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Boyanova L, Boyanova L, Hadzhiyski P, Kandilarov N, Yordanov D, Gergova R, Markovska R. Mixed (multiple-genotype) Helicobacter pylori infections in Bulgarian patients. Diagn Microbiol Infect Dis 2023; 107:116073. [PMID: 37717293 DOI: 10.1016/j.diagmicrobio.2023.116073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/19/2023]
Abstract
The aim of the study was to evaluate the frequency and characteristics of mixed (multiple-genotype) Helicobacter pylori infections (MGIs) in 155 Bulgarian symptomatic patients (21 children and 134 adults). MGIs were common (36.1%), including double-strain (34.8%) and triple-strain infections (1.3%). None of the 8 ulcer patients harbored multiple subtypes. We detected 18 multiple allelic combinations, of which the most frequent subtypes (17.4%) were vacA s1as2 and vacA s1cs2. The 2 patients with triple-strain infections had vacA s1bs1cs2i1i2/iceA1A2 and vacA s1as1cs2 subtypes. They were both adult men with chronic gastritis and both were examined in 2022. The prevalence of MGIs (51.7%) was 2-fold higher in 2020 to 2022 than in 2015 to 2019 (26.3%). Putative factors for the increase may be the patient's characteristics and COVID-19 pandemic-associated factors. MGI rates corresponded to the high infection seroprevalence (72.4% in 2011) in Bulgaria. The evolution and clinical importance of mixed H. pylori infections merit extensive evaluation.
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Affiliation(s)
- Lyudmila Boyanova
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.
| | - Liliya Boyanova
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Petyo Hadzhiyski
- Specialized Hospital for Active Pediatric Treatment, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Nayden Kandilarov
- Department of General and Hepatobiliary Pancreatic Surgery, Department of Surgery, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Daniel Yordanov
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Raina Gergova
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Rumyana Markovska
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
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Honjo Y, Fukumoto S, Sakamoto H, Hikosaka K. New PCR primers targeting the cytochrome b gene reveal diversity of Leucocytozoon lineages in an individual host. Parasitol Res 2022; 121:3313-3320. [PMID: 36121563 DOI: 10.1007/s00436-022-07667-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022]
Abstract
Avian haemosporidian parasites have received considerable attention in ecology and evolution as a result of their wide distribution and ease of detection. However, conventional PCR-based detection methods may sometimes underestimate haemosporidian mixed infections, which are frequent in natural populations. This underestimation is due to differences in PCR sensitivity for detection of lineages within the mixed infections. Therefore, we designed new primers to amplify sequences that were not detected by the conventional primers and examined if our primers were useful for accurate detection of mixed infections. Blood samples were collected from 32 wild birds captured in Hokkaido, and 16 of these were positive for Leucocytozoon using the conventional primers, while 15 were positive using our primers. All positively amplified samples were sequenced, and we found that the conventional primers detected 16% (5/32) of multiple infections and none of them was a novel lineage, whereas our primers detected 44% (14/32) of multiple infections and ten of them were novel lineages. A phylogenetic analysis showed that the new primers can detect a wide range of Leucocytozoon lineages compared with that detected by the conventional primers. The results indicate that our primers are particularly suitable for revealing unique strains from multiple infections. Highly variable multiple infections in the same population of birds at the same location were found for the first time. We revealed a higher diversity of Leucocytozoon lineages in nature than expected, which would provide more information to better understand parasite diversity and host-vector interactions in wildlife.
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Affiliation(s)
- Yui Honjo
- Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Shinya Fukumoto
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, Japan
| | - Hirokazu Sakamoto
- Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenji Hikosaka
- Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
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Hu Z, Zheng H, Zeng K. Patterns of multiple human papillomavirus clearance during 5-aminolevulinic acid-based photodynamic therapy in patients with genital warts. Photodiagnosis Photodyn Ther 2021; 35:102454. [PMID: 34303875 DOI: 10.1016/j.pdpdt.2021.102454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 11/21/2022]
Abstract
BACKGROUND Multiple human papillomavirus infections are commonly encountered in genital warts. Infection can be eliminated using 5-aminolevulinic acid-based photodynamic therapy. The aim of this study was to identify the preponderant genotypes and patterns of human papillomavirus co-infection clearance during photodynamic therapy in patients with genital warts. METHODS We conducted a retrospective study between January 2020 and February 2021 at two hospitals in Guangzhou, China. Human papillomavirus typing and quantitative detection were performed before starting treatment and after each session of photodynamic therapy. RESULTS A total of 97 patients participated in the study. Co-infections with low-risk and high-risk types were common in genital warts. Types 6 was the most common type detected, followed by types 52, 11, 58, 51 and 56. Patients with multiple infections were more likely to have high-risk human papillomavirus infection. The viral load of high-risk human papillomavirus before treatment was significantly lower than that of low-risk human papillomavirus, and decreased faster during therapy. In addition, high-risk types were cleared more readily than low-risk types, and 51.4% of high-risk types were eliminated after three rounds of therapy. A transient increase in viral load, especially low-risk types, was observed after two sessions of therapy. CONCLUSIONS Low-risk human papillomavirus was preponderant in patients co-infected with low-risk and high-risk types. Photodynamic therapy effectively eliminated multiple human papillomavirus infections. The response to photodynamic therapy was mainly determined by the low-risk types in patients infected with combinations of low-risk and high-risk types.
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Siqueira JD, Goes LR, Alves BM, da Silva ACP, de Carvalho PS, Cicala C, Arthos J, Viola JPB, Soares MA. Distinguishing SARS-CoV-2 bonafide re-infection from pre-existing minor variant reactivation. Infect Genet Evol 2021; 90:104772. [PMID: 33592317 PMCID: PMC7882217 DOI: 10.1016/j.meegid.2021.104772] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/22/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
Different groups have recently reported events of SARS-CoV-2 reinfection, where patients had a sequence of positive-negative-positive RT-PCR tests. However, such events could be explained by different scenarios such as intermittent viral shedding, bonafide re-infection or multiple infection with alternating predominance of different viruses. Analysis of minor variants is an important tool to distinguish between these scenarios. Using ARTIC network PCR amplification and next-generation sequencing, we obtained SARS-CoV-2 sequences from two timepoints (with a time span of 102 days) of a patient followed at the Brazilian National Cancer Institute. Within-host variant analysis evidenced three single nucleotide variants (SNVs) at the consensus viral sequence in the second timepoint that were already present in the first timepoint as minor variants. Another five SNVs found in the second timepoint were not detected in the first sample sequenced, suggesting an additional infection by a yet another new virus. Our observation shed light into the existence of different viral populations that are present in dynamic frequencies and fluctuate during the course of SARS-CoV-2 infection. The detection of these variants in distinct disease events of an individual highlights a complex interplay between viral reactivation from a pre-existing minority variant and reinfection by a different virus.
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Affiliation(s)
- Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil
| | - Livia R Goes
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10 Room 6A08, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil
| | - Ana Carla P da Silva
- Hospital do Câncer II, Instituto Nacional de Câncer, Avenida Via Binário do Porto, 831, Rio de Janeiro, RJ 20081-250, Brazil
| | - Pedro S de Carvalho
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10 Room 6A08, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10 Room 6A08, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - João P B Viola
- Programa de Imunologia e Biologia de Tumores, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua Andre Cavalcanti, 37, Rio de Janeiro, RJ 20231-050, Brazil; Departamento de Genética, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ 21941-402, Brazil.
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Abstract
Scarlet fever is an acute respiratory infectious disease and the incidence rate is increasing from 2011 throughout the world. In this paper, the mathematical models are proposed, which incorporate both direct transmissions and indirect transmissions of scarlet fever. The threshold conditions for disease invasion are obtained in terms of the basic reproduction number. The peak value, final size and epidemic time in a seasonal prevalence are investigated numerically. Furthermore, the effects of seasonal fluctuations on disease outbreak are also studied on the basis of real data in China.
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Affiliation(s)
- Haonan Zhong
- School of Mathematics and Statistics, Southwest University, Chongqing, People's Republic of China
| | - Wendi Wang
- School of Mathematics and Statistics, Southwest University, Chongqing, People's Republic of China
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Eleje GU, Mbachu II, Ogwaluonye UC, Kalu SO, Onubogu CU, Nweje SI, Uzochukwu CE, Nwankwo CH, Fiebai PO, Loto OM, Akaba GO, Usman HA, Rabiu A, Egeonu RO, Igue OE, Adesoji BA, Jibuaku CH, Aja PO, Chidozie CP, Ibrahim HS, Aliyu FE, Numan AI, Okoro OD, Omoruyi SA, Oppah IC, Anyang UI, Ahmed A, Chukwurah SN, Umeononihu OS, Chukwuanukwu RC, Umeh EO, Emeka EA, Ogbuagu CN, Yakasai IA, Ezechi OC, Ikechebelu JI. Prevalence, seroconversion and mother-to-child transmission of dual and triplex infections of HIV, hepatitis B and C viruses among pregnant women in Nigeria: study protocol. Reprod Health 2020; 17:144. [PMID: 32977846 PMCID: PMC7519506 DOI: 10.1186/s12978-020-00995-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022] Open
Abstract
Background Nigeria contributes significantly to the global burden of HIV, Hepatitis B and C infections, either singly or in combinations, despite progress in HIV care regionally and globally. Although some limited data on mono infection of HIV, Hepatitis B and C virus infections do exists, that of dual and triplex infections, including seroconversion and mother-to-child transmission (MTCT) rates necessary for planning to address the scourge of infections in pregnancy are not available. Objectives To determine the seroprevalence, rate of new infections, MTCT of dual and triple infections of HIV, Hepatitis B and C viruses and associated factors, among pregnant women in Nigeria. Method A multicenter prospective cohort study will be conducted in six tertiary health facilities randomly selected from the six geopolitical zones of Nigeria. All eligible pregnant women are to be tested at enrollment after informed consent for HIV, Hepatitis B and C virus infections. While those positive for at least two of the infections in any combination will be enrolled into the study and followed up to 6 weeks post-delivery, those negative for the three infections or positive for only one of the infections at enrolment will be retested at delivery using a rapid diagnostic test. On enrolment into the study relevant information, will be obtained, and laboratory test of CD4 count, liver function test and full blood counts, and prenatal ultrasonography will also be obtained/performed. Management of mother-newborns pairs will be according to appropriate national guidelines. All exposed newborns will be tested for HIV, HBV or HCV infection at birth and 6 weeks using PCR technique. The study data will be documented on the study case record forms. Data will be managed with SPSS for windows version 23. Ethical approval was obtained from National Health Research Ethics Committee (NHREC) (NHREC/01/01/2007–23/01/2020). Conclusion Pregnant women with multiple of HIV, HBV and HCV infections are at increased risk of hepatotoxicity, maternal and perinatal morbidity and mortality. Additionally, infected pregnant women transmit the virus to their unborn baby even when asymptomatic. Children born with any of the infection have significantly poorer quality of life and lower five-year survival rate. Unfortunately, the seroconversion and MTCT rates of dual or triplex infections among pregnant women in Nigeria have not been studied making planning for prevention and subsequent elimination of the viruses difficult. The study is expected to fill this knowledge gaps. Nigeria joining the rest of the world to eliminate the triple infection among children rest on the availability of adequate and reliable data generated from appropriately designed, and powered study using representative population sample. The establishment of the three-in-one study of prevalence, rate of new infection, rate and risk factor for MTCT of dual and triple infection of HIV, Hepatitis B and C viruses among pregnant women in Nigeria is urgently needed for policy development and planning for the improvement of the quality of life of mothers and the elimination of childhood triplex infection.
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Affiliation(s)
- George Uchenna Eleje
- Department of Obstetrics and Gynecology, Nnamdi Azikiwe University, Awka, Nigeria. .,Department of Obstetrics and Gynecology, Nnamdi Azikiwe University Teaching Hospital, PMB 5025, Nnewi, Anambra State, Nigeria.
| | - Ikechukwu Innocent Mbachu
- Department of Obstetrics and Gynecology, Nnamdi Azikiwe University, Awka, Nigeria.,Department of Obstetrics and Gynecology, Nnamdi Azikiwe University Teaching Hospital, PMB 5025, Nnewi, Anambra State, Nigeria
| | | | - Stephen Okoroafor Kalu
- HIV Care Laboratory/HIV Care Department, Nnamdi Azikiwe University Teaching Hospital, Nnewi, Nigeria
| | | | | | | | | | - Preye Owen Fiebai
- Department of Obstetrics and Gynecology, University of Port Harcourt, PortHarcourt, Nigeria.,Department of Obstetrics and Gynecology, University of Port Harcourt Teaching Hospital, PortHarcourt, Nigeria
| | - Olabisi Morebise Loto
- Department of Obstetrics and Gynecology, Obafemi Awolowo University, Ile Ife, Nigeria.,Department of Obstetrics and Gynecology, Obafemi Awolowo University Teaching Hospital Complex, Ile-Ife, Nigeria
| | - Godwin Otuodichinma Akaba
- Department of Obstetrics and Gynecology, University of Abuja, Abuja, Nigeria.,Department of Obstetrics and Gynecology, University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Hadiza Abdullahi Usman
- Department of Obstetrics and Gynecology, University of Maiduguri, Maiduguri, Nigeria.,Department of Obstetrics and Gynecology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Ayyuba Rabiu
- Department of Obstetrics and Gynecology, Bayero University, Kano, Nigeria.,Department of Obstetrics and Gynecology, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Richard Obinwanne Egeonu
- Department of Obstetrics and Gynecology, Nnamdi Azikiwe University Teaching Hospital, PMB 5025, Nnewi, Anambra State, Nigeria
| | - Odion Emmanuel Igue
- Department of Physiological Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Bukola Abimbola Adesoji
- Department of Nursing, Obafemi Awolowo University Teaching Hospital Complex, Ile-Ife, Nigeria
| | | | - Prince Ogbonnia Aja
- Immunology Unit, Department of Medical Laboratory Science, Nnamdi Azikiwe University, Awka, Nigeria
| | | | - Hadiza Sani Ibrahim
- Department of Obstetrics and Gynecology, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Fatima Ele Aliyu
- Department of Obstetrics and Gynecology, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Aisha Ismaila Numan
- Department of Obstetrics and Gynecology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Ogbonna Dennis Okoro
- Department of Parasitology & Entomology, Faculty of Veterinary Medicine, University of Maiduguri Borno State, Maiduguri, Nigeria
| | - Solace Amechi Omoruyi
- Department of Obstetrics and Gynecology, University of Port Harcourt Teaching Hospital, PortHarcourt, Nigeria
| | - Ijeoma Chioma Oppah
- Department of Obstetrics and Gynecology, University of Port Harcourt Teaching Hospital, PortHarcourt, Nigeria
| | - Ubong Inyang Anyang
- Department of Obstetrics and Gynecology, University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Aishat Ahmed
- Department of Obstetrics and Gynecology, University of Abuja Teaching Hospital, Abuja, Nigeria
| | | | - Osita Samuel Umeononihu
- Department of Obstetrics and Gynecology, Nnamdi Azikiwe University, Awka, Nigeria.,Department of Obstetrics and Gynecology, Nnamdi Azikiwe University Teaching Hospital, PMB 5025, Nnewi, Anambra State, Nigeria
| | | | - Eric Okechukwu Umeh
- Department of Radiology, Faculty of Medicine, Nnamdi Azikiwe University, Awka, Nigeria
| | - Ekene Agatha Emeka
- Department of Family Medicine, Faculty of Medicine, Nnamdi Azikiwe University, Awka, Nigeria
| | | | - Ibrahim Adamu Yakasai
- Department of Obstetrics and Gynecology, Bayero University, Kano, Nigeria.,Department of Obstetrics and Gynecology, Aminu Kano Teaching Hospital, Kano, Nigeria
| | | | - Joseph Ifeanyichukwu Ikechebelu
- Department of Obstetrics and Gynecology, Nnamdi Azikiwe University, Awka, Nigeria.,Department of Obstetrics and Gynecology, Nnamdi Azikiwe University Teaching Hospital, PMB 5025, Nnewi, Anambra State, Nigeria
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Groß U, Brzuszkiewicz E, Gunka K, Starke J, Riedel T, Bunk B, Spröer C, Wetzel D, Poehlein A, Chibani C, Bohne W, Overmann J, Zimmermann O, Daniel R, Liesegang H. Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile. BMC Genomics 2018; 19:1. [PMID: 29291715 PMCID: PMC5749029 DOI: 10.1186/s12864-017-4368-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/06/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Clostridioides difficile infections (CDI) have emerged over the past decade causing symptoms that
range from mild, antibiotic-associated diarrhea (AAD) to life-threatening toxic megacolon. In this study, we describe a multiple and isochronal (mixed) CDI caused by the isolates DSM 27638, DSM 27639 and DSM 27640 that already initially showed different morphotypes on solid media. RESULTS The three isolates belonging to the ribotypes (RT) 012 (DSM 27639) and 027 (DSM 27638 and DSM 27640)
were phenotypically characterized and high quality closed genome sequences were generated. The genomes were compared with seven reference strains including three strains of the RT 027, two of the RT 017, and one of the RT 078 as well as a multi-resistant RT 012 strain. The analysis of horizontal gene transfer events revealed gene acquisition incidents that sort the strains within the time line of the spread of their RTs within Germany. We could show as well that horizontal gene transfer between the members of different RTs occurred within this multiple infection. In addition, acquisition and exchange of virulence-related features including antibiotic resistance genes were observed. Analysis of the two genomes assigned to RT 027 revealed three single nucleotide polymorphisms (SNPs) and apparently a regional genome modification within the flagellar switch that regulates the fli operon. CONCLUSION Our findings show that (i) evolutionary events based on horizontal gene transfer occur within an ongoing
CDI and contribute to the adaptation of the species by the introduction of new genes into the genomes, (ii) within a multiple infection of a single patient the exchange of genetic material was responsible for a much higher genome variation than the observed SNPs.
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Affiliation(s)
- Uwe Groß
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Elzbieta Brzuszkiewicz
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Katrin Gunka
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Jessica Starke
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Daniela Wetzel
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Cynthia Chibani
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Wolfgang Bohne
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Ortrud Zimmermann
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany.
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Troell K, Hallström B, Divne AM, Alsmark C, Arrighi R, Huss M, Beser J, Bertilsson S. Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes. BMC Genomics 2016; 17:471. [PMID: 27338614 PMCID: PMC4917956 DOI: 10.1186/s12864-016-2815-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 06/07/2016] [Indexed: 12/11/2022] Open
Abstract
Background Infectious disease involving multiple genetically distinct populations of pathogens is frequently concurrent, but difficult to detect or describe with current routine methodology. Cryptosporidium sp. is a widespread gastrointestinal protozoan of global significance in both animals and humans. It cannot be easily maintained in culture and infections of multiple strains have been reported. To explore the potential use of single cell genomics methodology for revealing genome-level variation in clinical samples from Cryptosporidium-infected hosts, we sorted individual oocysts for subsequent genome amplification and full-genome sequencing. Results Cells were identified with fluorescent antibodies with an 80 % success rate for the entire single cell genomics workflow, demonstrating that the methodology can be applied directly to purified fecal samples. Ten amplified genomes from sorted single cells were selected for genome sequencing and compared both to the original population and a reference genome in order to evaluate the accuracy and performance of the method. Single cell genome coverage was on average 81 % even with a moderate sequencing effort and by combining the 10 single cell genomes, the full genome was accounted for. By a comparison to the original sample, biological variation could be distinguished and separated from noise introduced in the amplification. Conclusions As a proof of principle, we have demonstrated the power of applying single cell genomics to dissect infectious disease caused by closely related parasite species or subtypes. The workflow can easily be expanded and adapted to target other protozoans, and potential applications include mapping genome-encoded traits, virulence, pathogenicity, host specificity and resistance at the level of cells as truly meaningful biological units. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2815-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karin Troell
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden.
| | - Björn Hallström
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Anna-Maria Divne
- Microbial Single Cell Genomics Facility, Department of Cell and Molecular Biology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Cecilia Alsmark
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden.,Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Romanico Arrighi
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Mikael Huss
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Jessica Beser
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Morikawa S, Kohdera U, Hosaka T, Ishii K, Akagawa S, Hiroi S, Kase T. Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children. J Clin Virol 2015; 73:14-9. [PMID: 26521224 DOI: 10.1016/j.jcv.2015.10.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/29/2015] [Accepted: 10/04/2015] [Indexed: 11/20/2022]
Abstract
Nasal aspirates were subjected to real-time PCR to detect 16 respiratory viruses. One or more viruses were detected in 83% of specimens. Rhinoviruses were the most frequently detected viruses. Seasonal distribution was seen for each virus. The clinical severity did not differ among main respiratory viral infections.
Background Using the polymerase chain reaction (PCR) method it is possible to detect uncultivable viruses and discover multiple viral infections. However, the clinical importance of these findings in relation to symptoms is not known. Objectives The seasonal fluctuations of respiratory viruses and the clinical outcomes of single infections and dual infections were investigated. Study design Nasal aspirate samples were obtained from outpatients and inpatients of a children’s hospital and these samples were subjected to real-time PCR to detect 16 respiratory viruses. Seasonal variations of the 16 viruses and the clinical outcomes such as wheezing, the need for oxygenation and prolonged hospitalization of patients with single viral infections and multiple infections were determined for the 5 most often detected viruses. Results Among 512 specimens analyzed, one or more viruses were detected in 424 (83%) specimens. Two or more viruses were detected in 160 samples (31% of all samples). The epidemic peaks of the viruses did not coincide with each other. Rhinoviruses were the most frequently detected viruses and their coinfection rates were also higher. However, the disease severity in the lower respiratory tract did not differ in most respiratory viral infections regardless of whether there was single infection or dual infection with a rhinovirus and other respiratory virus. Conclusions Seasonal distribution was seen for each virus. There were no significant differences in clinical symptoms in the children studied. Because the infection of rhinoviruses is the common occurrence in children, it is hypothesized that the factors related to disease severity are mainly the underlying conditions of the children.
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Natsopoulou ME, McMahon DP, Paxton RJ. Parasites modulate within-colony activity and accelerate the temporal polyethism schedule of a social insect, the honey bee. Behav Ecol Sociobiol 2015; 70:1019-1031. [PMID: 27397965 PMCID: PMC4917585 DOI: 10.1007/s00265-015-2019-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 09/24/2015] [Accepted: 09/29/2015] [Indexed: 12/11/2022]
Abstract
Task allocation in social insect colonies is generally organised into an age-related division of labour, termed the temporal polyethism schedule, which may in part have evolved to reduce infection of the colony's brood by pests and pathogens. The temporal polyethism schedule is sensitive to colony perturbations that may lead to adaptive changes in task allocation, maintaining colony homeostasis. Though social insects can be infected by a range of parasites, little is known of how these parasites impact within-colony behaviour and the temporal polyethism schedule. We use honey bees (Apis mellifera) experimentally infected by two of their emerging pathogens, Deformed wing virus (DWV), which is relatively understudied concerning its behavioural impact on its host, and the exotic microsporidian Nosema ceranae. We examined parasite effects on host temporal polyethism and patterns of activity within the colony. We found that pathogens accelerated the temporal polyethism schedule, but without reducing host behavioural repertoire. Infected hosts exhibited increased hyperactivity, allocating more time to self-grooming and foraging-related tasks. The strength of behavioural alterations we observed was found to be pathogen specific; behavioural modifications were more pronounced in virus-treated hosts versus N. ceranae-treated hosts, with potential benefits for the colony in terms of reducing within-colony transmission. Investigating the effects of multiple pathogens on behavioural patterns of social insects could play a crucial role in understanding pathogen spread within a colony and their effects on colony social organisation.
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Affiliation(s)
- Myrsini E Natsopoulou
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Dino P McMahon
- Institute of Biology, Free University Berlin, Schwendenerstr.1, 14195 Berlin, Germany ; Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205 Berlin, Germany
| | - Robert J Paxton
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
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Mata VA, da Silva LP, Lopes RJ, Drovetski SV. The Strait of Gibraltar poses an effective barrier to host-specialised but not to host-generalised lineages of avian Haemosporidia. Int J Parasitol 2015; 45:711-9. [PMID: 26056737 DOI: 10.1016/j.ijpara.2015.04.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 12/14/2022]
Abstract
One of the major concerns with ongoing environmental global change is the ability of parasites to shift their distribution (both geographically and across hosts) and to increase in virulence. To understand the structure, diversity and connectivity of parasite communities across the Mediterranean Sea, we used avian haemosporidian communities associated with forest birds of northwestern Africa and northwestern Iberia as a model system. We characterised host specificity of lineages and tested whether host generalists are more likely to cross the biogeographic barrier imposed by the Strait of Gibraltar than host specialists. We sampled 321 birds of 43 species in northwestern Africa and 735 birds of 49 species in northwestern Iberia. Using a PCR-based approach to amplify Plasmodium, Haemoproteus and Leucocytozoon parasites, we retrieved 969 sequences representing 200 unique cytochrome-b lineages. Haemosporidians infected a significantly higher proportion of birds in northwestern Africa (78.5%) than in northwestern Iberia (50.5%). Relative diversity of different haemosporidian genera did not differ between our study areas, but Plasmodium was overrepresented among individual infections in northwestern Iberia. Haemoproteus and Leucocytozoon lineages were predominantly host-specialised and Plasmodium lineages were host-generalised. The number of regions occupied by lineages was significantly associated with their host specificity and abundance. These data are consistent with the positive abundance-occupancy relationship and patterns of host specificity among different haemosporidian genera observed in other studies.
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Affiliation(s)
- Vanessa A Mata
- CIBIO-InBIO - Research Center in Biodiversity and Genetic Resources, Research Network in Biodiversity and Evolutionary Biology, Associate Laboratory, University of Porto, 4485-661 Vairão, Portugal.
| | - Luís P da Silva
- MARE - Marine and Environmental Sciences Center, Department of Life Sciences, University of Coimbra, 3004-517 Coimbra, Portugal; CFE - Center for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Ricardo J Lopes
- CIBIO-InBIO - Research Center in Biodiversity and Genetic Resources, Research Network in Biodiversity and Evolutionary Biology, Associate Laboratory, University of Porto, 4485-661 Vairão, Portugal
| | - Sergei V Drovetski
- Division of Birds, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Ave, NW, Washington, DC 20004, USA
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Phan D, Wodarz D. Modeling multiple infection of cells by viruses: Challenges and insights. Math Biosci 2015; 264:21-8. [PMID: 25770053 DOI: 10.1016/j.mbs.2015.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 02/26/2015] [Accepted: 03/03/2015] [Indexed: 11/17/2022]
Abstract
The multiple infection of cells with several copies of a given virus has been demonstrated in experimental systems, and has been subject to previous mathematical modeling approaches. Such models, especially those based on ordinary differential equations, can be characterized by difficulties and pitfalls. One such difficulty arises from what we refer to as multiple infection cascades. That is, such models subdivide the infected cell population into sub-populations that are carry i viruses, and each sub-population can in principle always be further infected to contain i + 1 viruses. In order to study the model with numerical simulations, the infection cascade needs to be cut artificially, and this can influence the results. This is shown here in the context of the simplest setting that involves a single, homogeneous virus population. If the viral replication rate is sufficiently fast, then most infected cells will accumulate in the last member of the infection cascade, leading to incorrect numerical results. This can be observed even with relatively long infection cascades, and in this case computational costs associated with a sufficiently long infection cascade can render this approach impractical. We subsequently examine a more complex scenario where two virus types/strains with different fitness are allowed to compete. Again, we find that the length of the infection cascade can have a crucial influence on the results. Competitive exclusion can be observed for shorter infection cascades, while coexistence can be observed for longer infection cascades. More subtly, the length of the infection cascade can influence the equilibrium level of the populations in numerical simulations. Studying the model in a parameter regime where an increase in the infection cascade length does not influence the results, we examine the effect of multiple infection on the outcome of competition. We find that multiple infection can promote coexistence of virus types if there is a degree of intracellular niche separation. If this is not the case, the only outcome is competitive exclusion, similar to equivalent models that do not take into account multiple infection of cells. We further find that multiple infection has a reduced ability to allow coexistence if virus spread is spatially restricted compared to a well-mixed system. These results provide important insights when analyzing and interpreting multiple infection models.
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Affiliation(s)
- Dustin Phan
- Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine, CA 92617, United States
| | - Dominik Wodarz
- Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine, CA 92617, United States.
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