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Liang Q, Huang W, Xiao T, Zhang L, Lei G, Lv H, Yang X. Characteristics of Clinical Isolates of Listeria monocytogenes in Sichuan, China, in 2022 Based on Whole Genome Sequencing Analysis. Foodborne Pathog Dis 2024; 21:424-430. [PMID: 38597599 DOI: 10.1089/fpd.2023.0173] [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] [Indexed: 04/11/2024] Open
Abstract
Listeria monocytogenes is a foodborne pathogen. In 2022, we collected 15 strains of L. monocytogenes isolated from patients in some foodborne disease sentinel monitoring hospitals in Sichuan Province. Through whole genome sequencing (WGS), we obtained the virulence genes carried by the strains, multi-locus sequence typing (MLST), core genome MLST (cgMLST), clonal complex (CC), and serum groups and constructed a phylogenetic tree and minimum spanning tree with nonhuman strains. An analysis shows that all 15 strains of L. monocytogenes carry virulence genes LIPI-1 and LIPI-2, whereas the carrying rates of LIPI-3 and LIPI-4 virulence genes are relatively low. The MLST typing results showed a total of 10 sequence types (ST), including 10 CCs, with ST7 being the dominant type. The cgMLST clearly distinguishes strains of different lineages and CC types. The serum group is divided into three types: IIa, IIb, and IVb, with IIa being the dominant serum group. An analysis of antibiotic genes showed that all 15 strains carried FosX, lin, mprF, and norB with high carrying rates. The minimum inhibitory concentration results indicated that all were susceptible to eight antibiotics (ampicillin, penicillin, tetracycline, meropenem, erythromycin, vancomycin, ciprofloxacin, and trimethoprim-sulfamethoxazole). The analysis of strains isolated from different sources of Listeria revealed varying degrees of diversity, and the contamination of meat and environment within the province is closely related to clinical cases. L. monocytogenes isolated from clinical cases in Sichuan Province carry multiple virulence and antibiotic genes, with high potential pathogenicity. It is necessary to further strengthen the monitoring and control of food and environment by L. monocytogenes within Sichuan Province.
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Affiliation(s)
- Qian Liang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Weifeng Huang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Tao Xiao
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Lin Zhang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Gaopeng Lei
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Hong Lv
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Xiaorong Yang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
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Notarbartolo V, Badiane BA, Insinga V, Giuffrè M. Antimicrobial Stewardship: A Correct Management to Reduce Sepsis in NICU Settings. Antibiotics (Basel) 2024; 13:520. [PMID: 38927186 PMCID: PMC11200753 DOI: 10.3390/antibiotics13060520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/25/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
The discovery of antimicrobial drugs has led to a significant increase in survival from infections; however, they are very often prescribed and administered, even when their use is not necessary and appropriate. Newborns are particularly exposed to infections due to the poor effectiveness and the immaturity of their immune systems. For this reason, in Neonatal Intensive Care Units (NICUs), the use of antimicrobial drugs is often decisive and life-saving, and it must be started promptly to ensure its effectiveness in consideration of the possible rapid evolution of the infection towards sepsis. Nevertheless, the misuse of antibiotics in the neonatal period leads not only to an increase in the development and wide spreading of antimicrobial resistance (AMR) but it is also associated with various short-term (e.g., alterations of the microbiota) and long-term (e.g., increased risk of allergic disease and obesity) effects. It appears fundamental to use antibiotics only when strictly necessary; specific decision-making algorithms and electronic calculators can help limit the use of unnecessary antibiotic drugs. The aim of this narrative review is to summarize the right balance between the risks and benefits of antimicrobial therapy in NICUs; for this purpose, specific Antimicrobial Stewardship Programs (ASPs) in neonatal care and the creation of a specific antimicrobial stewardship team are requested.
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Affiliation(s)
- Veronica Notarbartolo
- Neonatology and Neonatal Intensive Care Unit, University Hospital “Paolo Giaccone”, 90127 Palermo, Italy;
| | - Bintu Ayla Badiane
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy; (B.A.B.); (M.G.)
| | - Vincenzo Insinga
- Neonatology and Neonatal Intensive Care Unit, University Hospital “Paolo Giaccone”, 90127 Palermo, Italy;
| | - Mario Giuffrè
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy; (B.A.B.); (M.G.)
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Feng Y, Arsenault D, Louyakis AS, Altman-Price N, Gophna U, Papke RT, Gogarten JP. Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense. mBio 2024; 15:e0040824. [PMID: 38619241 PMCID: PMC11078007 DOI: 10.1128/mbio.00408-24] [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: 03/04/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024] Open
Abstract
In this study, we use pan-genomics to characterize the genomic variability of the widely dispersed halophilic archaeal species Halorubrum ezzemoulense (Hez). We include a multi-regional sampling of newly sequenced, high-quality draft genomes. The pan-genome graph of the species reveals 50 genomic islands that represent rare accessory genetic capabilities available to members. Most notably, we observe rearrangements that have led to the insertion/recombination/replacement of mutually exclusive genomic islands in equivalent genome positions ("homeocassettes"). These conflicting islands encode for similar functions, but homologs from islands located between the same core genes exhibit high divergence on the amino acid level, while the neighboring core genes are nearly identical. Both islands of a homeocassette often coexist in the same geographic location, suggesting that either island may be beyond the reach of selective sweeps and that these loci of divergence between Hez members are maintained and persist long term. This implies that subsections of the population have different niche preferences and rare metabolic capabilities. After an evaluation of the gene content in the homeocassettes, we speculate that these islands may play a role in the speciation, niche adaptability, and group selection dynamics in Hez. Though homeocassettes are first described in this study, similar replacements and divergence of genes on genomic islands have been previously reported in other Haloarchaea and distantly related Archaea, suggesting that homeocassettes may be a feature in a wide range of organisms outside of Hez.IMPORTANCEThis study catalogs the rare genes discovered in strains of the species Halorubrum ezzemoulense (Hez), an obligate halophilic archaeon, through the perspective of its pan-genome. These rare genes are often found to be arranged on islands that confer metabolic and transport functions and contain genes that have eluded previous studies. The discovery of divergent, but homologous islands occupying equivalent genome positions ("homeocassettes") in different genomes, reveals significant new information on genome evolution in Hez. Homeocassette pairs encode for similar functions, but their dissimilarity and distribution imply high rates of recombination, different specializations, and niche preferences in Hez. The coexistence of both islands of a homeocassette pair in multiple environments demonstrates that both islands are beyond the reach of selective sweeps and that these genome content differences between strains persist long term. The switch between islands through recombination under different environmental conditions may lead to a greater range of niche adaptability in Hez.
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Affiliation(s)
- Yutian Feng
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Danielle Arsenault
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Artemis S. Louyakis
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Neta Altman-Price
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Avinoam Adam Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - R. Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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Chen Z, Toro M, Moreno-Switt AI, Adell AD, Delgado-Suárez EJ, Bonelli RR, Oliveira CJB, Reyes-Jara A, Huang X, Albee B, Grim CJ, Allard M, Tallent SM, Brown EW, Bell RL, Meng J. Unveiling the genomic landscape of Salmonella enterica serotypes Typhimurium, Newport, and Infantis in Latin American surface waters: a comparative analysis. Microbiol Spectr 2024; 12:e0004724. [PMID: 38546218 PMCID: PMC11064523 DOI: 10.1128/spectrum.00047-24] [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: 01/05/2024] [Accepted: 03/06/2024] [Indexed: 05/03/2024] Open
Abstract
Surface waters are considered ecological habitats where Salmonella enterica can persist and disseminate to fresh produce production systems. This study aimed to explore the genomic profiles of S. enterica serotypes Typhimurium, Newport, and Infantis from surface waters in Chile, Mexico, and Brazil collected between 2019 and 2022. We analyzed the whole genomes of 106 S. Typhimurium, 161 S. Newport, and 113 S. Infantis isolates. Our phylogenetic analysis exhibited distinct groupings of isolates by their respective countries except for a notable case involving a Chilean S. Newport isolate closely related to two Mexican isolates, showing 4 and 13 single nucleotide polymorphisms of difference, respectively. The patterns of the most frequently detected antimicrobial resistance genes varied across countries and serotypes. A strong correlation existed between integron carriage and genotypic multidrug resistance (MDR) across serotypes in Chile and Mexico (R > 0.90, P < 0.01), while integron(s) were not detected in any of the Brazilian isolates. By contrast, we did not identify any strong correlation between plasmid carriage and genotypic MDR across diverse countries and serotypes.IMPORTANCEUnveiling the genomic landscape of S. enterica in Latin American surface waters is pivotal for ensuring public health. This investigation sheds light on the intricate genomic diversity of S. enterica in surface waters across Chile, Mexico, and Brazil. Our research also addresses critical knowledge gaps, pioneering a comprehensive understanding of surface waters as a reservoir for multidrug-resistant S. enterica. By integrating our understanding of integron carriage as biomarkers into broader MDR control strategies, we can also work toward targeted interventions that mitigate the emergence and dissemination of MDR in S. enterica in surface waters. Given its potential implications for food safety, this study emphasizes the critical need for informed policies and collaborative initiatives to address the risks associated with S. enterica in surface waters.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
| | - Magaly Toro
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Andrea I. Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Aiko D. Adell
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Facultad de Agronomía y Sistemas Naturales, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andrés Bello, Santiago, Chile
| | - Enrique J. Delgado-Suárez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad de Nacional Autónoma de México, Mexico City, Mexico
| | - Raquel R. Bonelli
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Angélica Reyes-Jara
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Xinyang Huang
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
| | - Brett Albee
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Sandra M. Tallent
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Eric W. Brown
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Rebecca L. Bell
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition and Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
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Cohen E, Azriel S, Auster O, Gal A, Mikhlin S, Crauwels S, Rahav G, Gal-Mor O. A new Salmonella enterica serovar that was isolated from a wild sparrow presents a distinct genetic, metabolic and virulence profile. Microbes Infect 2024; 26:105249. [PMID: 37956735 DOI: 10.1016/j.micinf.2023.105249] [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: 08/27/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
Salmonella enterica is a ubiquitous and clinically-important bacterial pathogen, able to infect and cause different diseases in a wide range of hosts. Here, we report the isolation and characterization of a new S. enterica serovar (13,23:i:-; S. Tirat-Zvi), belonging to the Havana supper-lineage that was isolated from a wild house sparrow (Passer domesticus) in Israel. Whole genome sequencing and complete assembly of its genome indicated a plasmid-free, 4.7 Mb genome that carries the Salmonella pathogenicity islands 1-6, 9, 19 and an integrative and conjugative element (ICE), encoding arsenic resistance genes. Phenotypically, S. Tirat-Zvi isolate TZ282 was motile, readily formed biofilm, more versatile in carbon source utilization than S. Typhimurium and highly tolerant to arsenic, but impaired in host cell invasion. In-vivo infection studies indicated that while S. Tirat-Zvi was able to infect and cause an acute inflammatory enterocolitis in young chicks, it was compromised in mice colonization and did not cause an inflammatory colitis in mice compared to S. Typhimurium. We suggest that these phenotypes reflect the distinctive ecological niche of this new serovar and its evolutionary adaptation to passerine birds, as a permissive host. Moreover, these results further illuminate the genetic, phenotypic and ecological diversity of S. enterica pathovars.
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Affiliation(s)
- Emiliano Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Shalevet Azriel
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Oren Auster
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
| | - Adiv Gal
- Faculty of Sciences, Kibbutzim College, Tel-Aviv, Israel
| | | | - Sam Crauwels
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Galia Rahav
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel.
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M de Freitas Pereira R, de Oliveira Filho HS, C Duarte JL, R P Júnior F, de Sousa Lima T, Dos Santos KMOL, da Silva Pereira E, Jerônimo da Silva N, Bruno de Oliveira CJ, Leal de Araújo J, de Souza Mendonça F. Fibrinonecrotic enteritis and orchitis associated with Salmonella enterica subsp houtenae infection in a short-tailed boa (Boa constrictor amarali). J Comp Pathol 2024; 209:1-5. [PMID: 38306731 DOI: 10.1016/j.jcpa.2024.01.002] [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: 09/18/2023] [Revised: 11/28/2023] [Accepted: 01/08/2024] [Indexed: 02/04/2024]
Abstract
Salmonella enterica subsp houtenae has been recovered from a wide variety of species, including reptiles, and has been linked to important clinical manifestations in snakes and lizards. We describe a case of concomitant fibrinonecrotic enteritis and orchitis associated with S. enterica subsp houtenae infection in a short-tailed boa (Boa constrictor amarali). At necropsy, the mucosa of the large intestine was covered by a focally extensive fibrinonecrotic exudate (diphtheritic pseudomembrane). The left testicle was enlarged, firm and diffusely expanded by a thick fibrinous yellow exudate. Polymerase chain reaction and conclusive antigenic testing indicated that the bacteria isolated from the lesions were S. enterica subsp houtenae, and the virulence genes InvA, slyA, stn and spvC were identified. This report reinforces that, although S. enterica subsp houtenae has been isolated from asymptomatic reptiles, it has the potential to cause life-threatening disease in snakes.
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Affiliation(s)
- Raquel M de Freitas Pereira
- Animal Diagnostic Laboratory, Federal Rural University of Pernambuco, Manuel de Medeiros Street 97, Recife-PE, 52171-900, Brazil.
| | - Hodias S de Oliveira Filho
- Laboratory of Veterinary Pathology, Federal University of Paraíba, Highway PB-079, Areia-PB, 58051-900, Brazil
| | - José L C Duarte
- Laboratory of Veterinary Pathology, Federal University of Paraíba, Highway PB-079, Areia-PB, 58051-900, Brazil
| | - Fabiano R P Júnior
- Department of Wild Animals, Cesmac University Center, Highway Divaldo Suruagy S/N, Marechal Deodoro-AL, 57081-350, Brazil
| | - Telma de Sousa Lima
- Animal Diagnostic Laboratory, Federal Rural University of Pernambuco, Manuel de Medeiros Street 97, Recife-PE, 52171-900, Brazil
| | - Kin M O L Dos Santos
- Laboratory of Veterinary Pathology, Federal University of Paraíba, Highway PB-079, Areia-PB, 58051-900, Brazil
| | - Edivaldo da Silva Pereira
- Laboratory of Preventive Veterinary Medicine, Federal University of Paraíba, Highway PB-079, Areia-PB, 58051-900, Brazil
| | - Nádyra Jerônimo da Silva
- Laboratory for the Evaluation of Products of Animal Origin, Federal University of Paraíba, Highway PB-079, Areia-PB, 58051-900, Brazil
| | - Celso J Bruno de Oliveira
- Laboratory for the Evaluation of Products of Animal Origin, Federal University of Paraíba, Highway PB-079, Areia-PB, 58051-900, Brazil
| | - Jeann Leal de Araújo
- Laboratory of Veterinary Pathology, Federal University of Paraíba, Highway PB-079, Areia-PB, 58051-900, Brazil
| | - Fábio de Souza Mendonça
- Animal Diagnostic Laboratory, Federal Rural University of Pernambuco, Manuel de Medeiros Street 97, Recife-PE, 52171-900, Brazil
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Ilyas M, Purkait D, Atmakuri K. Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens. Brief Funct Genomics 2024; 23:55-68. [PMID: 36528816 DOI: 10.1093/bfgp/elac051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/03/2022] [Accepted: 11/11/2022] [Indexed: 01/21/2024] Open
Abstract
To survive and establish a niche for themselves, bacteria constantly evolve. Toward that, they not only insert point mutations and promote illegitimate recombinations within their genomes but also insert pieces of 'foreign' deoxyribonucleic acid, which are commonly referred to as 'genomic islands' (GEIs). The GEIs come in several forms, structures and types, often providing a fitness advantage to the harboring bacterium. In pathogenic bacteria, some GEIs may enhance virulence, thus altering disease burden, morbidity and mortality. Hence, delineating (i) the GEIs framework, (ii) their encoded functions, (iii) the triggers that help them move, (iv) the mechanisms they exploit to move among bacteria and (v) identification of their natural reservoirs will aid in superior tackling of several bacterial diseases, including sepsis. Given the vast array of comparative genomics data, in this short review, we provide an overview of the GEIs, their types and the compositions therein, especially highlighting GEIs harbored by two important pathogens, viz. Acinetobacter baumannii and Klebsiella pneumoniae, which prominently trigger sepsis in low- and middle-income countries. Our efforts help shed some light on the challenges these pathogens pose when equipped with GEIs. We hope that this review will provoke intense research into understanding GEIs, the cues that drive their mobility across bacteria and the ways and means to prevent their transfer, especially across pathogenic bacteria.
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Affiliation(s)
- Mohd Ilyas
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Dyuti Purkait
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Krishnamohan Atmakuri
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
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Danov A, Segev O, Bograd A, Ben Eliyahu Y, Dotan N, Kaplan T, Levy A. Toxinome-the bacterial protein toxin database. mBio 2024; 15:e0191123. [PMID: 38117054 PMCID: PMC10790787 DOI: 10.1128/mbio.01911-23] [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: 08/08/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Microbes use protein toxins as important tools to attack neighboring cells, microbial or eukaryotic, and for self-killing when attacked by viruses. These toxins work through different mechanisms to inhibit cell growth or kill cells. Microbes also use antitoxin proteins to neutralize the toxin activities. Here, we developed a comprehensive database called Toxinome of nearly two million toxins and antitoxins that are encoded in 59,475 bacterial genomes. We described the distribution of bacterial toxins and identified that they are depleted by bacteria that live in hot and cold temperatures. We found 5,161 cases in which toxins and antitoxins are densely clustered in bacterial genomes and termed these areas "Toxin Islands." The Toxinome database is a useful resource for anyone interested in toxin biology and evolution, and it can guide the discovery of new toxins.
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Affiliation(s)
- Aleks Danov
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ofir Segev
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avi Bograd
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yedidya Ben Eliyahu
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Dotan
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Tan YH, Arros P, Berríos-Pastén C, Wijaya I, Chu WHW, Chen Y, Cheam G, Mohamed Naim AN, Marcoleta AE, Ravikrishnan A, Nagarajan N, Lagos R, Gan YH. Hypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut. THE ISME JOURNAL 2024; 18:wrae054. [PMID: 38547398 PMCID: PMC11020217 DOI: 10.1093/ismejo/wrae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/24/2024] [Accepted: 03/25/2024] [Indexed: 04/18/2024]
Abstract
The hypervirulent lineages of Klebsiella pneumoniae (HvKp) cause invasive infections such as Klebsiella-liver abscess. Invasive infection often occurs after initial colonization of the host gastrointestinal tract by HvKp. Over 80% of HvKp isolates belong to the clonal group 23 sublineage I that has acquired genomic islands (GIs) GIE492 and ICEKp10. Our analysis of 12 361 K. pneumoniae genomes revealed that GIs GIE492 and ICEKp10 are co-associated with the CG23-I and CG10118 HvKp lineages. GIE492 and ICEKp10 enable HvKp to make a functional bacteriocin microcin E492 (mccE492) and the genotoxin colibactin, respectively. We discovered that GIE492 and ICEKp10 play cooperative roles and enhance gastrointestinal colonization by HvKp. Colibactin is the primary driver of this effect, modifying gut microbiome diversity. Our in vitro assays demonstrate that colibactin and mccE492 kill or inhibit a range of Gram-negative Klebsiella species and Escherichia coli strains, including Gram-positive bacteria, sometimes cooperatively. Moreover, mccE492 and colibactin kill human anaerobic gut commensals that are similar to the taxa found altered by colibactin in the mouse intestines. Our findings suggest that GIs GIE492 and ICEKp10 enable HvKp to kill several commensal bacterial taxa during interspecies interactions in the gut. Thus, acquisition of GIE492 and ICEKp10 could enable better carriage in host populations and explain the dominance of the CG23-I HvKp lineage.
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Affiliation(s)
- Yi Han Tan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, MD4, Level 2, Singapore 117545, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore 117596, Republic of Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore 138672, Republic of Singapore
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Departamento de Biología, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago, Chile
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Departamento de Biología, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago, Chile
| | - Indrik Wijaya
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore 138672, Republic of Singapore
| | - Wilson H W Chu
- National Public Health Laboratory, National Centre for Infectious Diseases, 16 Jln Tan Tock Seng, Singapore 308442, Republic of Singapore
| | - Yahua Chen
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, MD4, Level 2, Singapore 117545, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore 117596, Republic of Singapore
| | - Guoxiang Cheam
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, MD4, Level 2, Singapore 117545, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore 117596, Republic of Singapore
| | - Ahmad Nazri Mohamed Naim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore 138672, Republic of Singapore
| | - Andrés E Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Departamento de Biología, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago, Chile
| | - Aarthi Ravikrishnan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore 138672, Republic of Singapore
| | - Niranjan Nagarajan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, MD4, Level 2, Singapore 117545, Republic of Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore 138672, Republic of Singapore
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Departamento de Biología, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago, Chile
| | - Yunn-Hwen Gan
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, MD4, Level 2, Singapore 117545, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore 117596, Republic of Singapore
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10
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Han J, Aljahdali N, Zhao S, Tang H, Harbottle H, Hoffmann M, Frye JG, Foley SL. Infection biology of Salmonella enterica. EcoSal Plus 2024:eesp00012023. [PMID: 38415623 DOI: 10.1128/ecosalplus.esp-0001-2023] [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: 02/17/2023] [Accepted: 07/31/2023] [Indexed: 02/29/2024]
Abstract
Salmonella enterica is the leading cause of bacterial foodborne illness in the USA, with an estimated 95% of salmonellosis cases due to the consumption of contaminated food products. Salmonella can cause several different disease syndromes, with the most common being gastroenteritis, followed by bacteremia and typhoid fever. Among the over 2,600 currently identified serotypes/serovars, some are mostly host-restricted and host-adapted, while the majority of serotypes can infect a broader range of host species and are associated with causing both livestock and human disease. Salmonella serotypes and strains within serovars can vary considerably in the severity of disease that may result from infection, with some serovars that are more highly associated with invasive disease in humans, while others predominantly cause mild gastroenteritis. These observed clinical differences may be caused by the genetic make-up and diversity of the serovars. Salmonella virulence systems are very complex containing several virulence-associated genes with different functions that contribute to its pathogenicity. The different clinical syndromes are associated with unique groups of virulence genes, and strains often differ in the array of virulence traits they display. On the chromosome, virulence genes are often clustered in regions known as Salmonella pathogenicity islands (SPIs), which are scattered throughout different Salmonella genomes and encode factors essential for adhesion, invasion, survival, and replication within the host. Plasmids can also carry various genes that contribute to Salmonella pathogenicity. For example, strains from several serovars associated with significant human disease, including Choleraesuis, Dublin, Enteritidis, Newport, and Typhimurium, can carry virulence plasmids with genes contributing to attachment, immune system evasion, and other roles. The goal of this comprehensive review is to provide key information on the Salmonella virulence, including the contributions of genes encoded in SPIs and plasmids during Salmonella pathogenesis.
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Affiliation(s)
- Jing Han
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Nesreen Aljahdali
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
- Biological Science Department, College of Science, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, Maryland, USA
| | - Hailin Tang
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Heather Harbottle
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, Maryland, USA
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Jonathan G Frye
- Agricutlutral Research Service, U.S. Department of Agriculture, Athens, Georgia, USA
| | - Steven L Foley
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
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11
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Guo X, Guo Y, Chen H, Liu X, He P, Li W, Zhang MQ, Dai Q. Systematic comparison of genome information processing and boundary recognition tools used for genomic island detection. Comput Biol Med 2023; 166:107550. [PMID: 37826950 DOI: 10.1016/j.compbiomed.2023.107550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
Genomic islands are fragments of foreign DNA that are found in bacterial and archaeal genomes, and are typically associated with symbiosis or pathogenesis. While numerous genomic island detection methods have been proposed, there has been limited evaluation of the efficiency of the genome information processing and boundary recognition tools. In this study, we conducted a review of the statistical methods involved in genomic signatures, host signature extraction, informative signature selection, divergence measures, and boundary detection steps in genomic island prediction. We compared the performances of these methods on simulated experiments using alien fragments obtained from both artificial and real genomes. Our results indicate that among the nine genomic signatures evaluated, genomic signature frequency and full probability performed the best. However, their performance declined when normalized to their expectations and variances, such as Z-score and composition vector. Based on our experiments of the E. coli genome, we found that the confidence intervals of the window variances achieved the best performance in the signature extraction of the host, with the best confidence interval being 1.5-2 times the standard error. Ordered kurtosis was most effective in selecting informative signatures from a single genome, without requiring prior knowledge from other datasets. Among the three divergence measures evaluated, the two-sample t-test was the most successful, and a non-overlapping window with a small eye window (size 2) was best suited for identifying compositionally distinct regions. Finally, the maximum of the Markovian Jensen-Shannon divergence score, in terms of GC-content bias, was found to make boundary detection faster while maintaining a similar error rate.
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Affiliation(s)
- Xiangting Guo
- Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yichu Guo
- Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Hu Chen
- Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xiaoqing Liu
- College of Sciences, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Pingan He
- Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Wenshu Li
- Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Michael Q Zhang
- Center for Systems Biology, University of Texas at Dallas, Richardson, TX, 75080, USA; Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing, 100084, China
| | - Qi Dai
- Zhejiang Sci-Tech University, Hangzhou, 310018, China; Center for Systems Biology, University of Texas at Dallas, Richardson, TX, 75080, USA.
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12
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Schwarz MGA, Corrêa PR, Mendonça-Lima L. Transcriptional Profiling of Homologous Recombination Pathway Genes in Mycobacterium bovis BCG Moreau. Microorganisms 2023; 11:2534. [PMID: 37894192 PMCID: PMC10609372 DOI: 10.3390/microorganisms11102534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/17/2023] [Accepted: 08/29/2023] [Indexed: 10/29/2023] Open
Abstract
Mycobacterium bovis BCG Moreau is the main Brazilian strain for vaccination against tuberculosis. It is considered an early strain, more like the original BCG, whereas BCG Pasteur, largely used as a reference, belongs to the late strain clade. BCG Moreau, contrary to Pasteur, is naturally deficient in homologous recombination (HR). In this work, using a UV exposure test, we aimed to detect differences in the survival of various BCG strains after DNA damage. Transcription of core and regulatory HR genes was further analyzed using RT-qPCR, aiming to identify the molecular agent responsible for this phenotype. We show that early strains share the Moreau low survival rate after UV exposure, whereas late strains mimic the Pasteur phenotype, indicating that this increase in HR efficiency is linked to the evolutionary clade history. Additionally, RT-qPCR shows that BCG Moreau has an overall lower level of these transcripts than Pasteur, indicating a correlation between this gene expression profile and HR efficiency. Further assays should be performed to fully identify the molecular mechanism that may explain this differential phenotype between early and late BCG strains.
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Affiliation(s)
- Marcos Gustavo Araujo Schwarz
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (P.R.C.); (L.M.-L.)
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13
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Salamzade R, Tran P, Martin C, Manson AL, Gilmore MS, Earl AM, Anantharaman K, Kalan LR. zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544063. [PMID: 37333121 PMCID: PMC10274777 DOI: 10.1101/2023.06.07.544063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements (MGEs), such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous or homologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of protein-encoding ortholog groups for individual genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of statistics for each inferred ortholog group. These programs are showcased through application to: (i) longitudinal tracking of a virus in metagenomes, (ii) discovering novel population-genetic insights of two common BGCs in a fungal species, and (iii) uncovering large-scale evolutionary trends of a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.
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Affiliation(s)
- Rauf Salamzade
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Patricia Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Freshwater and Marine Science Doctoral Program, University of Wisconsin-Madison, WI, USA
| | - Cody Martin
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Abigail L. Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S. Gilmore
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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14
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Morales G, Abelson B, Reasoner S, Miller J, Earl AM, Hadjifrangiskou M, Schmitz J. The Role of Mobile Genetic Elements in Virulence Factor Carriage from Symptomatic and Asymptomatic Cases of Escherichia coli Bacteriuria. Microbiol Spectr 2023; 11:e0471022. [PMID: 37195213 PMCID: PMC10269530 DOI: 10.1128/spectrum.04710-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/01/2023] [Indexed: 05/18/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is extremely diverse genotypically and phenotypically. Individual strains can variably carry diverse virulence factors, making it challenging to define a molecular signature for this pathotype. For many bacterial pathogens, mobile genetic elements (MGEs) constitute a major mechanism of virulence factor acquisition. For urinary E. coli, the total distribution of MGEs and their role in the acquisition of virulence factors is not well defined, including in the context of symptomatic infection versus asymptomatic bacteriuria (ASB). In this work, we characterized 151 isolates of E. coli, derived from patients with either urinary tract infection (UTI) or ASB. For both sets of E. coli, we catalogued the presence of plasmids, prophage, and transposons. We analyzed MGE sequences for the presence of virulence factors and antimicrobial resistance genes. These MGEs were associated with only ~4% of total virulence associated genes, while plasmids contributed to ~15% of antimicrobial resistance genes under consideration. Our analyses suggests that, across strains of E. coli, MGEs are not a prominent driver of urinary tract pathogenesis and symptomatic infection. IMPORTANCE Escherichia coli is the most common etiological agent of urinary tract infections (UTIs), with UTI-associated strains designated "uropathogenic" E. coli or UPEC. Across urinary strains of E. coli, the global landscape of MGEs and its relationship to virulence factor carriage and clinical symptomatology require greater clarity. Here, we demonstrate that many of the putative virulence factors of UPEC are not associated with acquisition due to MGEs. The current work enhances our understanding of the strain-to-strain variability and pathogenic potential of urine-associated E. coli and points toward more subtle genomic differences distinguishing ASB from UTI isolates.
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Affiliation(s)
- Grace Morales
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Benjamin Abelson
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seth Reasoner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jordan Miller
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee, USA
| | - Jonathan Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee, USA
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15
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Wiktorczyk-Kapischke N, Skowron K, Wałecka-Zacharska E. Genomic and pathogenicity islands of Listeria monocytogenes-overview of selected aspects. Front Mol Biosci 2023; 10:1161486. [PMID: 37388250 PMCID: PMC10300472 DOI: 10.3389/fmolb.2023.1161486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Listeria monocytogenes causes listeriosis, a disease characterized by a high mortality rate (up to 30%). Since the pathogen is highly tolerant to changing conditions (high and low temperature, wide pH range, low availability of nutrients), it is widespread in the environment, e.g., water, soil, or food. L. monocytogenes possess a number of genes that determine its high virulence potential, i.e., genes involved in the intracellular cycle (e.g., prfA, hly, plcA, plcB, inlA, inlB), response to stress conditions (e.g., sigB, gadA, caspD, clpB, lmo1138), biofilm formation (e.g., agr, luxS), or resistance to disinfectants (e.g., emrELm, bcrABC, mdrL). Some genes are organized into genomic and pathogenicity islands. The islands LIPI-1 and LIPI-3 contain genes related to the infectious life cycle and survival in the food processing environment, while LGI-1 and LGI-2 potentially ensure survival and durability in the production environment. Researchers constantly have been searching for new genes determining the virulence of L. monocytogenes. Understanding the virulence potential of L. monocytogenes is an important element of public health protection, as highly pathogenic strains may be associated with outbreaks and the severity of listeriosis. This review summarizes the selected aspects of L. monocytogenes genomic and pathogenicity islands, and the importance of whole genome sequencing for epidemiological purposes.
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Affiliation(s)
- Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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16
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Rose TFA, Kannan P, Ruban SW, Srinivas K, Milton AAP, Ghatak S, Elango A, Rajalakshmi S, Sundaram S. Isolation, susceptibility profiles and genomic analysis of a colistin-resistant Salmonella enterica serovar Kentucky strain COL-R. 3 Biotech 2023; 13:140. [PMID: 37124985 PMCID: PMC10133420 DOI: 10.1007/s13205-023-03559-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Salmonella enterica serovar Kentucky is a frequent cause for clinical infections in human patients. They are isolated and reported with multidrug resistance from the foods of animal origin from various countries. However, studies inferring the colistin resistance are limited. Hence, the current study reports the genetic factors and genomic analysis of the colistin-resistant Salmonella enterica serovar Kentucky strain COL-R for better understanding of its pathogenic potential and phylogenetic relatedness. The S. Kentucky strain COL-R was successfully isolated from chicken meat during ongoing surveillance of food of animal origin. Antimicrobial susceptibility testing revealed resistance to cefoxitin, erythromycin, gentamicin, tetracycline, and most disturbingly to ciprofloxacin and colistin (broth microdilution method). Whole-genome sequence of the COL-R strain was subjected to various in silico analysis to identify the virulence factors, antimicrobial resistance genes, pathogenicity islands and sequence type. The S. Kentucky COL-R strain belonged to sequence type (ST) 198 with a high probability (0.943) of being a human pathogen. Besides presence of integrated phage in the S. Kentucky COL-R genome, 38 genes conferring resistance to various antimicrobials and disinfectants were also identified. Nucleotide Polymorphism analysis indicated triple mutations in gyrA and parC genes conferring fluoroquinolone resistance. Phylogenomic analysis with 31 other S. Kentucky genomes revealed discernible clusters with S. Kentucky COL-R strain latching onto a cluster of high diversity (geographic location and isolation sources). Taken together, our results document the first occurrence of colistin resistance in a fluoroquinolone resistant S. Kentucky COL-R strain isolated from retail chicken and provide crucial information on the genomic features of the strain. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03559-2.
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Affiliation(s)
- T. F. Amal Rose
- Department of Veterinary Public Health and Epidemiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
| | - Porteen Kannan
- Department of Veterinary Public Health and Epidemiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
| | - S. Wilfred Ruban
- Department of Livestock Products Technology, Veterinary College, KVAFSU, Hebbal, Bangalore, 560024 India
| | - Kandhan Srinivas
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122 India
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, 793103 India
| | | | - Sandeep Ghatak
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, 793103 India
| | - A. Elango
- Veterinary College and Research Institute, TANUVAS, Salem, 636112 India
| | - S. Rajalakshmi
- Department of Veterinary Microbiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
| | - Sureshkannan Sundaram
- Department of Veterinary Public Health and Epidemiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
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17
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Apari P, Földvári G. Domestication and microbiome succession may drive pathogen spillover. Front Microbiol 2023; 14:1102337. [PMID: 37007505 PMCID: PMC10065160 DOI: 10.3389/fmicb.2023.1102337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
Emerging infectious diseases have posed growing medical, social and economic threats to humanity. The biological background of pathogen spillover or host switch, however, still has to be clarified. Disease ecology finds pathogen spillovers frequently but struggles to explain at the molecular level. Contrarily, molecular biological traits of host-pathogen relationships with specific molecular binding mechanisms predict few spillovers. Here we aim to provide a synthetic explanation by arguing that domestication, horizontal gene transfer even between superkingdoms as well as gradual exchange of microbiome (microbiome succession) are essential in the whole scenario. We present a new perspective at the molecular level which can explain the observations of frequent pathogen spillover events at the ecological level. This proposed rationale is described in detail, along with supporting evidence from the peer-reviewed literature and suggestions for testing hypothesis validity. We also highlight the importance of systematic monitoring of virulence genes across taxonomical categories and in the whole biosphere as it helps prevent future epidemics and pandemics. We conclude that that the processes of domestication, horizontal gene transfer and microbial succession might be important mechanisms behind the many spillover events driven and accelerated by climate change, biodiversity loss and globalization.
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Affiliation(s)
- Péter Apari
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Gábor Földvári
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
- Centre for Eco-Epidemiology, National Laboratory for Health Security, Budapest, Hungary
- *Correspondence: Gábor Földvári,
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18
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Comparison of Phenotype and Genotype Virulence and Antimicrobial Factors of Salmonella Typhimurium Isolated from Human Milk. Int J Mol Sci 2023; 24:ijms24065135. [PMID: 36982209 PMCID: PMC10048834 DOI: 10.3390/ijms24065135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023] Open
Abstract
Salmonella is a common foodborne infection. Many serovars belonging to Salmonella enterica subsp. enterica are present in the gut of various animal species. They can cause infection in human infants via breast milk or cross-contamination with powdered milk. In the present study, Salmonella BO was isolated from human milk in accordance with ISO 6579-1:2017 standards and sequenced using whole-genome sequencing (WGS), followed by serosequencing and genotyping. The results also allowed its pathogenicity to be predicted. The WGS results were compared with the bacterial phenotype. The isolated strain was found to be Salmonella enterica subsp. enterica serovar Typhimurium 4:i:1,2_69M (S. Typhimurium 69M); it showed a very close similarity to S. enterica subsp. enterica serovar Typhimurium LT2. Bioinformatics sequence analysis detected eleven SPIs (SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-14, C63PI, CS54_island). Significant changes in gene sequences were noted, causing frameshift mutations in yeiG, rfbP, fumA, yeaL, ybeU (insertion) and lpfD, avrA, ratB, yacH (deletion). The sequences of several proteins were significantly different from those coded in the reference genome; their three-dimensional structure was predicted and compared with reference proteins. Our findings indicate the presence of a number of antimicrobial resistance genes that do not directly imply an antibiotic resistance phenotype.
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19
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The Xenogeneic Silencer Histone-Like Nucleoid-Structuring Protein Mediates the Temperature and Salinity-Dependent Regulation of the Type III Secretion System 2 in Vibrio parahaemolyticus. J Bacteriol 2023; 205:e0026622. [PMID: 36468869 PMCID: PMC9879105 DOI: 10.1128/jb.00266-22] [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: 12/12/2022] Open
Abstract
The marine bacterium Vibrio parahaemolyticus is a major seafood-borne pathogen that causes acute diarrhea in humans. A crucial virulence determinant of V. parahaemolyticus is the type III secretion system 2 (T3SS2), which is encoded on the Vibrio parahaemolyticus pathogenicity island (Vp-PAI), in which gene expression is dependent on environmental cues, such as temperature and salinity. This characteristic may implicate the adaptation of V. parahaemolyticus from its natural habitat to the human body environment during infection; however, the underlying mechanism remains unknown. Here, we describe the regulatory role of the histone-like nucleoid-structuring protein (H-NS), which is a xenogeneic silencing protein, in T3SS2 gene expression through the conditional silencing of the gene encoding a master regulator of Vp-PAI, VtrB. The hns deletion canceled the temperature- and salinity-dependent differential T3SS2 gene expression. H-NS bound to the vtrB promoter containing AT-rich sequences, and the binding sites partially overlapped the binding sites of two positive regulators of vtrB (i.e., VtrA and ToxR), which may block the transcriptional activation of vtrB. H-NS-family proteins multimerize along the DNA strand, forming stiffened filament and/or bridging DNA duplexes for its target silencing. In V. parahaemolyticus, mutations at conserved residues that are required for the multimerization of H-NS abolished the repressive activity on VtrB expression, supporting the contention that H-NS multimerization is also critical for vtrB silencing in V. parahaemolyticus. Taken together, these findings demonstrate the principal role of H-NS as a thermal and salt switch with sensory and regulatory properties for ensuring T3SS2 gene regulation in V. parahaemolyticus. IMPORTANCE In the major seafood-borne pathogen Vibrio parahaemolyticus, the type III secretion system 2 (T3SS2) is a major virulence factor that is responsible for the enterotoxicity of this bacterium. The expression of T3SS2 varies according to changes in temperature and salinity, but the mechanism via which T3SS2 expression is regulated in response to such physical cues remains unknown. Here, we report that H-NS, a xenogeneic silencer that is widespread in Gram-negative bacteria, modulates the entirety of T3SS2 gene expression through the transcriptional silencing of the gene encoding the T3SS2 master regulator VtrB in a temperature- and salinity-dependent manner. Thus, our findings provide insights into how this pathogen achieves the appropriate control of the expression of virulence genes in the transition between aquatic and human environments.
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20
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Ecology and evolution of phages encoding anti-CRISPR proteins. J Mol Biol 2023; 435:167974. [PMID: 36690071 DOI: 10.1016/j.jmb.2023.167974] [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: 10/27/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/21/2023]
Abstract
CRISPR-Cas are prokaryotic defence systems that provide protection against invasion by mobile genetic elements (MGE), including bacteriophages. MGE can overcome CRISPR-Cas defences by encoding anti-CRISPR (Acr) proteins. These proteins are produced in the early stages of the infection and inhibit the CRISPR-Cas machinery to allow phage replication. While research on Acr has mainly focused on their discovery, structure and mode of action, and their applications in biotechnology, the impact of Acr on the ecology of MGE as well as on the coevolution with their bacterial hosts only begins to be unravelled. In this review, we summarise our current understanding on the distribution of anti-CRISPR genes in MGE, the ecology of phages encoding Acr, and their coevolution with bacterial defence mechanisms. We highlight the need to use more diverse and complex experimental models to better understand the impact of anti-CRISPR in MGE-host interactions.
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Feng A, Akter S, Leigh SA, Wang H, Pharr GT, Evans J, Branton SL, Landinez MP, Pace L, Wan XF. Genomic diversity, pathogenicity and antimicrobial resistance of Escherichia coli isolated from poultry in the southern United States. BMC Microbiol 2023; 23:15. [PMID: 36647025 PMCID: PMC9841705 DOI: 10.1186/s12866-022-02721-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 11/30/2022] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli (E. coli) are typically present as commensal bacteria in the gastro-intestinal tract of most animals including poultry species, but some avian pathogenic E. coli (APEC) strains can cause localized and even systematic infections in domestic poultry. Emergence and re-emergence of antimicrobial resistant isolates (AMR) constrain antibiotics usage in poultry production, and development of an effective vaccination program remains one of the primary options in E. coli disease prevention and control for domestic poultry. Thus, understanding genetic and pathogenic diversity of the enzootic E. coli isolates, particularly APEC, in poultry farms is the key to designing an optimal vaccine candidate and to developing an effective vaccination program. This study explored the genomic and pathogenic diversity among E. coli isolates in southern United States poultry. A total of nine isolates were recovered from sick broilers from Mississippi, and one from Georgia, with epidemiological variations among clinical signs, type of housing, and bird age. The genomes of these isolates were sequenced by using both Illumina short-reads and Oxford Nanopore long-reads, and our comparative analyses suggested data from both platforms were highly consistent. The 16 s rRNA based phylogenetic analyses showed that the 10 bacteria strains are genetically closer to each other than those in the public database. However, whole genome analyses showed that these 10 isolates encoded a diverse set of reported virulence and AMR genes, belonging to at least nine O:H serotypes, and are genetically clustered with at least five different groups of E. coli isolates reported by other states in the United States. Despite the small sample size, this study suggested that there was a large extent of genomic and serological diversity among E. coli isolates in southern United States poultry. A large-scale comprehensive study is needed to understand the overall genomic diversity and the associated virulence, and such a study will be important to develop a broadly protective E. coli vaccine.
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Affiliation(s)
- Aijing Feng
- grid.134936.a0000 0001 2162 3504Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
| | - Sadia Akter
- grid.134936.a0000 0001 2162 3504Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
| | - Spencer A. Leigh
- Poultry Research Unit, USDA Agricultural Research Service, Mississippi State, MS USA
| | - Hui Wang
- grid.260120.70000 0001 0816 8287Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS USA
| | - G. Todd Pharr
- grid.260120.70000 0001 0816 8287Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS USA
| | - Jeff Evans
- Poultry Research Unit, USDA Agricultural Research Service, Mississippi State, MS USA
| | - Scott L. Branton
- Poultry Research Unit, USDA Agricultural Research Service, Mississippi State, MS USA
| | - Martha Pulido Landinez
- grid.260120.70000 0001 0816 8287Poultry Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University, Pearl, MS USA
| | - Lanny Pace
- grid.260120.70000 0001 0816 8287Mississippi Veterinary Research and Diagnostic Laboratory System, College of Veterinary Medicine, Mississippi State University, Pearl, MS USA
| | - Xiu-Feng Wan
- grid.134936.a0000 0001 2162 3504Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
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Dubin CA, Voorhies M, Sil A, Teixeira MM, Barker BM, Brem RB. Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii. J Fungi (Basel) 2022; 8:jof8121235. [PMID: 36547568 PMCID: PMC9782707 DOI: 10.3390/jof8121235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
The human fungal pathogen Coccidioides spp. causes valley fever, a treatment-refractory and sometimes deadly disease prevalent in arid regions of the western hemisphere. Fungal virulence in the mammalian host hinges on a switch between growth as hyphae and as large spherules containing infectious spores. How these virulence programs are encoded in the genome remains poorly understood. Drawing on Coccidioides genomic resources, we first discovered a new facet of genome organization in this system: spherule-gene islands, clusters of genes physically linked in the genome that exhibited specific mRNA induction in the spherule phase. Next, we surveyed copy-number variation genome-wide among strains of C. posadasii. Emerging from this catalog were spherule-gene islands with striking presence-absence differentiation between C. posadasii populations, a pattern expected from virulence factors subjected to different selective pressures across habitats. Finally, analyzing single-nucleotide differences across C. posadasii strains, we identified signatures of natural selection in spherule-expressed genes. Together, our data establish spherule-gene islands as candidate determinants of virulence and targets of selection in Coccidioides.
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Affiliation(s)
- Claire A. Dubin
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720-3102, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, UC San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Department of Microbiology and Immunology, UC San Francisco, San Francisco, CA 94143, USA
| | - Marcus M. Teixeira
- The Translational Genomics Research Institute (TGen)-Affiliate of City of Hope, Flagstaff, AZ 85004, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Bridget M. Barker
- The Translational Genomics Research Institute (TGen)-Affiliate of City of Hope, Flagstaff, AZ 85004, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Rachel B. Brem
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720-3102, USA
- Correspondence:
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23
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Zakaria AS, Edward EA, Mohamed NM. Pathogenicity Islands in Uropathogenic Escherichia coli Clinical Isolate of the Globally Disseminated O25:H4-ST131 Pandemic Clonal Lineage: First Report from Egypt. Antibiotics (Basel) 2022; 11:1620. [PMID: 36421264 PMCID: PMC9686529 DOI: 10.3390/antibiotics11111620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 10/25/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infections (UTIs). The pathogenesis of UTIs relies upon UPEC's acquisition of virulence determinants that are commonly inserted into large chromosomal blocks which are termed 'pathogenicity islands' (PAIs). In this study, we investigated the virulence-associated genes embedded in the chromosome of a UPEC Egyptian strain, EC14142. Additionally, we present a detailed characterization of the PAIs in the EGY_EC14142 chromosome. The isolate displayed a multidrug-resistant phenotype, and whole genome sequencing indicated that it belonged to the globally disseminated O25:H4-ST131 pandemic lineage and the H30-Rx clade. EGY_EC14142 carried genes that are responsible for resistance to aminoglycosides, fluoroquinolones, extended-spectrum β-lactams, macrolides, folate pathway antagonists, and tetracyclines. It encoded five PAIs with a high similarity to PAI II536, PAI IV536, PAI V536, PAI-536-icd, and PAIusp. The genome analysis of EGY_EC14142 with other closely related UPEC strains revealed that they have a high nucleotide sequence identity. The constructed maximum-likelihood phylogenetic tree showed the close clonality of EGY_EC14142 with the previously published ST131 UPEC international isolates, thus endorsing the broad geographical distribution of this clone. This is the first report characterizing PAIs in a UPEC Egyptian strain belonging to the globally disseminated pandemic clone O25:H4-ST131.
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Affiliation(s)
- Azza S. Zakaria
- Microbiology and Immunology Department, Faculty of Pharmacy, Alexandria University, Alexandria 25435, Egypt
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24
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Zhang D, Hu M, Chi S, Chen H, Lin C, Yu F, Zheng Z. Molecular Characteristics and Gonococcal Genetic Island Carrying Status of Thirty-Seven Neisseria gonorrhoeae Isolates in Eastern China. Infect Drug Resist 2022; 15:6545-6553. [DOI: 10.2147/idr.s385079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
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25
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Sardinha-Silva A, Alves-Ferreira EVC, Grigg ME. Intestinal immune responses to commensal and pathogenic protozoa. Front Immunol 2022; 13:963723. [PMID: 36211380 PMCID: PMC9533738 DOI: 10.3389/fimmu.2022.963723] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
The physical barrier of the intestine and associated mucosal immunity maintains a delicate homeostatic balance between the host and the external environment by regulating immune responses to commensals, as well as functioning as the first line of defense against pathogenic microorganisms. Understanding the orchestration and characteristics of the intestinal mucosal immune response during commensal or pathological conditions may provide novel insights into the mechanisms underlying microbe-induced immunological tolerance, protection, and/or pathogenesis. Over the last decade, our knowledge about the interface between the host intestinal mucosa and the gut microbiome has been dominated by studies focused on bacterial communities, helminth parasites, and intestinal viruses. In contrast, specifically how commensal and pathogenic protozoa regulate intestinal immunity is less well studied. In this review, we provide an overview of mucosal immune responses induced by intestinal protozoa, with a major focus on the role of different cell types and immune mediators triggered by commensal (Blastocystis spp. and Tritrichomonas spp.) and pathogenic (Toxoplasma gondii, Giardia intestinalis, Cryptosporidium parvum) protozoa. We will discuss how these various protozoa modulate innate and adaptive immune responses induced in experimental models of infection that benefit or harm the host.
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26
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Sadat A, Ramadan H, Elkady MA, Hammad AM, Soliman MM, Aboelenin SM, Al-Harthi HF, Abugomaa A, Elbadawy M, Awad A. Phylotypic Profiling, Distribution of Pathogenicity Island Markers, and Antimicrobial Susceptibility of Escherichia coli Isolated from Retail Chicken Meat and Humans. Antibiotics (Basel) 2022; 11:antibiotics11091197. [PMID: 36139976 PMCID: PMC9495032 DOI: 10.3390/antibiotics11091197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/20/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Escherichia coli (E.coli) found in retail chicken meat could be causing a wide range of infections in humans and constitute a potential risk. This study aimed to evaluate 60 E. coli isolates from retail chicken meat (n = 34) and human urinary tract infections (UTIs, n = 26) for phylogenetic diversity, presence of pathogenicity island (PAI) markers, antimicrobial susceptibility phenotypes, and antimicrobial resistance genes, and to evaluate their biofilm formation capacity. In that context, confirmed E.coli isolates were subjected to phylogrouping analysis using triplex PCR, antimicrobial susceptibility testing using the Kirby–Bauer disc diffusion method; PAI distribution was investigated by using two multiplex PCRs. Most of the chicken isolates (22/34, 64.7%) were identified as commensal E. coli (A and B1), while 12 isolates (35.3%) were classified as pathogenic virulent E. coli (B2 and D). Similarly, the commensal group dominated in human isolates. Overall, 23 PAIs were detected in the chicken isolates; among them, 39.1% (9/23) were assigned to group B1, 34.8% (8/23) to group A, 4.34% (1/23) to group B2, and 21.7% (5/23) to group D. However, 25 PAIs were identified from the human isolates. PAI IV536 was the most prevalent (55.9%, 69.2%) PAI detected in both sources. In total, 37 (61.7%) isolates of the chicken and human isolates were biofilm producers. Noticeably, 100% of E. coli isolates were resistant to penicillin and rifamycin. Markedly, all E. coli isolates displayed multiple antibiotic resistance (MAR) phenotypes, and the multiple antibiotic resistance index (MARI) among E. coli isolates ranged between 0.5 and 1. Several antibiotic resistance genes (ARGs) were identified by a PCR assay; the sul2 gene was the most prevalent (38/60, 63.3%) from both sources. Interestingly, a significant positive association (r = 0.31) between biofilm production and resistance to quinolones by the qnr gene was found by the correlation analysis. These findings were suggestive of the transmission of PAI markers and antibiotic resistance genes from poultry to humans or humans to humans through the food chain. To avoid the spread of virulent and multidrug-resistant E. coli, intensive surveillance of retail chicken meat markets is required.
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Affiliation(s)
- Asmaa Sadat
- Department of Bacteriology, Mycology, and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Hazem Ramadan
- Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed A. Elkady
- Mansoura Veterinary Laboratory Branch, Microbiology Research Department, Animal Health Research Institute, Kafrelsheikh 33516, Egypt
| | - Amal Mahmoud Hammad
- Biochemistry Department, Faculty of Medicine Damietta, Al-Azhar University, Cairo 11651, Egypt
| | - Mohamed M. Soliman
- Clinical Laboratory Sciences Department, Turabah University College, Taif University, Taif 21995, Saudi Arabia
| | - Salama M. Aboelenin
- Biology Department, Turabah University College, Taif University, Al Hawiyah 21995, Saudi Arabia
| | - Helal F. Al-Harthi
- Biology Department, Turabah University College, Taif University, Al Hawiyah 21995, Saudi Arabia
| | - Amira Abugomaa
- Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed Elbadawy
- Department of Pharmacology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt
| | - Amal Awad
- Department of Bacteriology, Mycology, and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
- Correspondence: ; Tel.: +2-0102-127-6993
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Whole-genome sequencing analysis of Shiga toxin-producing Escherichia coli O22:H8 isolated from cattle prediction pathogenesis and colonization factors and position in STEC universe phylogeny. J Microbiol 2022; 60:689-704. [DOI: 10.1007/s12275-022-1616-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/25/2022] [Accepted: 03/24/2022] [Indexed: 10/17/2022]
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28
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Werner KA, Schneider D, Poehlein A, Diederich N, Feyen L, Axtmann K, Hübner T, Brüggemann N, Prost K, Daniel R, Grohmann E. Metagenomic Insights Into the Changes of Antibiotic Resistance and Pathogenicity Factor Pools Upon Thermophilic Composting of Human Excreta. Front Microbiol 2022; 13:826071. [PMID: 35432262 PMCID: PMC9009411 DOI: 10.3389/fmicb.2022.826071] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/17/2022] [Indexed: 01/12/2023] Open
Abstract
In times of climate change, practicing a form of sustainable, climate-resilient and productive agriculture is of primordial importance. Compost could be one form of sustainable fertilizer, which is increasing humus, water holding capacity, and nutrient contents of soils. It could thereby strengthen agriculture toward the adverse effects of climate change, especially when additionally combined with biochar. To get access to sufficient amounts of suitable materials for composting, resources, which are currently treated as waste, such as human excreta, could be a promising option. However, the safety of the produced compost regarding human pathogens, pharmaceuticals (like antibiotics) and related resistance genes must be considered. In this context, we have investigated the effect of 140- and 154-days of thermophilic composting on the hygienization of human excreta and saw dust from dry toilets together with straw and green cuttings with and without addition of biochar. Compost samples were taken at the beginning and end of the composting process and metagenomic analysis was conducted to assess the fate of antibiotic resistance genes (ARGs) and pathogenicity factors of the microbial community over composting. Potential ARGs conferring resistance to major classes of antibiotics, such as beta-lactam antibiotics, vancomycin, the MLSB group, aminoglycosides, tetracyclines and quinolones were detected in all samples. However, relative abundance of ARGs decreased from the beginning to the end of composting. This trend was also found for genes encoding type III, type IV, and type VI secretion systems, that are involved in pathogenicity, protein effector transport into eukaryotic cells and horizontal gene transfer between bacteria, respectively. The results suggest that the occurrence of potentially pathogenic microorganisms harboring ARGs declines during thermophilic composting. Nevertheless, ARG levels did not decline below the detection limit of quantitative PCR (qPCR). Thresholds for the usage of compost regarding acceptable resistance gene levels are yet to be evaluated and defined.
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Affiliation(s)
- Katharina A. Werner
- Department of Microbiology, Faculty of Life Sciences and Technology, Berliner Hochschule für Technik, Berlin, Germany
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Nina Diederich
- Department of Microbiology, Faculty of Life Sciences and Technology, Berliner Hochschule für Technik, Berlin, Germany
| | - Lara Feyen
- Department of Microbiology, Faculty of Life Sciences and Technology, Berliner Hochschule für Technik, Berlin, Germany
| | - Katharina Axtmann
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Tobias Hübner
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research GmbH—Umweltforschungszentrum Leipzig (UFZ), Leipzig, Germany
| | - Nicolas Brüggemann
- Institute of Bio- and Geosciences—Agrosphere (IBG-3), Forschungszentrum Jülich, Jülich, Germany
| | - Katharina Prost
- Institute of Bio- and Geosciences—Agrosphere (IBG-3), Forschungszentrum Jülich, Jülich, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Elisabeth Grohmann
- Department of Microbiology, Faculty of Life Sciences and Technology, Berliner Hochschule für Technik, Berlin, Germany
- *Correspondence: Elisabeth Grohmann,
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29
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Recombination resolves the cost of horizontal gene transfer in experimental populations of Helicobacter pylori. Proc Natl Acad Sci U S A 2022; 119:e2119010119. [PMID: 35298339 PMCID: PMC8944584 DOI: 10.1073/pnas.2119010119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Horizontal gene transfer (HGT)—the transfer of DNA between lineages—is responsible for a large proportion of the genetic variation that contributes to evolution in microbial populations. While HGT can bring beneficial genetic innovation, the transfer of DNA from other species or strains can also have deleterious effects. In this study, we evolve populations of the bacteria Helicobacter pylori and use DNA sequencing to identify over 40,000 genetic variants transferred by HGT. We measure the cost of many of these and find that both strongly beneficial mutations and deleterious mutations are genetic variants transferred by natural transformation. Importantly, we also show how recombination that separates linked beneficial and deleterious mutations resolves the cost of HGT. Horizontal gene transfer (HGT) is important for microbial evolution, yet we know little about the fitness effects and dynamics of horizontally transferred genetic variants. In this study, we evolve laboratory populations of Helicobacter pylori, which take up DNA from their environment by natural transformation, and measure the fitness effects of thousands of transferred genetic variants. We find that natural transformation increases the rate of adaptation but comes at the cost of significant genetic load. We show that this cost is circumvented by recombination, which increases the efficiency of selection by decoupling deleterious and beneficial genetic variants. Our results show that adaptation with HGT, pervasive in natural microbial populations, is shaped by a combination of selection, recombination, and genetic drift not accounted for in existing models of evolution.
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30
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Cohen H, Adani B, Cohen E, Piscon B, Azriel S, Desai P, Bähre H, McClelland M, Rahav G, Gal-Mor O. The ancestral stringent response potentiator, DksA has been adapted throughout Salmonella evolution to orchestrate the expression of metabolic, motility, and virulence pathways. Gut Microbes 2022; 14:1997294. [PMID: 34923900 PMCID: PMC8726615 DOI: 10.1080/19490976.2021.1997294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
DksA is a conserved RNA polymerase-binding protein known to play a key role in the stringent response of proteobacteria species, including many gastrointestinal pathogens. Here, we used RNA-sequencing of Escherichia coli, Salmonella bongori and Salmonella enterica serovar Typhimurium, together with phenotypic comparison to study changes in the DksA regulon, during Salmonella evolution. Comparative RNA-sequencing showed that under non-starved conditions, DksA controls the expression of 25%, 15%, and 20% of the E. coli, S. bongori, and S. enterica genes, respectively, indicating that DksA is a pleiotropic regulator, expanding its role beyond the canonical stringent response. We demonstrate that DksA is required for the growth of these three enteric bacteria species in minimal medium and controls the expression of the TCA cycle, glycolysis, pyrimidine biosynthesis, and quorum sensing. Interestingly, at multiple steps during Salmonella evolution, the type I fimbriae and various virulence genes encoded within SPIs 1, 2, 4, 5, and 11 have been transcriptionally integrated under the ancestral DksA regulon. Consequently, we show that DksA is necessary for host cells invasion by S. Typhimurium and S. bongori and for intracellular survival of S. Typhimurium in bone marrow-derived macrophages (BMDM). Moreover, we demonstrate regulatory inversion of the conserved motility-chemotaxis regulon by DksA, which acts as a negative regulator in E. coli, but activates this pathway in S. bongori and S. enterica. Overall, this study demonstrates the regulatory assimilation of multiple horizontally acquired virulence genes under the DksA regulon and provides new insights into the evolution of virulence genes regulation in Salmonella spp.
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Affiliation(s)
- Helit Cohen
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Boaz Adani
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Emiliano Cohen
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Bar Piscon
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
| | - Shalhevet Azriel
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel
| | - Prerak Desai
- Janssen Research & Development, LLC, Raritan, New Jersey, USA,Department of Microbiology and Molecular Genetics, University of California, Irvine, California, USA
| | - Heike Bähre
- Hannover Medical School, Research Core Unit Metabolomics, Hannover, Germany
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, California, USA
| | - Galia Rahav
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ohad Gal-Mor
- Sheba Medical Center, The Infectious Diseases Research Laboratory, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel,Contact Ohad Gal-Mor The Infectious Diseases Research Laboratory Sheba Medical Cente, Tel-Hashomer, Israel
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31
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Tilahun M, Gedefie A, Belayhun C, Sahle Z, Abera A. Helicobacter pylori Pathogenicity Islands and Giardia lamblia Cysteine Proteases in Role of Coinfection and Pathogenesis. Infect Drug Resist 2022; 15:21-34. [PMID: 35023934 PMCID: PMC8747529 DOI: 10.2147/idr.s346705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/21/2021] [Indexed: 12/18/2022] Open
Abstract
Helicobacter pylori is a well-known human-specific stomach pathogen that infects more than half of the world’s population. The infection with this bacterium can cause a variety of gastrointestinal problems, including chronic gastritis, peptic ulcers, and even cancer. H. pylori is a highly infectious bacterium. H. pylori causes an increase in gastric mucosa pH or gastric mucosa intestinal metaplasia. These modifications in the stomach environment are necessary for G. lamblia colonization to occur. Giardia lamblia is a flagellate protozoan parasite that can cause giardiasis in humans and other mammals. It dwells in the duodenum and upper jejunum. Globally, over 280 million cases of human giardiasis are predicted to occur each year. Simultaneous human colonization by G. lamblia and H. pylori is a typical occurrence since the viruses’ predisposing factors are similar in both groups. Giardiasis is a parasitic infection that affects both children and adults worldwide. Infection with Giardia is more common in underdeveloped countries. Globally, more than 200 million cases of giardiasis are detected each year. In contrast, the presence of G. lamblia in the host body triggers an immunological response comparable to that of H. pylori, with lymphocytes strongly polarized towards Th1. As a result, their combined presence exacerbates host tissue damage. The major goal of this seminar is to describe the pathophysiology, immunology, and clinical aspects of G. lamblia and H. pylori coinfection using a comprehensive search of PubMed, Lancet, and Google Scholar sources. Upper gastrointestinal problems such as upper abdominal pain, abdominal bloating, nausea, vomiting, epigastric pain/burning, and belching are all caused by both organisms. Differentiation by physical examination is impossible in people infected with both bacteria. For this coinfection distinction, a laboratory diagnosis is required. G. lamblia and H. pylori, when present together, have a synergistic effect on the host and can cause serious damage. As a result, researchers should delve deeper into the mechanics underlying this potential microbial interaction.
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Affiliation(s)
- Mihret Tilahun
- Department of Medical Laboratory Sciences, College of Medicine and Health Science, Wollo University, Dessie, Ethiopia
| | - Alemu Gedefie
- Department of Medical Laboratory Sciences, College of Medicine and Health Science, Wollo University, Dessie, Ethiopia
| | - Chernet Belayhun
- Department of Medical Laboratory Science, Mehal Meda Hospital, North Showa, Ethiopia
| | - Zenawork Sahle
- Department of Medical Laboratory Science, Debre Birhan Health Science College, North Showa, Ethiopia
| | - Admasu Abera
- Department of Medical Laboratory Science, Debre Birhan Health Science College, North Showa, Ethiopia
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Thiam M, Barreto Sánchez AL, Zhang J, Wen J, Zhao G, Wang Q. Investigation of the Potential of Heterophil/Lymphocyte Ratio as a Biomarker to Predict Colonization Resistance and Inflammatory Response to Salmonella enteritidis Infection in Chicken. Pathogens 2022; 11:pathogens11010072. [PMID: 35056020 PMCID: PMC8778401 DOI: 10.3390/pathogens11010072] [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: 11/29/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 12/10/2022] Open
Abstract
Salmonella causes significant economic loss to the poultry industry and represents a real threat to human health. The region of difference 21 (ROD21) pathogenicity island removal is a genetic mechanism by which Salmonellaenteritidis (SE) invades the intestinal epithelium and induces systemic infection in mice. The heterophil/lymphocyte (H/L) ratio reflects the chicken’s robustness and immune system status. The H/L ratio is considered a disease resistance trait, and it could be used as a marker for selecting Salmonella resistance in live chickens. However, the association of the H/L ratio with Salmonella resistance and the inflammatory response remains to be elucidated. Moreover, the kinetics of ROD21 excision in the intestine and immune organs of chickens is unknown. Therefore, this study aimed to investigate the bacterial load, the ROD21 excision, the IL-1β, IL-8, and INF-γ blood serum concentration kinetics, and the association with the H/L ratio in chicken at 1, 3, 7, and 21 days post-SE infection. The results showed a significant correlation between the H/L ratio and the bacterial load in the ileum and caecum at 7 dpi. The ROD21 pathogenicity island absolute and relative excision in the caecum were positively correlated at 1 dpi but negatively correlated at 7 dpi with the H/L ratio. However, in the liver, we found the opposite tendency. The association of the H/L ratio with IL-1β, IL-8, and INF-γ blood serum concentrations showed that a low H/L ratio is correlated with increased IL-1β and INF-γ at 21 dpi. This study confirmed that the H/L ratio is associated with robustness and Salmonella-resistance in chicken. The methodology used in this study can separate individuals into susceptible and resistant and can help in the selection and breeding of Salmonella-resistant chickens.
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Hasan CM, Dutta D, Nguyen ANT. Revisiting Antibiotic Resistance: Mechanistic Foundations to Evolutionary Outlook. Antibiotics (Basel) 2021; 11:antibiotics11010040. [PMID: 35052917 PMCID: PMC8773413 DOI: 10.3390/antibiotics11010040] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022] Open
Abstract
Antibiotics are the pivotal pillar of contemporary healthcare and have contributed towards its advancement over the decades. Antibiotic resistance emerged as a critical warning to public wellbeing because of unsuccessful management efforts. Resistance is a natural adaptive tool that offers selection pressure to bacteria, and hence cannot be stopped entirely but rather be slowed down. Antibiotic resistance mutations mostly diminish bacterial reproductive fitness in an environment without antibiotics; however, a fraction of resistant populations 'accidentally' emerge as the fittest and thrive in a specific environmental condition, thus favouring the origin of a successful resistant clone. Therefore, despite the time-to-time amendment of treatment regimens, antibiotic resistance has evolved relentlessly. According to the World Health Organization (WHO), we are rapidly approaching a 'post-antibiotic' era. The knowledge gap about antibiotic resistance and room for progress is evident and unified combating strategies to mitigate the inadvertent trends of resistance seem to be lacking. Hence, a comprehensive understanding of the genetic and evolutionary foundations of antibiotic resistance will be efficacious to implement policies to force-stop the emergence of resistant bacteria and treat already emerged ones. Prediction of possible evolutionary lineages of resistant bacteria could offer an unswerving impact in precision medicine. In this review, we will discuss the key molecular mechanisms of resistance development in clinical settings and their spontaneous evolution.
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Affiliation(s)
- Chowdhury M. Hasan
- School of Biological Sciences, University of Queensland, Brisbane 4072, Australia
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary & Ecological Sciences (IVES), University of Liverpool, Liverpool L7 3EA, UK;
- School of Biological Sciences, Monash University, Melbourne 3800, Australia;
- Correspondence:
| | - Debprasad Dutta
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary & Ecological Sciences (IVES), University of Liverpool, Liverpool L7 3EA, UK;
- Department of Human Genetics, National Institute of Mental Health & Neurosciences (NIMHANS), Bangalore 560029, India
| | - An N. T. Nguyen
- School of Biological Sciences, Monash University, Melbourne 3800, Australia;
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Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages. THE ISME JOURNAL 2021; 15:3195-3206. [PMID: 33990706 PMCID: PMC8528876 DOI: 10.1038/s41396-021-01002-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 02/03/2023]
Abstract
The alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the world's soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that the vast majority of nif-carrying free-living members comprise an independent cluster, indicating that horizontal gene transfer promotes nif expansion among the free-living Bradyrhizobium. Comparative genomics analysis identifies that the nif genes found in free-living Bradyrhizobium are located on a unique genomic island of ~50 kb equipped with genes potentially involved in coping with oxygen tension. We further analyze amplicon sequencing data to show that Bradyrhizobium members presumably carrying this nif island are widespread in a variety of environments. Given the dominance of Bradyrhizobium in world's soils, our findings have implications for global nitrogen cycles and agricultural research.
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Qasemi A, Rahimi F, Katouli M. Genetic diversity and virulence characteristics of biofilm-producing uropathogenic Escherichia coli. Int Microbiol 2021; 25:297-307. [PMID: 34705131 DOI: 10.1007/s10123-021-00221-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022]
Abstract
Uropathogenic E. coli (UPEC) strains exhibit different levels of biofilm formation that help adhesion of the bacteria to uroepithelial cells. We investigated the genetic diversity and virulence-associated genes (VAGs) of biofilm-producing UPEC. A collection of 107 biofilm-producing (BFP) UPEC strains isolated from patients with UTI in Iran were divided into three groups of strong, moderate, and weak BFPs after a quantitative microtiter plate assay, and the involvement of curli and cellulose in adhesion of the strains to T24 cell line was confirmed by the construction of csgD and yedQ mutants of two representative UPEC strains. BFP strains were tested for their genetic diversity, phylogenetic groups, and the presence of 15 VAGs. A significant decrease in adhesion of csgD and yedQ mutant strains confirmed the role of biofilm production in adhesion to uroepithelial cells. A high diversity was found among all three groups of strong (Di = 0.998), moderate (Di = 0.998), and weak (Di = 0.988) BFPs with majority of the strains belonging to phylogroups B2 (44.9%) and A (24.3%). Strong BFP strains carried significantly higher level papEF, hlyA, and iutA than other BFP groups. In contrast, the presence of fimH, focG, sfaS, set-1, and cvaC was more pronounced among weak BFP strains. There exists a high genetic diversity among the BFP strains with different VGA profiles. However, the high prevalence of phylogroup A among BFP strains suggests the fitness of commensal E. coli strains to cause UTI in this country.
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Affiliation(s)
- Ali Qasemi
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezarjarib St., Isfahan, Iran
| | - Fateh Rahimi
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezarjarib St., Isfahan, Iran.
| | - Mohammad Katouli
- Genecology Research Center, Maroochydore, QLD, Australia.,School of Science, Technology and Education, University of the Sunshine Coast, Maroochydore, QLD, Australia
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36
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Johnson CN, Sheriff EK, Duerkop BA, Chatterjee A. Let Me Upgrade You: Impact of Mobile Genetic Elements on Enterococcal Adaptation and Evolution. J Bacteriol 2021; 203:e0017721. [PMID: 34370561 PMCID: PMC8508098 DOI: 10.1128/jb.00177-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and pathogens, largely due to their accumulation of mobile genetic elements via horizontal gene transfer (HGT). Common agents of HGT include plasmids, transposable elements, and temperate bacteriophages. These vehicles of HGT have facilitated the evolution of the enterococci, specifically Enterococcus faecalis and Enterococcus faecium, into multidrug-resistant hospital-acquired pathogens. On the other hand, commensal strains of Enterococcus harbor CRISPR-Cas systems that prevent the acquisition of foreign DNA, restricting the accumulation of mobile genetic elements. In this review, we discuss enterococcal mobile genetic elements by highlighting their contributions to bacterial fitness, examine the impact of CRISPR-Cas on their acquisition, and identify key areas of research that can improve our understanding of enterococcal evolution and ecology.
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Affiliation(s)
- Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Emma K. Sheriff
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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Sabbadin F, Urresti S, Henrissat B, Avrova AO, Welsh LRJ, Lindley PJ, Csukai M, Squires JN, Walton PH, Davies GJ, Bruce NC, Whisson SC, McQueen-Mason SJ. Secreted pectin monooxygenases drive plant infection by pathogenic oomycetes. Science 2021; 373:774-779. [PMID: 34385392 DOI: 10.1126/science.abj1342] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/06/2021] [Indexed: 01/19/2023]
Abstract
The oomycete Phytophthora infestans is a damaging crop pathogen and a model organism to study plant-pathogen interactions. We report the discovery of a family of copper-dependent lytic polysaccharide monooxygenases (LPMOs) in plant pathogenic oomycetes and its role in plant infection by P. infestans We show that LPMO-encoding genes are up-regulated early during infection and that the secreted enzymes oxidatively cleave the backbone of pectin, a charged polysaccharide in the plant cell wall. The crystal structure of the most abundant of these LPMOs sheds light on its ability to recognize and degrade pectin, and silencing the encoding gene in P. infestans inhibits infection of potato, indicating a role in host penetration. The identification of LPMOs as virulence factors in pathogenic oomycetes opens up opportunities in crop protection and food security.
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Affiliation(s)
- Federico Sabbadin
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
| | - Saioa Urresti
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Anna O Avrova
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Lydia R J Welsh
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter J Lindley
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Michael Csukai
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Julie N Squires
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Paul H Walton
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Gideon J Davies
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Stephen C Whisson
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
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El-Mahdy R, Mahmoud R, Shrief R. Characterization of E. coli Phylogroups Causing Catheter-Associated Urinary Tract Infection. Infect Drug Resist 2021; 14:3183-3193. [PMID: 34429618 PMCID: PMC8378909 DOI: 10.2147/idr.s325770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/28/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Characterization of different uropathogenic E. coli (UPEC) phylogroups is crucial to understand pathogenesis of urinary tract infection (UTI). The objective of our study was to evaluate the antibiotic resistance pattern, biofilm formation and pathogenicity islands (PAIs) of UPEC phylogroups isolated from catheter-associated UTI (CAUTI) compared to community UTI (Com-UTI). PATIENTS AND METHODS This study included 90 UPEC strains recovered from CAUTI and Com-UTI. Antimicrobial susceptibility was tested by the Kirby-Bauer method and extended spectrum beta-lactamase (ESBL) production was confirmed using the combined disk. The biofilm formation was tested using the microtiter plate assay. Main E. coli phylogroups (A, B1, B2 and D) were detected by multiplex PCR and 2 multiplex PCR detected the 8 PAIs. RESULTS Antibiotic resistance of UPEC strains showed a similar high resistance in CAUTI and Com-UTI. Isolates from CAUTI significantly produced biofilm higher than Com-UTI strains (68.9% vs 44.4%). In CAUTI and Com-UTI isolates, phylogroup A was the commonest (53.3% vs 48.9%, respectively). PAI IV536 was the most common in the strains from CAUTI (71.1%) and Com-UTI (73.3%). No significant relationship was detected between the studied characters and different phylogroups except the significant resistance to cefotaxime, ceftazidime and aztreonam among phylogroups from CAUTI isolates. CONCLUSION Increased antibiotic resistance and ESBLs were detected in UPEC strains from CAUTI and Com-UTI. The strains from CAUTI significantly produced biofilm higher than Com-UTI strains. Phylogroup A was the predominate phylogroup and PAI IV536 was the most prevalent marker in all phylogroups from both types of UTI.
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Affiliation(s)
- Rasha El-Mahdy
- Medical Microbiology and Immunology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Rasha Mahmoud
- Internal Medicine Department, Nephrology and Dialysis Unit, Mansoura University, Mansoura, Egypt
| | - Raghdaa Shrief
- Medical Microbiology and Immunology Department, Faculty of Medicine, Damietta University, Damietta, Egypt
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Sabbadin F, Henrissat B, Bruce NC, McQueen-Mason SJ. Lytic Polysaccharide Monooxygenases as Chitin-Specific Virulence Factors in Crayfish Plague. Biomolecules 2021; 11:biom11081180. [PMID: 34439846 PMCID: PMC8393829 DOI: 10.3390/biom11081180] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 11/19/2022] Open
Abstract
The oomycete pathogen Aphanomyces astaci, also known as “crayfish plague”, is an obligate fungal-like parasite of freshwater crustaceans and is considered responsible for the ongoing decline of native European crayfish populations. A. astaci is thought to secrete a wide array of effectors and enzymes that facilitate infection, however their molecular mechanisms have been poorly characterized. Here, we report the identification of AA15 lytic polysaccharide monooxygenases (LPMOs) as a new group of secreted virulence factors in A. astaci. We show that this enzyme family has greatly expanded in A. astaci compared to all other oomycetes, and that it may facilitate infection through oxidative degradation of crystalline chitin, the most abundant polysaccharide found in the crustacean exoskeleton. These findings reveal new roles for LPMOs in animal–pathogen interactions, and could help inform future strategies for the protection of farmed and endangered species.
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Affiliation(s)
- Federico Sabbadin
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK;
- Correspondence: (F.S.); (S.J.M.-M.)
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark;
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Neil C. Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK;
| | - Simon J. McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK;
- Correspondence: (F.S.); (S.J.M.-M.)
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40
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Minnullina L, Kostennikova Z, Evtugin V, Akosah Y, Sharipova M, Mardanova A. Diversity in the swimming motility and flagellar regulon structure of uropathogenic Morganella morganii strains. Int Microbiol 2021; 25:111-122. [PMID: 34363151 DOI: 10.1007/s10123-021-00197-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
In current times, the opportunistic pathogen Morganella morganii is increasingly becoming a cause of urinary tract infections. The condition has been further complicated by the multiple drug resistance of most isolates. Swimming motility plays an important role in the development of urinary tract infections, allowing bacteria to colonize the upper urinary tract. We determined the differences between the growth, swimming motility, and biofilm formation of two M. morganii strains MM 1 and MM 190 isolated from the urine of patients who had community-acquired urinary tract infections. MM 190 showed a lower growth rate but better-formed biofilms in comparison to MM 1. In addition, MM 190 possessed autoaggregation abilities. It was found that a high temperature (37 °C) inhibits the flagellation of strains and makes MM 190 less motile. At the same time, the MM 1 strain maintained its rate of motility at this temperature. We demonstrated that urea at a concentration of 1.5% suppresses the growth and swimming motility of both strains. Genome analysis showed that MM 1 has a 17.7-kb-long insertion in flagellar regulon between fliE and glycosyltransferase genes, which was not identified in corresponding loci of MM 190 and 9 other M. morganii strains with whole genomes. Both strains carry two genes encoding flagellin, which may indicate flagellar antigen phase variation. However, the fliC2 genes have only 91% identity to each other and exhibit some variability in the regulatory region. We assume that all these differences influence the swimming motility of the strains.
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Affiliation(s)
- Leyla Minnullina
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russia.
| | - Zarina Kostennikova
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russia
| | - Vladimir Evtugin
- Interdisciplinary Center for Analytical Microscopy, Kazan (Volga region) Federal University, Kazan, Russia
| | - Yaw Akosah
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russia
| | - Margarita Sharipova
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russia
| | - Ayslu Mardanova
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russia
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Genomic Island Prediction via Chi-Square Test and Random Forest Algorithm. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:9969751. [PMID: 34122622 PMCID: PMC8169257 DOI: 10.1155/2021/9969751] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/14/2021] [Indexed: 12/02/2022]
Abstract
Genomic islands are related to microbial adaptation and carry different genomic characteristics from the host. Therefore, many methods have been proposed to detect genomic islands from the rest of the genome by evaluating its sequence composition. Many sequence features have been proposed, but many of them have not been applied to the identification of genomic islands. In this paper, we present a scheme to predict genomic islands using the chi-square test and random forest algorithm. We extract seven kinds of sequence features and select the important features with the chi-square test. All the selected features are then input into the random forest to predict the genome islands. Three experiments and comparison show that the proposed method achieves the best performance. This understanding can be useful to design more powerful method for the genomic island prediction.
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42
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Lin Y, Wang G, Yu J, Sung JJY. Artificial intelligence and metagenomics in intestinal diseases. J Gastroenterol Hepatol 2021; 36:841-847. [PMID: 33880764 DOI: 10.1111/jgh.15501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/24/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
Gut microbiota has been shown to associate with the development of gastrointestinal diseases. In the last decade, development in whole metagenome sequencing and 16S rRNA sequencing technology has dramatically accelerated the gut microbiome's research and revealed its association with gastrointestinal disorders. Because of high dimensionality and complexity's intrinsic data characteristics, traditional bioinformatical methods could only explain the most significant changes with limited prediction accuracy. In contrast, machine learning is the application of artificial intelligence that provides the computational systems to automatically learn and improve from experience (training cohort) without being explicitly programmed. It is thus capable of unwiring high dimensionality and complicated correlational hitches. With modern computation power, machine learning is widely utilized to analyze microorganisms related to disease onset and other clinical features. It could help explore and identify novel biomarkers or improve the accuracy rate of disease diagnostic. This review summarized the most recent research that utilized machine learning to reveal the role of gut microbiota in intestinal disorders.
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Affiliation(s)
- Yufeng Lin
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Guoping Wang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Joseph J Y Sung
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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VanAken SM, Newton D, VanEpps JS. Improved diagnostic prediction of the pathogenicity of bloodstream isolates of Staphylococcus epidermidis. PLoS One 2021; 16:e0241457. [PMID: 33770084 PMCID: PMC7997010 DOI: 10.1371/journal.pone.0241457] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/27/2021] [Indexed: 12/27/2022] Open
Abstract
With an estimated 440,000 active cases occurring each year, medical device associated infections pose a significant burden on the US healthcare system, costing about $9.8 billion in 2013. Staphylococcus epidermidis is the most common cause of these device-associated infections, which typically involve isolates that are multi-drug resistant and possess multiple virulence factors. S. epidermidis is also frequently a benign contaminant of otherwise sterile blood cultures. Therefore, tests that distinguish pathogenic from non-pathogenic isolates would improve the accuracy of diagnosis and prevent overuse/misuse of antibiotics. Attempts to use multi-locus sequence typing (MLST) with machine learning for this purpose had poor accuracy (~73%). In this study we sought to improve the diagnostic accuracy of predicting pathogenicity by focusing on phenotypic markers (i.e., antibiotic resistance, growth fitness in human plasma, and biofilm forming capacity) and the presence of specific virulence genes (i.e., mecA, ses1, and sdrF). Commensal isolates from healthy individuals (n = 23), blood culture contaminants (n = 21), and pathogenic isolates considered true bacteremia (n = 54) were used. Multiple machine learning approaches were applied to characterize strains as pathogenic vs non-pathogenic. The combination of phenotypic markers and virulence genes improved the diagnostic accuracy to 82.4% (sensitivity: 84.9% and specificity: 80.9%). Oxacillin resistance was the most important variable followed by growth rate in plasma. This work shows promise for the addition of phenotypic testing in clinical diagnostic applications.
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Affiliation(s)
- Shannon M. VanAken
- Department of Emergency Medicine, University of Michigan, Ann Arbor, MI, United States of America
| | - Duane Newton
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
| | - J. Scott VanEpps
- Department of Emergency Medicine, University of Michigan, Ann Arbor, MI, United States of America
- Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States of America
- Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, United States of America
- Michigan Center for Integrative Research in Critical Care, University of Michigan, Ann Arbor, MI, United States of America
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, United States of America
- * E-mail:
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The molecular mechanisms of listeriolysin O-induced lipid membrane damage. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183604. [PMID: 33722646 DOI: 10.1016/j.bbamem.2021.183604] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 12/22/2022]
Abstract
Listeria monocytogenes is an intracellular food-borne pathogen that causes listeriosis, a severe and potentially life-threatening disease. Listeria uses a number of virulence factors to proliferate and spread to various cells and tissues. In this process, three bacterial virulence factors, the pore-forming protein listeriolysin O and phospholipases PlcA and PlcB, play a crucial role. Listeriolysin O belongs to a family of cholesterol-dependent cytolysins that are mostly expressed by gram-positive bacteria. Its unique structural features in an otherwise conserved three-dimensional fold, such as the acidic triad and proline-glutamate-serine-threonine-like sequence, enable the regulation of its intracellular activity as well as distinct extracellular functions. The stability of listeriolysin O is pH- and temperature-dependent, and this provides another layer of control of its activity in cells. Moreover, many recent studies have demonstrated a unique mechanism of pore formation by listeriolysin O, i.e., the formation of arc-shaped oligomers that can subsequently fuse to form membrane defects of various shapes and sizes. During listerial invasion of host cells, these membrane defects can disrupt phagosome membranes, allowing bacteria to escape into the cytosol and rapidly multiply. The activity of listeriolysin O is profoundly dependent on the amount and accessibility of cholesterol in the lipid membrane, which can be modulated by the phospholipase PlcB. All these prominent features of listeriolysin O play a role during different stages of the L. monocytogenes life cycle by promoting the proliferation of the pathogen while mitigating excessive damage to its replicative niche in the cytosol of the host cell.
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Mao G, Liang J, Wang Q, Zhao C, Bai Y, Liu R, Liu H, Qu J. Epilithic biofilm as a reservoir for functional virulence factors in wastewater-dominant rivers after WWTP upgrade. J Environ Sci (China) 2021; 101:27-35. [PMID: 33334522 DOI: 10.1016/j.jes.2020.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 06/12/2023]
Abstract
Virulence factors (VFs) confer upon pathogens the ability to cause various types of damage or diseases. Wastewater treatment plants (WWTPs) are important point sources for the emission of pathogens and VFs into receiving rivers. Conventional WWTP upgrades are often implemented to improve the water quality of receiving ecosystems. However, knowledge on the pathogens, VFs, and health risks to receiving aquatic ecosystems after upgrade remains limited. In this study, we investigated detailed pathogenic information, including taxa, pathogenicity, and health risk, in two wastewater-dominant rivers after WWTP upgrade. Using 16S rRNA gene sequencing, we screened 14 potential pathogens in water and epilithic biofilm samples, though they were significantly more enriched in the biofilms. Combining 16S rRNA and metagenomic sequencing data, we identified Pseudomonas and Aeromonas as the dominant pathogenic taxa carrying functional VFs (e.g., mobility and offensive) in the epilithic biofilm. Moreover, strong pathogen-specific VF-host co-occurrence events were observed in the epilithic biofilm samples, indicating the importance of biofilms as reservoirs and vehicles for VFs. Further, we demonstrated that mobility VF is crucial for biofilm formation and pathogens in biofilm carrying offensive VF may be highly invasive. Quantification and health risk assessment suggested that the skin contact risk of P. aeruginosa carrying VFs was higher than the acceptable probability of 10-4 in both water and epilithic biofilm samples, which may threaten ecological and human health.
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Affiliation(s)
- Guannan Mao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Jinsong Liang
- Harbin Institute of Technology, School of Civil and Environmental Engineering, Shenzhen 518055, China.
| | - Qiaojuan Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Ruiping Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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Ranjan M, Khokhani D, Nayaka S, Srivastava S, Keyser ZP, Ranjan A. Genomic diversity and organization of complex polysaccharide biosynthesis clusters in the genus Dickeya. PLoS One 2021; 16:e0245727. [PMID: 33571209 PMCID: PMC7877592 DOI: 10.1371/journal.pone.0245727] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 01/07/2021] [Indexed: 11/18/2022] Open
Abstract
The pectinolytic genus Dickeya (formerly Erwinia chrysanthemi) comprises numerous pathogenic species which cause diseases in various crops and ornamental plants across the globe. Their pathogenicity is governed by complex multi-factorial processes of adaptive virulence gene regulation. Extracellular polysaccharides and lipopolysaccharides present on bacterial envelope surface play a significant role in the virulence of phytopathogenic bacteria. However, very little is known about the genomic location, diversity, and organization of the polysaccharide and lipopolysaccharide biosynthetic gene clusters in Dickeya. In the present study, we report the diversity and structural organization of the group 4 capsule (G4C)/O-antigen capsule, putative O-antigen lipopolysaccharide, enterobacterial common antigen, and core lipopolysaccharide biosynthesis clusters from 54 Dickeya strains. The presence of these clusters suggests that Dickeya has both capsule and lipopolysaccharide carrying O-antigen to their external surface. These gene clusters are key regulatory components in the composition and structure of the outer surface of Dickeya. The O-antigen capsule/group 4 capsule (G4C) coding region shows a variation in gene content and organization. Based on nucleotide sequence homology in these Dickeya strains, two distinct groups, G4C group I and G4C group II, exist. However, comparatively less variation is observed in the putative O-antigen lipopolysaccharide cluster in Dickeya spp. except for in Dickeya zeae. Also, enterobacterial common antigen and core lipopolysaccharide biosynthesis clusters are present mostly as conserved genomic regions. The variation in the O-antigen capsule and putative O-antigen lipopolysaccharide coding region in relation to their phylogeny suggests a role of multiple horizontal gene transfer (HGT) events. These multiple HGT processes might have been manifested into the current heterogeneity of O-antigen capsules and O-antigen lipopolysaccharides in Dickeya strains during its evolution.
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Affiliation(s)
- Manish Ranjan
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, Uttar Pradesh, India
| | - Devanshi Khokhani
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Plant Pathology, University of Minnesota—Twin Cities, St. Paul, Minnesota, United States of America
| | - Sanjeeva Nayaka
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, Uttar Pradesh, India
| | - Suchi Srivastava
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, Uttar Pradesh, India
| | - Zachary P. Keyser
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ashish Ranjan
- Department of Plant Pathology, University of Minnesota—Twin Cities, St. Paul, Minnesota, United States of America
- Department of Plant Sciences (SLS), University of Hyderabad, Hyderabad, India
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Escherichia coli Sequence Type 457 Is an Emerging Extended-Spectrum-β-Lactam-Resistant Lineage with Reservoirs in Wildlife and Food-Producing Animals. Antimicrob Agents Chemother 2020; 65:AAC.01118-20. [PMID: 33020161 DOI: 10.1128/aac.01118-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/18/2020] [Indexed: 01/16/2023] Open
Abstract
Silver gulls carry phylogenetically diverse Escherichia coli, including globally dominant extraintestinal pathogenic E. coli (ExPEC) sequence types and pandemic ExPEC-ST131 clades; however, our large-scale study (504 samples) on silver gulls nesting off the coast of New South Wales identified E. coli ST457 as the most prevalent. A phylogenetic analysis of whole-genome sequences (WGS) of 138 ST457 samples comprising 42 from gulls, 2 from humans (Australia), and 14 from poultry farmed in Paraguay were compared with 80 WGS deposited in public databases from diverse sources and countries. E. coli ST457 strains are phylogenetic group F, carry fimH145, and partition into five main clades in accordance to predominant flagella H-antigen carriage. Although we identified considerable phylogenetic diversity among the 138 ST457 strains, closely related subclades (<100 SNPs) suggested zoonotic or zooanthroponosis transmission between humans, wild birds, and food-producing animals. Australian human clinical and gull strains in two of the clades were closely related (≤80 SNPs). Regarding plasmid content, country, or country/source, specific connections were observed, including I1/ST23, I1/ST314, and I1/ST315 disseminating bla CMY-2 in Australia, I1/ST113 carrying bla CTX-M-8 and mcr-5 in Paraguayan poultry, and F2:A-:B1 plasmids of Dutch origin being detected across multiple ST457 clades. We identified a high prevalence of nearly identical I1/ST23 plasmids carrying bla CMY-2 among Australian gull and clinical human strains. In summary, ST457 is a broad host range, geographically diverse E. coli lineage that can cause human extraintestinal disease, including urinary tract infection, and displays a remarkable ability to capture mobile elements that carry and transmit genes encoding resistance to critically important antibiotics.
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Riley LW. Distinguishing Pathovars from Nonpathovars: Escherichia coli. Microbiol Spectr 2020; 8:10.1128/microbiolspec.ame-0014-2020. [PMID: 33385193 PMCID: PMC10773148 DOI: 10.1128/microbiolspec.ame-0014-2020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.
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Affiliation(s)
- Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
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Sidhu JPS, Gupta VVSR, Stange C, Ho J, Harris N, Barry K, Gonzalez D, Van Nostrand JD, Zhou J, Page D, Tiehm A, Toze S. Prevalence of antibiotic resistance and virulence genes in the biofilms from an aquifer recharged with stormwater. WATER RESEARCH 2020; 185:116269. [PMID: 32798893 DOI: 10.1016/j.watres.2020.116269] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
An improved understanding of the diversity and composition of microbial communities carrying antibiotic resistance genes (ARGs) and virulence genes (VGs) in aquifers recharged with stormwater is essential to comprehend potential human health risks from water reuse. A high-throughput functional gene array was used to study the prevalence of ARGs and VGs in aquifer biofilms (n = 27) taken from three boreholes over three months. Bacterial genera annotated as opportunistic pathogens such as Aeromonas, Burkholderia, Pseudomonas, Shewanella, and Vibrio were ubiquitous and abundant in all biofilms. Bacteria from clinically relevant genera, Campylobacter, Enterobacter, Klebsiella, Mycobacterium, Mycoplasma, and Salmonella were detected in biofilms. The mean travel time of stormwater from the injection well to P1 and P3 boreholes was 260 and 360 days respectively. The presence of ARGs and VGs in the biofilms from these boreholes suggest a high spatial movement of ARGs and VGs in the aquifer. The ARGs with the highest abundance were small multidrug resistance efflux pumps (SMR) and multidrug efflux (Mex) followed by β-lactamase C genes. β- lactamase C encoding genes were primarily detected in Enterobacteriaceae, Pseudomonadaceae, Bacillaceae, and Rhodobacteraceae families. The VGs encoding siderophores, including aerobactin (iro and iuc genes), followed by pilin, hemolysin, and type III secretion were ubiquitous. Canonical correspondence analysis suggested that Total Organic Carbon (TOC), Dissolved Organic Carbon (DOC), turbidity, and Fe concentration has a significant impact on the microbial community structure of bacteria carrying ARGs and VGs. Post abstraction treatment of groundwater may be prudent to improve water security and reduce potential health risks.
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Affiliation(s)
- J P S Sidhu
- CSIRO Oceans and Atmosphere, Ecoscience Precinct, 41 Boggo Road, Brisbane 4102, Australia.
| | - V V S R Gupta
- CSIRO Agriculture and Food, Locked Bag No. 2, Glen Osmond, SA 5064, Australia
| | - C Stange
- DVGW-Technologiezentrum Wasser (TZW), Karlsruher Street 84, D-76139 Karlsruhe, Germany
| | - J Ho
- DVGW-Technologiezentrum Wasser (TZW), Karlsruher Street 84, D-76139 Karlsruhe, Germany
| | - N Harris
- CSIRO Agriculture and Food, Locked Bag No. 2, Glen Osmond, SA 5064, Australia
| | - K Barry
- CSIRO Land and Water Private Bag 2, Glen Osmond, SA 5064, Australia
| | - D Gonzalez
- CSIRO Land and Water Private Bag 2, Glen Osmond, SA 5064, Australia
| | - J D Van Nostrand
- Institute of Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
| | - J Zhou
- Institute of Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
| | - D Page
- CSIRO Land and Water Private Bag 2, Glen Osmond, SA 5064, Australia
| | - A Tiehm
- DVGW-Technologiezentrum Wasser (TZW), Karlsruher Street 84, D-76139 Karlsruhe, Germany
| | - S Toze
- CSIRO Land and Water, Ecoscience Precinct, 41 Boggo Road, Brisbane 4102, Australia
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Gonçalves OS, de Queiroz MV, Santana MF. Potential evolutionary impact of integrative and conjugative elements (ICEs) and genomic islands in the Ralstonia solanacearum species complex. Sci Rep 2020; 10:12498. [PMID: 32719415 PMCID: PMC7385641 DOI: 10.1038/s41598-020-69490-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/13/2020] [Indexed: 11/09/2022] Open
Abstract
Ralstonia solanacearum, a soil-borne plant pathogen, encompasses a large number of strains known as R. solanacearum species complex (RSSC). Although it has been suggested that mobile genetic elements (MGEs) may play an important role in the RSSC genome, the evolutionary impact of these elements remains unknown. Here, we identified and analysed Integrative and Conjugative Elements (ICEs) and Genomic Islands (GIs) in the 121 genomes published for Ralstonia spp., including RSSC strains and three other non-plant pathogenic Ralstonia spp. Our results provided a dataset of 12 ICEs and 31 GIs distributed throughout Ralstonia spp. Four novel ICEs in RSSC were found. Some of these elements cover 5% of the host genome and carry accessory genes with a potential impact on the fitness and pathogenicity of RSSC. In addition, phylogenetic analysis revealed that these MGEs clustered to the same species, but there is evidence of strains from different countries that host the same element. Our results provide novel insight into the RSSC adaptation, opening new paths to a better understanding of how these elements affect this soil-borne plant pathogen.
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Affiliation(s)
- Osiel Silva Gonçalves
- Departamento de Microbiologia, Instituto de Bsiotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Marisa Vieira de Queiroz
- Departamento de Microbiologia, Instituto de Bsiotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia, Instituto de Bsiotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil.
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