CONCLUSION DHPS and DHFR mutations exist but are infrequent in our cohort. The contribution of gene polymorphisms to treatment failure needs further research. In immunocompromised HIV-negative patients PCP is associated with high mortality rates. Prophylactic treatment is warranted in this patient subset.
Collapse
|
20
|
Abstract
Pneumocystis pneumonia (PCP) is an opportunistic infection that occurs in humans and other mammals with debilitated immune systems. These infections are caused by fungi in the genus Pneumocystis, which are not susceptible to standard antifungal agents. Despite decades of research and drug development, the primary treatment and prophylaxis for PCP remains a combination of trimethoprim (TMP) and sulfamethoxazole (SMX) that targets two enzymes in folic acid biosynthesis, dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS), respectively. There is growing evidence of emerging resistance by Pneumocystis jirovecii (the species that infects humans) to TMP-SMX associated with mutations in the targeted enzymes. In the present study, we report the development of an accurate quantitative model to predict changes in the binding affinity of inhibitors (Ki, IC50) to the mutated proteins. The model is based on evolutionary information and amino acid covariance analysis. Predicted changes in binding affinity upon mutations highly correlate with the experimentally measured data. While trained on Pneumocystis jirovecii DHFR/TMP data, the model shows similar or better performance when evaluated on the resistance data for a different inhibitor of PjDFHR, another drug/target pair (PjDHPS/SMX) and another organism (Staphylococcus aureus DHFR/TMP). Therefore, we anticipate that the developed prediction model will be useful in the evaluation of possible resistance of the newly sequenced variants of the pathogen and can be extended to other drug targets and organisms.
Collapse
|
21
|
Luraschi A, Cissé OH, Pagni M, Hauser PM. Identification and Functional Ascertainment of the Pneumocystis jirovecii Potential Drug Targets Gsc1 and Kre6 Involved in Glucan Synthesis. J Eukaryot Microbiol 2016; 64:481-490. [PMID: 27859907 DOI: 10.1111/jeu.12385] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/11/2016] [Accepted: 11/11/2016] [Indexed: 12/23/2022]
Abstract
The most efficient drug against the human pathogenic fungus Pneumocystis jirovecii is cotrimoxazole targeting the folate biosynthesis. However, resistance toward it is emerging and adverse effects occur in some patients. Studies in rodent models suggested that echinocandins could be useful to treat Pneumocystis pneumonia. Echinocandins inhibit the catalytic subunit Gsc1 of the enzymatic complex ensuring the synthesis of 1,3-β glucan, an essential constituent of cell walls of most fungi. Besides, inhibitors of the enzyme Kre6 involved in the synthesis of 1,6-β glucan, another essential component of fungal walls, were recently described. We identified and functionally characterized these two potential drug targets in the human pathogen P. jirovecii by rescue of the null allele of the orthologous gene in Saccharomyces cerevisiae. The P. jirovecii proteins Gsc1 and Kre6 identified using those of the relative Pneumocystis carinii as the query sequence showed high sequence identity to the putative fungal orthologs (53-97% in conserved functional domains). The expression of their encoding genes on plasmid rescued the increased sensitivity to, respectively, caspofungin or calcofluor white of the corresponding S. cerevisiae null allele. The uniqueness and likely essentiality of these proteins suggest that they are potential good drug targets.
Collapse
Affiliation(s)
- Amanda Luraschi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, 1011, Switzerland
| | - Ousmane H Cissé
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, 1011, Switzerland.,Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Marco Pagni
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Philippe M Hauser
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, 1011, Switzerland
| |
Collapse
|
22
|
Abstract
Pneumocystis pneumonia remains one of the leading causes of morbidity and mortality in the HIV-infected population. Trimethoprim-sulfamethoxazole remains the drug of choice for both the treatment and prevention of this infection, although a high rate of side effects in HIV-infected patients often necessitates alternative treatment regimens. This article will review pneumocystis pneumonia, with a focus on the various therapeutic options, their side effects, and the immune reconstitution inflammatory syndrome as it relates to pneumocystis pneumonia infection.
Collapse
Affiliation(s)
- Stephanie A. Lee
- Christiana Care Health Systems, J32 Omega Drive, Newark, DE 19713
| |
Collapse
|
23
|
Abstract
Pneumocystis carinii pneumonia (PCP) remains a serious infection in the immunocompromised host (in the absence of HIV infection) and presents significant management and diagnostic challenges to ICU physicians. Non-HIV PCP is generally abrupt in onset, and follows a fulminate course with high rates of hospitalization, ICT admission, respiratory failure, and requirement for intubation. Mortality is generally high, especially if mechanical ventilation is required. Non-invasive ventilatory support may be considered, although the rapid progression to respiratory failure often necessitates intubation at the time of presentation. Bronchoscopy is often required to establish the diagnosis, and empirical antimicrobial treatment specifically targeted to P. carinii should be initiated while awaiting confirmation. Adjunctive corticosteroids may accelerate recovery, although their use has not yet been established in non-HIV PCP. For the ICU physicians to diagnose PCP, the non-specific presentation of an acute febrile illness and respiratory distress with diffuse pulmonary infiltrates requires a high clinical index of suspician, familiarity with clinical conditions associated with increased risk for PCP, and a low threshold for bronchoscopy to establish the diagnosis.
Collapse
Affiliation(s)
- Geoffrey S. Gilmartin
- Division of Pulmonary and Critical Care, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Henry Koziel
- Division of Pulmonary and Critical Care, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA.,
| |
Collapse
|
24
|
Cooley L, Dendle C, Wolf J, Teh BW, Chen SC, Boutlis C, Thursky KA. Consensus guidelines for diagnosis, prophylaxis and management of Pneumocystis jirovecii pneumonia in patients with haematological and solid malignancies, 2014. Intern Med J 2015; 44:1350-63. [PMID: 25482745 DOI: 10.1111/imj.12599] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pneumocystis jirovecii infection (PJP) is a common cause of pneumonia in patients with cancer-related immunosuppression. There are well-defined patients who are at risk of PJP due to the status of their underlying malignancy, treatment-related immunosuppression and/or concomitant use of corticosteroids. Prophylaxis is highly effective and should be given to all patients at moderate to high risk of PJP. Trimethoprim-sulfamethoxazole is the drug of choice for prophylaxis and treatment, although several alternative agents are available.
Collapse
Affiliation(s)
- L Cooley
- Department of Microbiology and Infectious Diseases, Royal Hobart Hospital, Hobart, Tasmania
| | | | | | | | | | | | | |
Collapse
|
25
|
Mogoye BK, Du Plessis D, Poonsamy B, Frean J. Characterisation of Pneumocystis jiroveciiDHPS genotypes using a simple, inexpensive restriction fragment length polymorphism analysis. S Afr J Infect Dis 2015. [DOI: 10.1080/23120053.2015.1054180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
26
|
Lee SM, Cho YK, Sung YM, Chung DH, Jeong SH, Park JW, Lee SP. A Case of Pneumonia Caused by Pneumocystis jirovecii Resistant to Trimethoprim-Sulfamethoxazole. THE KOREAN JOURNAL OF PARASITOLOGY 2015; 53:321-7. [PMID: 26174826 PMCID: PMC4510680 DOI: 10.3347/kjp.2015.53.3.321] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 11/23/2022]
Abstract
A 50-year-old male visited the outpatient clinic and complained of fever, poor oral intake, and weight loss. A chest X-ray demonstrated streaky and fibrotic lesions in both lungs, and chest CT revealed multifocal peribronchial patchy ground-glass opacities with septated cystic lesions in both lungs. Cell counts in the bronchoalveolar lavage fluid revealed lymphocyte-dominant leukocytosis, and further analysis of lymphocyte subsets showed a predominance of cytotoxic T cells and few T helper cells. Video-assisted wedge resection of the left upper lobe was performed, and the histologic examination was indicative of a Pneumocystis jirovecii infection. Trimethoprim-sulfamethoxazole (TMP-SMX) was orally administered for 3 weeks; however, the patient complained of cough, and the pneumonia was aggravated in the follow-up chest X-ray and chest CT. Molecular studies demonstrated mutations at codons 55 and 57 of the dihydropteroate synthase (DHPS) gene, which is associated with the resistance to TMP-SMX. Clindamycin-primaquine was subsequently administered for 3 weeks replacing the TMP-SMX. A follow-up chest X-ray showed that the pneumonia was resolving, and the cough was also alleviated. A positive result of HIV immunoassay and elevated titer of HCV RNA indicated HIV infection as an underlying condition. This case highlights the importance of careful monitoring of patients with P. jirovecii pneumonia (PCP) during the course of treatment, and the molecular study of DHPS mutations. Additionally, altering the anti-PCP drug utilized as treatment must be considered when infection with drug-resistant P. jirovecii is suspected. To the best of our knowledge, this is the first case of TMP-SMX-resistant PCP described in Korea.
Collapse
Affiliation(s)
- Sang Min Lee
- Division of Pulmonology and Allergy, Gachon University Gil Medical Center, Incheon 405-760, Korea
| | - Yong Kyun Cho
- Division of Infection, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon 405-760, Korea
| | - Yon Mi Sung
- Department of Radiology, Gachon University Gil Medical Center, Incheon 405-760, Korea
| | - Dong Hae Chung
- Departement of Pathology, Gachon University Gil Medical Center, Incheon 405-760, Korea
| | - Sung Hwan Jeong
- Division of Pulmonology and Allergy, Gachon University Gil Medical Center, Incheon 405-760, Korea
| | - Jeong-Woong Park
- Division of Pulmonology and Allergy, Gachon University Gil Medical Center, Incheon 405-760, Korea
| | - Sang Pyo Lee
- Division of Pulmonology and Allergy, Gachon University Gil Medical Center, Incheon 405-760, Korea
| |
Collapse
|
27
|
Kim T, Lee SO, Hong HL, Lee JY, Kim SH, Choi SH, Kim MN, Kim YS, Woo JH, Sung H. Clinical characteristics of hospital-onset Pneumocystis pneumonia and genotypes of Pneumocystis jirovecii in a single tertiary centre in Korea. BMC Infect Dis 2015; 15:102. [PMID: 25884420 PMCID: PMC4359516 DOI: 10.1186/s12879-015-0847-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/19/2015] [Indexed: 01/13/2023] Open
Abstract
Background Pneumocystis pneumonia (PCP) may develop as a clinical manifestation of nosocomial pneumonia by means of either reactivation of resident P. jirovecii or de novo infection. However, there have been no studies describing the clinical characteristics of hospital-onset PCP. Methods A retrospective review of medical records was performed to identify episodes of hospital-onset PCP in a tertiary care centre in Korea between May 2007 and January 2013. We investigated whether human-to-human contact during hospitalisation contributed to PCP development by molecular analysis of the genes encoding mitochondrial large ribosomal subunit (mtLSU) rRNA and dihydropteroate synthase (DHPS) and a review of hospitalisation history. Results During the study period, 129 patients (130 episodes) were diagnosed with PCP. Of these, respiratory specimens from 94 patients during 95 PCP episodes were available for analysis. Sixteen episodes (16.8%) were categorised as hospital-onset PCP. There was a trend toward a higher proportion of haematological malignancy (43.8% [7/16] vs. 20.3% [16/79]; P = 0.058) in patients with hospital-onset PCP compared to patients with community-onset PCP. mtLSU genotype 1 was the most common, occurring in 41 (43.2%) patients. There were four possible cases of nosocomial transmission. Mutation in DHPS was not observed in any PCP episode. Conclusions PCP can be one of the causes of nosocomial pneumonia, although the mode of acquisition and transmission of P. jirovecii remains uncertain. mtLSU genotype 1 is the predominant P. jirovecii strain in Korea.
Collapse
Affiliation(s)
- Tark Kim
- Department of Internal Medicine, Soonchunhyang University Bucheon Hospital 170 Jomaru-ro, Bucheon-si, Gyeonggi-do, 420-767, Republic of Korea. .,Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea.
| | - Sang-Oh Lee
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea.
| | - Hyo-Lim Hong
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea.
| | - Ju Young Lee
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea.
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea.
| | - Sang-Ho Choi
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea.
| | - Mi-Na Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea.
| | - Yang Soo Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea.
| | - Jun Hee Woo
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea.
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea.
| |
Collapse
|
28
|
Functional characterization of the Pneumocystis jirovecii potential drug targets dhfs and abz2 involved in folate biosynthesis. Antimicrob Agents Chemother 2015; 59:2560-6. [PMID: 25691634 DOI: 10.1128/aac.05092-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/07/2015] [Indexed: 01/12/2023] Open
Abstract
Pneumocystis species are fungal parasites colonizing mammal lungs with strict host specificity. Pneumocystis jirovecii is the human-specific species and can turn into an opportunistic pathogen causing severe pneumonia in immunocompromised individuals. This disease is currently the second most frequent life-threatening invasive fungal infection worldwide. The most efficient drug, cotrimoxazole, presents serious side effects, and resistance to this drug is emerging. The search for new targets for the development of new drugs is thus of utmost importance. The recent release of the P. jirovecii genome sequence opens a new era for this task. It can now be carried out on the actual targets to be inhibited instead of on those of the relatively distant model Pneumocystis carinii, the species infecting rats. We focused on the folic acid biosynthesis pathway because (i) it is widely used for efficient therapeutic intervention, and (ii) it involves several enzymes that are essential for the pathogen and have no human counterparts. In this study, we report the identification of two such potential targets within the genome of P. jirovecii, the dihydrofolate synthase (dhfs) and the aminodeoxychorismate lyase (abz2). The function of these enzymes was demonstrated by the rescue of the null allele of the orthologous gene of Saccharomyces cerevisiae.
Collapse
|
29
|
Sheikholeslami MF, Sadraei J, Farnia P, Forozandeh Moghadam M, Emadikochak H. Dihydropteroate synthase gene mutation rates in Pneumocystis jirovecii strains obtained from Iranian HIV-positive and non-HIV-positive patients. Med Mycol 2015; 53:361-8. [PMID: 25631478 DOI: 10.1093/mmy/myu095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 12/15/2014] [Indexed: 12/17/2022] Open
Abstract
The dihydropteroate sulfate (DHPS) gene is associated with resistance to sulfa/sulfone drugs in Pneumocystis jirovecii. We investigated the DHPS mutation rate in three groups of Iranian HIV-positive and HIV-negative patients by polymerase chain reaction-restricted fragment length polymorphism analysis. Furthermore, an association between P. jirovecii DHPS mutations and strain typing was investigated based on direct sequencing of internal transcribed spacer region 1 (ITS1) and ITS2. The overall P. jirovecii DHPS mutation rate was (5/34; 14.7%), the lowest rate identified was in HIV-positive patients (1/16; 6.25%) and the highest rate was in malignancies patients (3/11; 27.3%). A moderate rate of mutation was detected in chronic obstructive pulmonary disease (COPD) patients (1/7; 14.3%). Most of the isolates were wild type (29/34; 85.3%). Double mutations in DHPS were detected in patients with malignancies, whereas single mutations at codons 55 and 57 were identified in the HIV-positive and COPD patients, respectively. In this study, two new and rare haplotypes were identified with DHPS mutations. Additionally, a positive relationship between P. jirovecii strain genotypes and DHPS mutations was identified. In contrast, no DHPS mutations were detected in the predominant (Eg) haplotype. This should be regarded as a warning of an increasing incidence of drug-resistant P. jirovecii strains.
Collapse
Affiliation(s)
- Maryam-Fatemeh Sheikholeslami
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran Tarbiat Modares University, Medical Faculty, Parasitology Department, Tehran, Iran
| | - Javid Sadraei
- Tarbiat Modares University, Medical Faculty, Parasitology Department, Tehran, Iran
| | - Parisa Farnia
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Hamid Emadikochak
- Iranian HIV/AIDS Research Center, Imam Khomini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
30
|
Long Y, Zhang C, Su L, Que C. Pneumocystis jirovecii dihydropteroate synthase gene mutations in a group of HIV-negative immunocompromised patients with Pneumocystis pneumonia. Exp Ther Med 2014; 8:1825-1830. [PMID: 25371739 PMCID: PMC4218695 DOI: 10.3892/etm.2014.2002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 09/04/2014] [Indexed: 12/28/2022] Open
Abstract
The purpose of this study was to investigate dihydropteroate synthase (DHPS) mutations and their clinical context in non-HIV-infected patients with Pneumocystis pneumonia (PCP). DHPS genes in respiratory samples collected from HIV-negative patients with PCP presented between January 2008 and April 2011 were amplified by polymerase chain reaction (PCR) and sequenced. Basic clinical data from the medical records of the patients were also reviewed. The most common point mutations, which result in Thr55Ala and Pro57Ser amino acid substitutions, were not detected in the Pneumocystis jirovecii sampled from the HIV-negative patients. Two other point mutations, which result in nonsynonymous mutation, Asp90Asn and Glu98Lys, were identified in P. jirovecii from two patients. Among the patients, the levels of lactate dehydrogenase (LDH), C-reactive protein (CRP) and plasma (1-3) β-D-glucan were elevated in 75, 92.31 and 42.86% of patients, respectively. The percentage of circulating lymphocytes was significantly lower in non-survivors than in survivors [4.2%, interquartile range (IQR) 2.4-5.85 versus 10.1%, IQR 5.65-23.4; P=0.019]. The neutrophil proportion in bronchoalveolar lavage fluid (BALF) was significantly higher in non-survivors than in survivors (49.78±27.67 versus 21.33±15.03%; P=0.047). Thirteen patients had received adjunctive corticosteroids (1 mg/kg/day prednisone equivalent) and nine (69.23%) of them eventually experienced treatment failure. No common DHPS gene mutations of P. jirovecii were detected in the HIV-negative PCP patients. However, other mutations did exist, the significance of which remains to be further identified. The elevation of neutrophil counts in BALF and reduction of the number of lymphocytes in peripheral blood may be associated with poor outcome. The efficacy of adjunctive steroid therapy in HIV-negative patients with P. jirovecii infection requires further investigation.
Collapse
Affiliation(s)
- Yingjiao Long
- Department of Pulmonary Medicine, First Hospital, Peking University, Beijing 100034, P.R. China
| | - Cheng Zhang
- Department of Pulmonary Medicine, First Hospital, Peking University, Beijing 100034, P.R. China
| | - Li Su
- Department of Pulmonary Medicine, First Hospital, Peking University, Beijing 100034, P.R. China
| | - Chengli Que
- Department of Pulmonary Medicine, First Hospital, Peking University, Beijing 100034, P.R. China
| |
Collapse
|
31
|
Vanspauwen MJ, Knops VEJ, Bruggeman CA, van Mook WNKA, Linssen CFM. Molecular epidemiology of Pneumocystis jiroveci in human immunodeficiency virus-positive and -negative immunocompromised patients in The Netherlands. J Med Microbiol 2014; 63:1294-1302. [PMID: 25060971 DOI: 10.1099/jmm.0.076257-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pneumocystis jiroveci infections can cause pneumocystis pneumonia (PCP) or lead to colonization without signs of PCP. Over the years, different genotypes of P. jiroveci have been discovered. Genomic typing of P. jiroveci in different subpopulations can contribute to unravelling the pathogenesis, transmission and spread of the different genotypes. In this study, we wanted to determine the distribution of P. jiroveci genotypes in immunocompetent and immunocompromised patients in The Netherlands and determine the clinical relevance of these detected mutations. A real-time PCR targeting the major surface glycoprotein gene (MSG) was used as a screening test for the presence of P. jiroveci DNA. Samples positive for MSG were genotyped based on the internal transcribed spacer (ITS) and dihydropteroate synthase (DHPS) genes. Of the 595 included bronchoalveolar lavage fluid samples, 116 revealed the presence of P. jiroveci DNA. A total of 52 of the 116 samples were ITS genotyped and 58 DHPS genotyped. The ITS genotyping revealed 17 ITS types, including two types that have not been described previously. There was no correlation between ITS genotype and underlying disease. All ITS- and DHPS-genotyped samples were found in immunocompromised patients. Of the 58 DHPS-genotyped samples, 50 were found to be WT. The other eight samples revealed a mixed genotype consisting of WT and type 1. The majority of the latter recovered on trimethoprim-sulfamethoxazole suggesting no clinical relevance for this mutation.
Collapse
Affiliation(s)
- Marijke J Vanspauwen
- Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Vera E J Knops
- Department of Medical Microbiology, Atrium Medical Centre, Heerlen, The Netherlands.,Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Cathrien A Bruggeman
- Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Walther N K A van Mook
- Department of Internal Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands.,Department of Intensive Care Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Catharina F M Linssen
- Department of Medical Microbiology, Atrium Medical Centre, Heerlen, The Netherlands.,Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| |
Collapse
|
32
|
Prevalence and genotype distribution of Pneumocystis jirovecii in Cuban infants and toddlers with whooping cough. J Clin Microbiol 2013; 52:45-51. [PMID: 24131683 DOI: 10.1128/jcm.02381-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes the prevalence and genotype distribution of Pneumocystis jirovecii obtained from nasopharyngeal (NP) swabs from immunocompetent Cuban infants and toddlers with whooping cough (WC). A total of 163 NP swabs from 163 young Cuban children with WC who were admitted to the respiratory care units at two pediatric centers were studied. The prevalence of the organism was determined by a quantitative PCR (qPCR) assay targeting the P. jirovecii mitochondrial large subunit (mtLSU) rRNA gene. Genotypes were identified by direct sequencing of mtLSU ribosomal DNA (rDNA) and restriction fragment length polymorphism (RFLP) analysis of the dihydropteroate synthase (DHPS) gene amplicons. qPCR detected P. jirovecii DNA in 48/163 (29.4%) samples. mtLSU rDNA sequence analysis revealed the presence of three different genotypes in the population. Genotype 2 was most common (48%), followed in prevalence by genotypes 1 (23%) and 3 (19%); mixed-genotype infections were seen in 10% of the cases. RFLP analysis of DHPS PCR products revealed four genotypes, 18% of which were associated with resistance to sulfa drugs. Only contact with coughers (prevalence ratio [PR], 3.51 [95% confidence interval {CI}, 1.79 to 6.87]; P = 0.000) and exposure to tobacco smoke (PR, 1.82 [95% CI, 1.14 to 2.92]; P = 0.009) were statistically associated with being colonized by P. jirovecii. The prevalence of P. jirovecii in infants and toddlers with WC and the genotyping results provide evidence that this population represents a potential reservoir and transmission source of P. jirovecii.
Collapse
|
33
|
Multilocus sequence typing of Pneumocystis jirovecii from clinical samples: how many and which loci should be used? J Clin Microbiol 2013; 51:2843-9. [PMID: 23784120 DOI: 10.1128/jcm.01073-13] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PCP) is an opportunistic infection with airborne transmission and remains a major cause of respiratory illness among immunocompromised individuals. In recent years, several outbreaks of PCP, occurring mostly in kidney transplant recipients, have been reported. Currently, multilocus sequence typing (MLST) performed on clinical samples is considered to be the gold standard for epidemiological investigations of nosocomial clusters of PCP. However, until now, no MLST consensus scheme has emerged. The aim of this study was to evaluate the discriminatory power of eight distinct loci previously used for the molecular typing of P. jirovecii (internal transcribed spacer 1 [ITS1], cytochrome b [CYB], mitochondrial rRNA gene [mt26S], large subunit of the rRNA gene [26S], superoxide dismutase [SOD], β-tubulin [β-TUB], dihydropteroate synthase [DHPS], and dihydrofolate reductase [DHFR]) using a cohort of 33 epidemiologically unrelated patients having respiratory samples that were positive for P. jirovecii and who were admitted to our hospital between 2006 and 2011. Our results highlight that the choice of loci for MLST is crucial, as the discriminatory power of the method was highly variable from locus to locus. In all, the eight-locus-based scheme we used displayed a high discriminatory power (Hunter [H] index, 0.996). Based on our findings, a simple and alternative MLST scheme relying on three loci only (mt26S, CYB, and SOD) provides enough discriminatory power (H-index, 0.987) to be used for preliminary investigations of nosocomial clusters of PCP.
Collapse
|
34
|
Porollo A, Meller J, Joshi Y, Jaiswal V, Smulian AG, Cushion MT. Analysis of current antifungal agents and their targets within the Pneumocystis carinii genome. Curr Drug Targets 2013; 13:1575-85. [PMID: 22934582 DOI: 10.2174/138945012803530107] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Revised: 07/11/2012] [Accepted: 08/29/2012] [Indexed: 11/22/2022]
Abstract
Pneumocystis pneumonia (PCP) remains a leading opportunistic infection in patients with weakened immune systems. The fungus causing the infection belongs to the genus, Pneumocystis, and its members are found in a large variety of mammals. Adaptation to the lung environment of a host with an intact immune system has been a key to its successful survival. Unfortunately, the metabolic strategies used by these fungi to grow and survive in this context are largely unknown. There were considerable impediments to standard approaches for investigation of this unique pathogen, the most problematic being the lack of a long term in vitro culture system. The absence of an ex vivo cultivation method remains today, and many fundamental scientific questions about the basic biology, metabolism, and life cycle of Pneumocystis are unanswered. Recent progress in sequencing of the Pneumocystis carinii genome, a species infecting rats, permitted a more informative search for genes and biological pathways within this pathogen that are known to be targets for existing antifungal agents. In this work, we review the classes of antifungal drugs with respect to their potential applicability to the treatment of PCP. Classes covered in the review are the azoles, polyenes, allylamines, and echinocandins. Factors limiting the use of standard antifungal treatments and the currently available alternatives (trimethoprim-sulfamethoxazole, atovaquone, and pentamidine) are discussed. A summary of genomic sequences within Pneumocystis carinii associated with the corresponding targeted biological pathways is provided. All sequences are available via the Pneumocystis Genome Project at http://pgp.cchmc.org/.
Collapse
Affiliation(s)
- Aleksey Porollo
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA.
| | | | | | | | | | | |
Collapse
|
35
|
Le Gal S, Robert-Gangneux F, Perrot M, Rouillé A, Virmaux M, Damiani C, Totet A, Gangneux JP, Nevez G. Absence of Pneumocystis dihydropteroate synthase mutants in Brittany, France. Diagn Microbiol Infect Dis 2013; 76:113-5. [PMID: 23433532 DOI: 10.1016/j.diagmicrobio.2013.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/16/2013] [Accepted: 01/16/2013] [Indexed: 11/15/2022]
Abstract
Archival Pneumocystis jirovecii specimens from 84 patients monitored at Rennes University Hospital (Rennes, France) were assayed at the dihydropteroate synthase (DHPS) locus. No patient was infected with mutants. The results provide additional data showing that P. jirovecii infections involving DHPS mutants do not represent a public health issue in Brittany, western France.
Collapse
Affiliation(s)
- Solène Le Gal
- University of Brest, LUBEM EA 3882, SFR 148, Brest, France; Laboratory of Parasitology and Mycology, Brest University Hospital, Brest, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Circulation of Pneumocystis dihydropteroate synthase mutants in France. Diagn Microbiol Infect Dis 2012; 74:119-24. [PMID: 22795965 DOI: 10.1016/j.diagmicrobio.2012.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 06/01/2012] [Accepted: 06/04/2012] [Indexed: 11/21/2022]
Abstract
Data on the prevalence of Pneumocystis jirovecii (P. jirovecii) dihydropteroate synthase (DHPS) mutants in France are still limited. In this study, mutant prevalence in the Brest region (western France) was determined. Archival pulmonary specimens from 85 patients infected with P. jirovecii and admitted to our institution (University Hospital, Brest) from October 2007 to February 2010 were retrospectively typed at the DHPS locus using a polymerase chain reaction-restriction fragment length polymorphism assay. Type identification was successful in 66 of 85 patients. Sixty-four patients were infected with a wild type, whereas mutants were found in 2 patients (2/66, 3%). Medical chart analysis revealed that these 2 patients usually lived in Paris. Another patient usually lived on the French Riviera, whereas 63 patients were from the city of Brest. Thus, the corrected prevalence of mutants in patients who effectively lived in our geographic area was 0% (0/63). Taking into account that i) Paris is characterized by a high prevalence of mutants from 18.5% to 40%, ii) infection diagnoses were performed in the 2 Parisians during their vacation <30 days, iii) infection incubation is assumed to last about 2 months, the results provide evidence of mutant circulation from Paris to Brest through infected vacationers. The study shows that the usual city of patient residence, rather than the city of infection diagnosis, is a predictor of mutants and that P. jirovecii infections involving mutants do not represent a public health issue in western France.
Collapse
|
37
|
Muñoz C, Zuluaga A, Restrepo A, Tobón A, Cano LE, Gonzalez A. Molecular diagnosis and detection of Pneumocystis jirovecii DHPS and DHFR genotypes in respiratory specimens from Colombian patients. Diagn Microbiol Infect Dis 2012; 72:204-13. [PMID: 22321995 DOI: 10.1016/j.diagmicrobio.2011.11.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/17/2011] [Accepted: 11/19/2011] [Indexed: 11/16/2022]
Abstract
A total of 98 respiratory specimens from 88 patients suspected of having Pneumocystis jirovecii pneumonia (PcP) were evaluated using a previously reported nested polymerase chain reaction (PCR) assay for mitochondrial large subunit rRNA (mtLSUrRNA). In addition, samples from patients with other pulmonary infections and a sizeable DNA collection from other fungal pathogens were studied. A panfungal PCR assay amplifying the ITS1-ITS2 regions were also used to identify all fungal DNAs. All samples positive for mtLSUrRNA-PCR were evaluated to determine mutations in dihydropteroate synthase (DHPS) and dihydrofolate reductase (DHFR) genes. All PCR-amplified products were sequenced. Of the 98 clinical specimens, 13 (13.2%) were positive by GMS stain and mtLSUrRNA-PCR, while 32 (32.6%) that were GMS stain-negative gave positive results with mtLSUrRNA-PCR. All the sequences corresponding to the 45 products amplified by mtLSUrRNA-PCR showed 99% or greater identity with P. jirovecii. The mtLSUrRNA-PCR exhibited 86% sensitivity and 98% and 96.6% specificity when results were compared to those corresponding to negative controls and other proven clinical entities, respectively. We found mutations in the DHPS gene in 3 (7.7%) patients, 2 located at codon 55 and 1 at codon 57. One patient showed a synonymous substitution at nucleotide position 312 in the DHFR gene. These results suggest that mtLSUrRNA-PCR is a useful test for diagnosing PcP. In contrast to other studies, this study found a low prevalence of mutations in the DHPS and DHFR genes in Colombian patients.
Collapse
Affiliation(s)
- Cesar Muñoz
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas, Medellín, Colombia
| | | | | | | | | | | |
Collapse
|
38
|
Le Gal S, Damiani C, Rouille A, Grall A, Treguer L, Virmaux M, Moalic E, Quinio D, Moal MC, Berthou C, Saliou P, Le Meur Y, Totet A, Nevez G. A Cluster of Pneumocystis Infections Among Renal Transplant Recipients: Molecular Evidence of Colonized Patients as Potential Infectious Sources of Pneumocystis jirovecii. Clin Infect Dis 2012; 54:e62-71. [DOI: 10.1093/cid/cir996] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
39
|
Huang L, Cattamanchi A, Davis JL, den Boon S, Kovacs J, Meshnick S, Miller RF, Walzer PD, Worodria W, Masur H. HIV-associated Pneumocystis pneumonia. PROCEEDINGS OF THE AMERICAN THORACIC SOCIETY 2011; 8:294-300. [PMID: 21653531 PMCID: PMC3132788 DOI: 10.1513/pats.201009-062wr] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 11/26/2010] [Indexed: 11/20/2022]
Abstract
During the past 30 years, major advances have been made in our understanding of HIV/AIDS and Pneumocystis pneumonia (PCP), but significant gaps remain. Pneumocystis is classified as a fungus and is host-species specific, but an understanding of its reservoir, mode of transmission, and pathogenesis is incomplete. PCP remains a frequent AIDS-defining diagnosis and is a frequent opportunistic pneumonia in the United States and in Europe, but comparable epidemiologic data from other areas of the world that are burdened with HIV/AIDS are limited. Pneumocystis cannot be cultured, and bronchoscopy with bronchoalveolar lavage is the gold standard procedure to diagnose PCP, but noninvasive diagnostic tests and biomarkers show promise that must be validated. Trimethoprim-sulfamethoxazole is the recommended first-line treatment and prophylaxis regimen, but putative trimethoprim-sulfamethoxazole drug resistance is an emerging concern. The International HIV-associated Opportunistic Pneumonias (IHOP) study was established to address these knowledge gaps. This review describes recent advances in the pathogenesis, epidemiology, diagnosis, and management of HIV-associated PCP and ongoing areas of clinical and translational research that are part of the IHOP study and the Longitudinal Studies of HIV-associated Lung Infections and Complications (Lung HIV).
Collapse
Affiliation(s)
- Laurence Huang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, San Francisco General Hospital, University of California, San Francisco, California 94110, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Miller RF, Evans HER, Copas AJ, Huggett JF, Edwards SG, Walzer PD. Seasonal variation in mortality of Pneumocystis jirovecii pneumonia in HIV-infected patients. Int J STD AIDS 2011; 21:497-503. [PMID: 20852200 DOI: 10.1258/ijsa.2010.010148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A seasonal variation in the presentation of Pneumocystis jirovecii pneumonia (PCP) has been reported and a previous study from this centre noted a seasonal variation in mortality rates. This study examined seasonal influences (including climatic factors) within-host factors (clinical and laboratory-derived variables), the infectious burden of P. jirovecii in bronchoalveolar lavage (BAL) fluid, the presence of dihydropteroate synthase (DHPS) mutations in P. jirovecii, variations in knowledge and skills of junior medical staff, and mortality in 547 episodes of PCP occurring in 494 HIV-infected patients. The overall mortality rate was 13.5%. There was a seasonal variation in mortality: highest in autumn (21.2%) and lowest in spring (9.7%), P = 0.047. After adjustment was made for prognostic factors previously identified as being associated with mortality (increasing patient age, second/third episode of PCP, low haemoglobin, low PaO(2), presence of medical co-morbidity and pulmonary Kaposi sarcoma), there was no seasonal association with mortality, P = 0.249. The quantity of P. jirovecii DNA in BAL fluid showed no evidence of seasonal variation, P = 0.67; DHPS mutations were identified with equal frequency in each season and the mortality rate for February and August (when junior medical staff arrive in new posts) was 16.7%, only slightly greater than for other months (13.0%).
Collapse
Affiliation(s)
- R F Miller
- Centre for Sexual Health and HIV Research, Research Department of Infection and Population Health, Division of Population Health, University College London, UK.
| | | | | | | | | | | |
Collapse
|
41
|
Alvarez-Martínez MJ, Miró JM, Valls ME, Mas J, de la Bellacasa JP, Sued O, Solé M, Rivas PV, de Lazzari E, Benito N, García F, Agustí C, Wilson PE, Gatell JM, Jiménez de Anta MT, Meshnick SR, Moreno A. Prevalence of dihydropteroate synthase genotypes before and after the introduction of combined antiretroviral therapy and their influence on the outcome of Pneumocystis pneumonia in HIV-1-infected patients. Diagn Microbiol Infect Dis 2010; 68:60-5. [PMID: 20727472 DOI: 10.1016/j.diagmicrobio.2010.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 04/08/2010] [Accepted: 04/09/2010] [Indexed: 02/08/2023]
Abstract
The objective of this study was to determine whether the prevalence of Pneumocystis jirovecii dihydropteroate synthase (DHPS) gene mutations has changed since the introduction of combined antiretroviral therapy (cART) and whether the mutations are associated with poor outcome in Spanish HIV-1-infected patients with Pneumocystis pneumonia (PcP). We studied 167 PcP episodes in HIV-1-infected patients diagnosed during the pre-cART (1989-1995) and cART (2001-2004) periods. Molecular genotyping of DHPS was successfully performed in 98 patients (43 pre-cART and 55 cART). Seventeen patients (17/98, 17%; 95% confidence interval [CI], 10-25%) had mutations in the DHPS gene: 14 patients (14/43, 33%; 95% CI, 19-49%) from the pre-cART period and 3 patients (3/55, 5.5%; 95% CI, 1.3-16%) from the cART period (P < 0.01). In the multivariate analysis, the pre-cART period, previous PcP prophylaxis with sulfa drugs, and homosexuality as an HIV risk factor were found to be associated with a higher risk of presenting DHPS mutations. Overall, 95% of patients were treated with trimethoprim and sulfamethoxazole (TMP-SMX). In-hospital mortality was similar in patients with (out) mutations (6% versus 11%, P = 0.84). DHPS gene mutations were more common during the pre-cART period and were associated with previous sulfa exposure and homosexuality. However, their presence did not worsen prognosis of PcP. The response to TMP-SMX with therapeutic doses was successful in most cases.
Collapse
Affiliation(s)
- Míriam J Alvarez-Martínez
- Hospital Clínic-IDIBAPS (Institut d'Investigació August Pi i Sunyer), Universitat de Barcelona, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Wissmann G, Morilla R, Friaza V, Calderón E, Varela JM. El ser humano como reservorio de Pneumocystis. Enferm Infecc Microbiol Clin 2010; 28:38-43. [DOI: 10.1016/j.eimc.2008.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 07/22/2008] [Accepted: 07/25/2008] [Indexed: 10/20/2022]
|
43
|
Moukhlis R, Boyer J, Lacube P, Bolognini J, Roux P, Hennequin C. Linking Pneumocystis jiroveci sulfamethoxazole resistance to the alleles of the DHPS gene using functional complementation in Saccharomyces cerevisiae. Clin Microbiol Infect 2009; 16:501-7. [PMID: 19673964 DOI: 10.1111/j.1469-0691.2009.02833.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Curative and prophylactic therapy for Pneumocystis jiroveci pneumonia relies mainly on cotrimoxazole, an association of trimethoprim and sulfamethoxazole (SMX). SMX inhibits the folic acid pathway through competition with para-aminobenzoic acid (pABA), one of the two substrates of the dihydropteroate synthase (DHPS), a key enzyme in de novo folic acid synthesis. The most frequent non-synonymous single nucleotide polymorphisms (SNPs) in P. jiroveci DHPS are seen at positions 165 and 171, the combination leading to four possible different genetic alleles. A number of reports correlate prophylaxis failure and mutation in the P. jiroveci DHPS but, because of the impossibility of reliably cultivating P. jiroveci, the link between DHPS mutation(s) and SMX susceptibility is not definitively proven. To circumvent this limitation, the yeast Saccharomyces cerevisiae was used as a model. The introduction of the P. jiroveci DHPS gene, with or without point mutations, directly amplified from a clinical specimen and cloned in a centromeric plasmid into a DHPS-deleted yeast strain, allowed a fully effective complementation. However, in the presence of SMX at concentrations >250 mg/L, yeasts complemented with the double mutated allele showed a lower susceptibility compared with strains complemented with either a single mutated allele or wild-type alleles. These results confirm the need for prospective study of pneumocystosis, including systematic determination of the DHPS genotype, to clarify further the impact of mutations on clinical outcome. Additionally, the S. cerevisiae model proves to be useful for the study of still uninvestigated biological properties of P. jiroveci.
Collapse
Affiliation(s)
- R Moukhlis
- Université Pierre et Marie Curie, Paris, France
| | | | | | | | | | | |
Collapse
|
44
|
Costa MC, Gaspar J, Mansinho K, Esteves F, Antunes F, Matos O. Detection of Pneumocystis jirovecii dihydropteroate synthase polymorphisms in patients with Pneumocystis pneumonia. ACTA ACUST UNITED AC 2009; 37:766-71. [PMID: 16191898 DOI: 10.1080/00365540510038505] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In the present study, in order to improve the detection of Pneumocystis jirovecii dihydropteroate synthase (DHPS) mutations in pulmonary specimens of HIV-infected patients with P. jirovecii pneumonia, we evaluated a microfiltration procedure for the removal of human cell contamination and a nested-PCR method, for amplification in specimens with low parasite load. In the studied population, PCR amplification of the DHPS gene was more successful in unfiltered than in filtered specimens, with both touchdown-PCR and nested-PCR procedures (p<0.05 and p<0.001, respectively), but the amount of host DNA in the samples analysed seems to be inversely related with the successful PCR parasite detection. Amplification of P. jirovecii DHPS gene with nested-PCR was achieved in 77.5% of the specimens studied, demonstrating that this is a useful method for the identification of mutations in pulmonary specimens, including samples with low parasite loads, and will facilitate the evaluation of the relationship between the P. jirovecii DHPS polymorphisms and clinical resistance to sulfa drugs.
Collapse
Affiliation(s)
- M C Costa
- Unidade de Protozoários Oportunistas/VIH e outras Protozooses, Unidade de Parasitologia e Microbiologia Médicas (UPMM), Instituto de Higiene e Medicina Tropical, Lisboa, Portugal
| | | | | | | | | | | |
Collapse
|
45
|
|
46
|
Alvarez-Martínez MJ, Moreno A, Miró JM, Valls ME, Rivas PV, de Lazzari E, Sued O, Benito N, Domingo P, Ribera E, Santín M, Sirera G, Segura F, Vidal F, Rodríguez F, Riera M, Cordero ME, Arribas JR, Jiménez de Anta MT, Gatell JM, Wilson PE, Meshnick SR. Pneumocystis jirovecii pneumonia in Spanish HIV-infected patients in the combined antiretroviral therapy era: prevalence of dihydropteroate synthase mutations and prognostic factors of mortality. Diagn Microbiol Infect Dis 2008; 62:34-43. [PMID: 18554841 DOI: 10.1016/j.diagmicrobio.2008.04.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 03/14/2008] [Accepted: 04/16/2008] [Indexed: 02/08/2023]
Abstract
The incidence of Pneumocystis jirovecii pneumonia (PCP) in HIV-infected patients has decreased thanks to sulfa prophylaxis and combined antiretroviral therapy. The influence of P. jirovecii dihydropteroate synthase (DHPS) gene mutations on survival is controversial and has not been reported in Spain. This prospective multicenter study enrolled 207 HIV-infected patients with PCP from 2000 to 2004. Molecular genotyping was performed on stored specimens. Risk factors for intensive care unit (ICU) admission and mortality were identified using a logistic regression model. Seven patients (3.7%; 95% confidence interval [CI], 1.5-7.5%) had DHPS mutations. Overall mortality was 15% (95% CI, 10-21%), rising to 80% (95% CI, 61-92%) in patients requiring mechanical ventilation. None of the patients with DHPS mutants died, nor did they need ICU admission or mechanical ventilation. PaO(2) <60 mm Hg at admission was a predictor of ICU admission (P = 0.01), and previous antiretroviral therapy predicted non-ICU admission (P = 0.009). PaO(2) <60 mm Hg at admission and ICU admission during the 1st week were predictors of mortality (P = 0.03 and P < 0.001, respectively). The prevalence of DHPS mutants in Spain is low and is not associated with a worse outcome. Severe respiratory failure at admission is the strongest predictor of PCP outcome.
Collapse
|
47
|
Aliouat-Denis CM, Chabé M, Demanche C, Aliouat EM, Viscogliosi E, Guillot J, Delhaes L, Dei-Cas E. Pneumocystis species, co-evolution and pathogenic power. INFECTION GENETICS AND EVOLUTION 2008; 8:708-26. [DOI: 10.1016/j.meegid.2008.05.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Revised: 05/02/2008] [Accepted: 05/03/2008] [Indexed: 01/13/2023]
|
48
|
Huang L, Welsh DA, Miller RF, Beard CB, Lawrence GG, Fox M, Swartzman A, Bensley MR, Carbonnet D, Davis JL, Chi A, Yoo BJ, Jones JL. Pneumocystis jirovecii dihydropteroate synthase gene mutations and human immunodeficiency virus-associated Pneumocystis pneumonia. J Eukaryot Microbiol 2007; 53 Suppl 1:S114-6. [PMID: 17169022 DOI: 10.1111/j.1550-7408.2006.00195.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Laurence Huang
- HIV/AIDS Division, Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California 94110, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Valerio A, Tronconi E, Mazza F, Cargnel A, Fantoni G, Atzori C. DHPS-mutated isolates of Pneumocystis jirovecii from HIV-infected individuals: analysis of related ITS genotypes. J Eukaryot Microbiol 2007; 53 Suppl 1:S108-9. [PMID: 17169019 DOI: 10.1111/j.1550-7408.2006.00192.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Antonella Valerio
- 2nd Department of Infectious Diseases, L. Sacco Hospital, 20157 Milan, Italy
| | | | | | | | | | | |
Collapse
|
50
|
Valerio A, Tronconi E, Mazza F, Fantoni G, Atzori C, Tartarone F, Duca P, Cargnel A. Genotyping of Pneumocystis jiroveci pneumonia in Italian AIDS patients. Clinical outcome is influenced by dihydropteroate synthase and not by internal transcribed spacer genotype. J Acquir Immune Defic Syndr 2007; 45:521-8. [PMID: 17558331 DOI: 10.1097/qai.0b013e3180decbe2] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Two Pneumocystis jiroveci independent genomic regions, internal transcribed spacer (ITS) 1 and ITS2, and dihydropteroate synthase (DHPS) gene have been used for typing a cohort of HIV-infected Italian patients with P jiroveci pneumonia (PcP). METHODS Bronchoalveolar lavage samples isolated from 207 HIV-infected adults were ITS and DHPS genotyped by DNA sequencing and by restriction fragment length polymorphism analysis, respectively. Mutant DHPS samples were cloned and ITS typed. Data on severity, treatment, and outcome of PcP were obtained by chart review. RESULTS High diversity with 46 different ITS genotypes was observed. At the DHPS locus, 9.1% of samples analyzed were found to be mutated. A correlation was observed between DHPS mutants and greater severity of PcP, as defined by higher lactate dehydrogenase (P = 0.015) and need for intubation (P = 0.002), and worse outcomes, as defined by failure of sulfa treatment (P = 0.04), death, and/or relapse of PcP (P = 0.008). There was a significant difference in ITS genotype patterns between DHPS wild-type and mutants (P = 0.028). CONCLUSIONS The present data suggest the absence of a correlation between P jiroveci ITS types and specific clinical characteristics. DHPS mutations correlate with possible failure of anti-P jiroveci sulfa therapy, and a trend of association is shown between DHPS mutations and some clinical PcP features.
Collapse
Affiliation(s)
- Antonella Valerio
- II Department of Infectious Diseases, Luigi Sacco Hospital, Milan, Italy
| | | | | | | | | | | | | | | |
Collapse
|