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Ackermann MR, Bannantine JP. Progress and persistence of diseases of high consequence to livestock in the United States. One Health 2024; 19:100865. [PMID: 39185352 PMCID: PMC11344017 DOI: 10.1016/j.onehlt.2024.100865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/27/2024] Open
Abstract
The USDA/ARS-National Disease Center (NADC) will celebrate its 65th anniversary of existence in November 2026. NADC continues as one of the world's premier animal health research centers conducting basic and applied research on endemic diseases with economic impact on U.S. livestock and wildlife. This research center also supports a program studying important food safety pathogens such as Salmonella, E. coli and Campylobacter. NADC has contributed significantly to the elimination of a few diseases, notably hog cholera and milk fever, and made progress in reducing the impact of many other animal diseases through vaccines, therapies and managerial recommendations. Despite nearly 65 years of targeted research on these diseases and much progress, some of these continue to persist. The reasons for such persistence varies for each disease condition and they are often multifactorial involving host susceptibility, virulence and even environmental conditions. Individually and in aggregate, these disease conditions have a massive economic impact and can be devasting to animal producers, owners and individuals that become infected through zoonotic disease agents such as tuberculosis, leptospirosis and avian influenza. They also diminish the health, well-being and welfare of affected animals, which directly affects the food supply. The NADC is using all available technologies including genomic, biochemical, reverse genetics, and vaccine trials in the target host to combat these significant diseases. We review the progress and reasons for persistence of selected diseases and food safety pathogens as well as the progress and potential outcomes should research and programmatic plans to eliminate these disease conditions cease.
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Affiliation(s)
- Mark R. Ackermann
- US Department of Agriculture-Agricultural Research Service, National Animal Disease Center, Ames, IA, USA
| | - John P. Bannantine
- US Department of Agriculture-Agricultural Research Service, National Animal Disease Center, Ames, IA, USA
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Lin Y, Peng Q, Chen B. Clinical characterization of brucellosis in children from non-pastoral areas: a report of five cases. BMC Infect Dis 2024; 24:929. [PMID: 39245722 PMCID: PMC11382466 DOI: 10.1186/s12879-024-09843-7] [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: 05/16/2024] [Accepted: 08/30/2024] [Indexed: 09/10/2024] Open
Abstract
BACKGROUND Brucellosis is a global public health concern and occurs mainly in young adults and the elderly, with children having a lower incidence, thus often leading to delayed treatment. This study aimed to describe the epidemiologic features and clinical characteristics of brucellosis in children. METHODS In this retrospective study, the clinical data of five children diagnosed with brucellosis in Anhui Provincial Children's Hospital between January 1, 2021 and December 30, 2022 were analyzed. RESULTS All five cases were from non-pastoral areas, among which three have a history of livestock exposure and originated from the countryside. All patients had medium-high grade fever, mostly accompanied by night sweats and malaise, and three had joint pains. Laboratory tests showed that their white blood cell count was normal or mildly raised, with lymphocytes as the predominant cell population. Four patients had anemia, four had aspartate aminotransferase and alanine aminotransferase abnormality, and two had elevated ferritin levels. All blood samples were positive for Brucella culture, one of which had positive bone marrow culture, and all had positive serology test results. All patients were treated with rifampicin, in combination with sulfamethoxazole or doxycycline for 6 weeks following diagnosis. Four children had a good prognosis, but one child had recurrent joint pain. CONCLUSIONS The epidemiologic history of children from non-pastoral areas with brucellosis is often unclear; clinical manifestations and laboratory tests lack specificity; and they are easily delayed diagnosis. Clinicians should remain vigilant regarding the possibility of this disease in children with fever of unknown origin. The epidemiological history should be investigated in detail to improve the diagnostic ability of brucellosis. We recommend emphasizing serological testing. Children with brucellosis who receive timely diagnosis and standardized treatment can expect a favorable prognosis.
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Affiliation(s)
- Yuan Lin
- Department of Infectious Diseases, Anhui Provincial Children's Hospital, Hefei, 230001, China
| | - Qin Peng
- Department of Infectious Diseases, Anhui Provincial Children's Hospital, Hefei, 230001, China
| | - Biquan Chen
- Department of Infectious Diseases, Anhui Provincial Children's Hospital, Hefei, 230001, China.
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Yang C, Gao J, Xian R, Liu X, Kuai W, Yin C, Fan H, Tian J, Ma X, Ma J. Molecular epidemiology of Brucella abortus isolated from the environment in Ningxia Hui autonomous region, China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105635. [PMID: 38969194 DOI: 10.1016/j.meegid.2024.105635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/18/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Brucellosis is among the key zoonotic infectious diseases in China, and The Ningxia Hui Autonomous Region represents a major endemic area, and it is one of the main causes of poverty in the region due to illness. In Ningxia, there is substantial research on Brucella melitensis, studies on the molecular epidemiology of Brucella abortus are notably scarce. Consequently, this study aims to undertake pathogenic isolation and molecular epidemiological research on Brucella abortus isolated from the environment in Ningxia, providing insights and evidence to advance the prevention and control measures for brucellosis in the region. Building on traditional pathogenic detection methods, this research employs whole-genome sequencing(WGS) techniques and bioinformatics software to conduct a phylogenetic comparison of Ningxia strains and strains of Brucella abortus from various geographical origins. The results indicate that four Brucella abortus strains are classified as biovar 3 and MLST type ST2. It is shown that the local strains were closer phylogenetic relationships with strains from Asian and European countries. The presence of Brucella abortus in certain environmental sectors of Ningxia indicates a risk of transmission from the environment to animals and subsequently to humans. In conclusion, the Brucella abortus exists in some farming environments in Ningxia, and exists for a long time. Therefore, it is necessary to strengthen the monitoring of the disinfection effect of the farming environment to provide a basis for the forward movement of the gate of brucellosis prevention and control.
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Affiliation(s)
- Cong Yang
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan, 750004 Ningxia, China
| | - Jianwei Gao
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan, 750004 Ningxia, China
| | - Ran Xian
- Ningxia Medical University, Yinchuan, 750004 Ningxia, China
| | - Xiang Liu
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan, 750004 Ningxia, China
| | - Wenhe Kuai
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan, 750004 Ningxia, China
| | - Cai Yin
- Ningxia Hui Autonomous Region Animal Center for Disease Control and Prevention, Yinchuan, 750004 Ningxia, China
| | - Haohao Fan
- Ningxia Medical University, Yinchuan, 750004 Ningxia, China
| | - Jinhua Tian
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan, 750004 Ningxia, China
| | - Xueping Ma
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan, 750004 Ningxia, China
| | - Jiangtao Ma
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan, 750004 Ningxia, China.
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Alirezaei A, Khalili M, Baseri N, Esmaeili S, Mohammadi Damaneh E, Kazeminia S. Molecular detection of Brucella species among aborted small ruminants in southeast Iran. Braz J Microbiol 2024; 55:911-917. [PMID: 37999910 PMCID: PMC10920489 DOI: 10.1007/s42770-023-01191-z] [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: 09/21/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
Brucellosis, caused by Brucella bacteria, is a common zoonotic infectious disease with various clinical manifestations in humans and animals. The disease is endemic in human and ruminant populations in Iran, with a particular prevalence in areas where humans have close interactions with livestock. Since domestic animals serve as the primary reservoir for brucellosis, this study aimed to identify the presence of Brucella spp. among aborted small ruminants in southeast Iran. Between 2021 and 2022, aborted fetuses of small ruminants (46 sheep and 4 goats) were collected from Zarand County in the Kerman province. Swab samples from the abomasum contents of these fetuses were obtained and subjected to DNA extraction. The samples were then tested for Brucella spp. detection using the polymerase chain reaction (PCR) method. Out of the 50 aborted fetuses examined, Brucella spp. was detected in 15 (30%) specimens, comprising 13 (28%) sheep and 2 (50%) goats. Species typing revealed the presence of Brucella ovis (6 sheep and 1 goat), Brucella melitensis (6 sheep), and Brucella abortus (1 sheep) among the positive specimens. This cross-sectional study highlights the high prevalence of various Brucella species in samples from small ruminant abortions in southeast Iran. Additionally, the identified Brucella species were not limited to their primary host livestock. These indicated potential cross-species transmission among small ruminants.
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Affiliation(s)
- Amin Alirezaei
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mohammad Khalili
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Neda Baseri
- National Reference Laboratory of Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran.
- Department of Epidemiology and Biostatics, Pasteur Institute of Iran, Tehran, Iran.
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Saber Esmaeili
- National Reference Laboratory of Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran.
- Department of Epidemiology and Biostatics, Pasteur Institute of Iran, Tehran, Iran.
| | - Elham Mohammadi Damaneh
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
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Liu Z, Wang M, Shi Q, Dong X, Gao L, Li Z. Original and introduced lineages co-driving the persistence of Brucella abortus circulating in West Africa. Front Public Health 2023; 11:1106361. [PMID: 37006545 PMCID: PMC10050740 DOI: 10.3389/fpubh.2023.1106361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/20/2023] [Indexed: 03/17/2023] Open
Abstract
IntroductionBrucellosis, a serious public health issue affecting animals and humans, is neglected in West Africa (WA).MethodsIn the present study, bio-typing, multi-locus sequence typing (MLST), multiple-locus variable-number tandem repeat analysis (MLVA), and whole genome sequencing single-nucleotide polymorphism (WGS-SNP) analysis were used to characterize the Brucella abortus (B. abortus) strains from WA.ResultsAll of the 309 strains analyzed in this study were extracted and downloaded from the international MLVA bank and were from 10 hosts (cattle, humans, ovine, buffalo, dromedaries, horse, sheep, zebu, dog, and cat) distributed in 17 countries in WA. Based on the bio-typing, three biovars, dominated by B. abortus bv.3, were observed and reported across seven decades (1958–2019). With MLST, 129 B. abortus strains from the present study were sorted into 14 STs, with ST34 as the predicted founder. These 14 STs clustered into the global MLST data into three clone complexes (C I–C III) with the majority of strains clustering in C I, while C II forms an independent branch, and C III harbors three STs shared by different continents. These data revealed that most cases were caused by strains from native lineages. According to the MLVA-11 comparison, 309 strains were divided into 22 MLVA-11 genotypes, 15 of which were unique to WA and the remaining seven had a global distribution. MLVA-16 analysis showed that there were no epidemiological links among these strains. Based on the MLVA data, B. abortus strains from WA have high genetic diversity, and predominated genotypes were descended from a native lineage. While the MLVA-16 globally highlights that the dominant native and few introduced lineages (from Brazil, the USA, South Korea, Argentina, India, Italy, Portugal, the UK, Costa Rica, and China) co-driving the B. abortus ongoing prevalence in WA. The high-resolution SNP analysis implied the existence of introduced B. abortus lineages, which may be reasonably explained by the movement and trade of dominant hosts (cattle) and/or their products.DiscussionOur results indicated that B. abortus strains in WA consist of native and introduced strains that necessitate control such as vaccination, testing, slaughtering, and movement control by the relevant country authorities to reduce brucellosis in livestock.
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Affiliation(s)
- Zhiguo Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Vocational and Technical College, Inner Mongolia Agricultural University, Baotou, China
| | - Miao Wang
- Comprehensive Office, Ulanqab Center for Disease Control and Prevention, Jining, Inner Mongolia, China
| | - Qi Shi
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoping Dong
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Liping Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Changzhi Medical College, Changzhi, Shanxi, China
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Giuliano CJ, Wei KJ, Harling FM, Waldman BS, Farringer MA, Boydston EA, Lan TCT, Thomas RW, Herneisen AL, Sanderlin AG, Coppens I, Dvorin JD, Lourido S. Functional profiling of the Toxoplasma genome during acute mouse infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.05.531216. [PMID: 36945434 PMCID: PMC10028831 DOI: 10.1101/2023.03.05.531216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Within a host, pathogens encounter a diverse and changing landscape of cell types, nutrients, and immune responses. Examining host-pathogen interactions in animal models can therefore reveal aspects of infection absent from cell culture. We use CRISPR-based screens to functionally profile the entire genome of the model apicomplexan parasite Toxoplasma gondii during mouse infection. Barcoded gRNAs were used to track mutant parasite lineages, enabling detection of bottlenecks and mapping of population structures. We uncovered over 300 genes that modulate parasite fitness in mice with previously unknown roles in infection. These candidates span multiple axes of host-parasite interaction, including determinants of tropism, host organelle remodeling, and metabolic rewiring. We mechanistically characterized three novel candidates, including GTP cyclohydrolase I, against which a small-molecule inhibitor could be repurposed as an antiparasitic compound. This compound exhibited antiparasitic activity against T. gondii and Plasmodium falciparum, the most lethal agent of malaria. Taken together, we present the first complete survey of an apicomplexan genome during infection of an animal host, and point to novel interfaces of host-parasite interaction that may offer new avenues for treatment.
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Affiliation(s)
| | - Kenneth J. Wei
- Whitehead Institute, Cambridge, MA
- Biology Department, MIT, Cambridge, MA
| | - Faye M. Harling
- Whitehead Institute, Cambridge, MA
- Biology Department, MIT, Cambridge, MA
| | | | - Madeline A. Farringer
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, Massachusetts, USA
- Biological Sciences in Public Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | - Raina W. Thomas
- Whitehead Institute, Cambridge, MA
- Biology Department, MIT, Cambridge, MA
| | - Alice L. Herneisen
- Whitehead Institute, Cambridge, MA
- Biology Department, MIT, Cambridge, MA
| | | | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Jeffrey D. Dvorin
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sebastian Lourido
- Whitehead Institute, Cambridge, MA
- Biology Department, MIT, Cambridge, MA
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Aggarwal SD, Lees JA, Jacobs NT, Bee GCW, Abruzzo AR, Weiser JN. BlpC-mediated selfish program leads to rapid loss of Streptococcus pneumoniae clonal diversity during infection. Cell Host Microbe 2023; 31:124-134.e5. [PMID: 36395758 PMCID: PMC9839470 DOI: 10.1016/j.chom.2022.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/27/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022]
Abstract
Successful colonization of a host requires bacterial adaptation through genetic and population changes that are incompletely defined. Using chromosomal barcoding and high-throughput sequencing, we investigate the population dynamics of Streptococcus pneumoniae during infant mouse colonization. Within 1 day post inoculation, diversity was reduced >35-fold with expansion of a single clonal lineage. This loss of diversity was not due to immune factors, microbiota, or exclusive genetic drift. Rather, bacteriocins induced by the BlpC-quorum sensing pheromone resulted in predation of kin cells. In this intra-strain competition, the subpopulation reaching a quorum likely eliminates others that have yet to activate the blp locus. Additionally, this reduced diversity restricts the number of unique clones that establish colonization during transmission between hosts. Genetic variation in the blp locus was also associated with altered transmissibility in a human population, further underscoring the importance of BlpC in clonal selection and its role as a selfish element.
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Affiliation(s)
- Surya D Aggarwal
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - John A Lees
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA; European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W12 7TA, UK
| | - Nathan T Jacobs
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Gavyn Chern Wei Bee
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Annie R Abruzzo
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jeffrey N Weiser
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA.
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Chen S, Wang C, Chen Q, Zhao D, Liu Y, Zhao S, Fu S, He X, Yang B, Zhao Q, An Q, Zhang Z, Cheng Y, Man C, Liu G, Wei X, Zhang W, Du L, Wang F. Downregulation of Three Novel miRNAs in the Lymph Nodes of Sheep Immunized With the Brucella suis Strain 2 Vaccine. Front Vet Sci 2022; 9:813170. [PMID: 35274021 PMCID: PMC8902169 DOI: 10.3389/fvets.2022.813170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/13/2022] [Indexed: 02/02/2023] Open
Abstract
Ovine and caprine brucellosis, both caused by Brucella melitensis, lead to substantial economic losses in the animal industry and health problems in human populations. Brucella suis strain 2 (B.suis S2), as a live attenuated vaccine, is used extensively in China to prevent brucellosis. It has been proven that microRNA (miRNAs) are involved in the immunopathogenesis of brucellosis; however, the miRNA-driven mechanism of immune response to B.suis S2 in vivo remains unknown. To determine which new miRNAs are involved in the host immune response to B.suis S2 and elucidate the function of these miRNAs, we performed a comprehensive analysis of miRNA expression profiles in sheep immunized with B.suis S2 using the high-throughput sequencing approach. The submandibular lymphatic nodes from sheep seropositive for Brucella were collected at 7, 14, 21, 30, 60 and 90 days post-immunization. MiRNA sequencing analysis revealed that 282 differentially expressed miRNAs (|log2 fold-change |>0.5 and p < 0.05) were significantly enriched in the immune pathways, including the NF-kappa B signaling pathway, B cell receptor signaling pathway, p53 signaling pathway and complement and coagulation cascades. Increasing the threshold to |log2 fold change|>1 and p < 0.01 revealed 48 differentially expressed miRNAs, 31 of which were novel miRNAs. Thirteen of these novel miRNAs, which were differentially expressed for at least two time points, were detected via RT-qPCR assays. The novel_229, novel_609, novel_973 and oar-miR-181a assessed by RT-qPCR were detectable and consistent with the expression patterns obtained by miRNA sequencing. Functional analyses of these miRNAs demonstrated that their target genes participated in the immune response pathways, including the innate and adaptive immunity pathways. The immune-related target genes of novel_229 included ENSOARG00000000649 and TMED1, as well as LCN2, PDPK1 and LPO were novel_609 target genes. The immune-related target genes of novel_973 included C6orf58, SPPL3, BPIFB1, ENSOARG00000021083, MPTX1, CCL28, FGB, IDO1, OLR1 and ENSOARG00000020393. The immune-related target genes of oar-miR-181a included ENSOARG00000002722, ARHGEF2, MFAP4 and DOK2. These results will deepen our understanding of the host miRNA-driven defense mechanism in sheep immunized with B.suis S2 vaccine, and provide the valuable information for optimizing vaccines and developing molecular diagnostic targets.
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Affiliation(s)
- Si Chen
- Hainan Key Lab of Tropical Animal Reproduction, Animal Genetic Engineering Key Lab of Haikou, Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Chengqiang Wang
- Hainan Key Lab of Tropical Animal Reproduction, Animal Genetic Engineering Key Lab of Haikou, Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Qiaoling Chen
- Hainan Key Lab of Tropical Animal Reproduction, Animal Genetic Engineering Key Lab of Haikou, Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Dantong Zhao
- Jinyu Baoling Bio-Pharmaceutical Co., Ltd., Hohhot, China
| | | | - Shihua Zhao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Shaoyin Fu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Xiaolong He
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Bin Yang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Qinan Zhao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Qi An
- Hainan Key Lab of Tropical Animal Reproduction, Animal Genetic Engineering Key Lab of Haikou, Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Zhenxing Zhang
- Hainan Key Lab of Tropical Animal Reproduction, Animal Genetic Engineering Key Lab of Haikou, Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Yiwen Cheng
- Hainan Key Lab of Tropical Animal Reproduction, Animal Genetic Engineering Key Lab of Haikou, Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Churiga Man
- Hainan Key Lab of Tropical Animal Reproduction, Animal Genetic Engineering Key Lab of Haikou, Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
| | - Guoying Liu
- Jinyu Baoling Bio-Pharmaceutical Co., Ltd., Hohhot, China
| | - Xuefeng Wei
- Jinyu Baoling Bio-Pharmaceutical Co., Ltd., Hohhot, China
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Li Du
| | - Li Du
- Hainan Key Lab of Tropical Animal Reproduction, Animal Genetic Engineering Key Lab of Haikou, Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
- Li Du
| | - Fengyang Wang
- Hainan Key Lab of Tropical Animal Reproduction, Animal Genetic Engineering Key Lab of Haikou, Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou, China
- *Correspondence: Fengyang Wang
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Hullahalli K, Waldor MK. Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during murine systemic infection. eLife 2021; 10:e70910. [PMID: 34636322 PMCID: PMC8545400 DOI: 10.7554/elife.70910] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/07/2021] [Indexed: 12/31/2022] Open
Abstract
The dissemination of pathogens through blood and their establishment within organs lead to severe clinical outcomes. However, the within-host dynamics that underlie pathogen spread to and clearance from systemic organs remain largely uncharacterized. In animal models of infection, the observed pathogen population results from the combined contributions of bacterial replication, persistence, death, and dissemination, each of which can vary across organs. Quantifying the contribution of each these processes is required to interpret and understand experimental phenotypes. Here, we leveraged STAMPR, a new barcoding framework, to investigate the population dynamics of extraintestinal pathogenic Escherichia coli, a common cause of bacteremia, during murine systemic infection. We show that while bacteria are largely cleared by most organs, organ-specific clearance failures are pervasive and result from dramatic expansions of clones representing less than 0.0001% of the inoculum. Clonal expansion underlies the variability in bacterial burden between animals, and stochastic dissemination of clones profoundly alters the pathogen population structure within organs. Despite variable pathogen expansion events, host bottlenecks are consistent yet highly sensitive to infection variables, including inoculum size and macrophage depletion. We adapted our barcoding methodology to facilitate multiplexed validation of bacterial fitness determinants identified with transposon mutagenesis and confirmed the importance of bacterial hexose metabolism and cell envelope homeostasis pathways for organ-specific pathogen survival. Collectively, our findings provide a comprehensive map of the population biology that underlies bacterial systemic infection and a framework for barcode-based high-resolution mapping of infection dynamics.
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Affiliation(s)
- Karthik Hullahalli
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
- Division of Infectious Diseases, Brigham & Women’s HospitalBostonUnited States
| | - Matthew K Waldor
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
- Division of Infectious Diseases, Brigham & Women’s HospitalBostonUnited States
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Abstract
Pathogen population dynamics during infection are critical determinants of infection susceptibility and define patterns of dissemination. However, deciphering these dynamics, particularly founding population sizes in host organs and patterns of dissemination between organs, is difficult because measuring bacterial burden alone is insufficient to observe these patterns. Introduction of allelic diversity into otherwise identical bacteria using DNA barcodes enables sequencing-based measurements of these parameters, in a method known as STAMP (Sequence Tag-based Analysis of Microbial Populations). However, bacteria often undergo unequal expansion within host organs, resulting in marked differences in the frequencies of barcodes in input and output libraries. Here, we show that these differences confound STAMP-based analyses of founding population sizes and dissemination patterns. We present STAMPR, a successor to STAMP, which accounts for such population expansions. Using data from systemic infection of barcoded extraintestinal pathogenic E. coli, we show that this new framework, along with the metrics it yields, enhances the fidelity of measurements of bottlenecks and dissemination patterns. STAMPR was also validated on an independent barcoded Pseudomonas aeruginosa data set, uncovering new patterns of dissemination within the data. This framework (available at https://github.com/hullahalli/stampr_rtisan), when coupled with barcoded data sets, enables a more complete assessment of within-host bacterial population dynamics. IMPORTANCE Barcoded bacteria are often employed to monitor pathogen population dynamics during infection. The accuracy of these measurements is diminished by unequal bacterial expansion rates. Here, we develop computational tools to circumvent this limitation and establish additional metrics that collectively enhance the fidelity of measuring within-host pathogen founding population sizes and dissemination patterns. These new tools will benefit future studies of the dynamics of pathogens and symbionts within their respective hosts and may have additional barcode-based applications beyond host-microbe interactions.
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