Tracking resistomes, virulence genes, and bacterial pathogens in long-term manure-amended greenhouse soils

2020 ◽  
Vol 396 ◽  
pp. 122618 ◽  
Author(s):  
Houpu Zhang ◽  
Qianke Zhang ◽  
Jiajin Song ◽  
Zihan Zhang ◽  
Shiyu Chen ◽  
...  
Keyword(s):  
Virulence Genes ◽  
Bacterial Pathogens ◽  
Greenhouse Soils

scholarly journals Transmission of Novel Bacterial Pathogens through Pigs Transported from Myanmar to Mizoram

2021 ◽  
Author(s):  
C. Lalremruata ◽  
T.K. Dutta ◽  
P. Roychoudhury ◽  
Sanjeev Kumar ◽  
A. Sen ◽  
...  
Keyword(s):  
Pasteurella Multocida ◽  
Virulence Genes ◽  
Bacterial Pathogens ◽  
Bacterial Species ◽  
Microbial Pathogens ◽  
Identification System ◽  
Bacterial Strains ◽  
Illegal Migration ◽  
Isolation And Identification ◽  
Specific Pcr

Background: Illegal migration of pigs/piglets from Myanmar to Mizoram is a common practice to meet the local demands. The migrated animals are suspected as potential carrier of various microbial pathogens. The present study was conducted on isolation, identification and molecular characterization of major bacterial pathogens (Actinobacillus pleuropneumoniae, Bordetella bronchiseptica, Haemophilus parasuis, Mycoplasma hyopneumoniae and Pasteurella multocida) in pigs illegally migrated from Myanmar to Mizoram. Methods: A total of 209 rectal swabs and 209 nasal swabs were collected from apparently healthy migrated pigs during October 2018 to April, 2019. All the samples were processed for PCR based detection of target bacterial species followed by isolation and identification by bacteriological techniques. The bacterial species were further confirmed by BD Phoenix automated bacterial identification system and selected virulence genes of the bacterial species were determined by specific PCR assay. Result: By species specific PCR, 110 samples were found to be positive for selected bacterial species, of which 20 (9.57%), 1 (0.478%), 86 (41.15%), 2 (0.956%) and 1 (0.478%) were A. pleuropneumoniae, B. bronchiseptica, H. parasuis, M. hyopneumoniae and P. multocida, respectively. A total of 52 bacterial strains were isolated and identified, of which 11, 1, 39 and 1 were A. pleuropneumoniae, B. bronchiseptica, H. parasuis, M. hyopneumoniae and P. multocida, respectively. Virulence genes were detected in A. pleuropneumoniae and H. parasuis isolates. Based upon the published literatures, this is the first ever report of isolation and identification of pathogenic A. pleuropneumoniae and H. parasuis in pigs in India.

scholarly journals Escherichia coli EDL933 Requires Gluconeogenic Nutrients To Successfully Colonize the Intestines of Streptomycin-Treated Mice Precolonized with E. coli Nissle 1917

2015 ◽  
Vol 83 (5) ◽  
pp. 1983-1991 ◽  
Author(s):  
Silvia A. C. Schinner ◽  
Matthew E. Mokszycki ◽  
Jimmy Adediran ◽  
Mary Leatham-Jensen ◽  
Tyrrell Conway ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Genes ◽  
Probiotic Strain ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Mouse Intestine ◽  
K 12 ◽  
Rule Out

Escherichia coliMG1655, a K-12 strain, uses glycolytic nutrients exclusively to colonize the intestines of streptomycin-treated mice when it is the onlyE. colistrain present or when it is confronted withE. coliEDL933, an O157:H7 strain. In contrast,E. coliEDL933 uses glycolytic nutrients exclusively when it is the onlyE. colistrain in the intestine but switches in part to gluconeogenic nutrients when it colonizes mice precolonized withE. coliMG1655 (R. L. Miranda et al., Infect Immun 72:1666–1676, 2004,http://dx.doi.org/10.1128/IAI.72.3.1666-1676.2004). Recently, J. W. Njoroge et al. (mBio 3:e00280-12, 2012,http://dx.doi.org/10.1128/mBio.00280-12) reported thatE. coli86-24, an O157:H7 strain, activates the expression of virulence genes under gluconeogenic conditions, suggesting that colonization of the intestine with a probioticE. colistrain that outcompetes O157:H7 strains for gluconeogenic nutrients could render them nonpathogenic. Here we report thatE. coliNissle 1917, a probiotic strain, uses both glycolytic and gluconeogenic nutrients to colonize the mouse intestine between 1 and 5 days postfeeding, appears to stop using gluconeogenic nutrients thereafter in a large, long-term colonization niche, but continues to use them in a smaller niche to compete with invadingE. coliEDL933. Evidence is also presented suggesting that invadingE. coliEDL933 uses both glycolytic and gluconeogenic nutrients and needs the ability to perform gluconeogenesis in order to colonize mice precolonized withE. coliNissle 1917. The data presented here therefore rule out the possibility thatE. coliNissle 1917 can starve the O157:H7E. colistrain EDL933 of gluconeogenic nutrients, even thoughE. coliNissle 1917 uses such nutrients to compete withE. coliEDL933 in the mouse intestine.

scholarly journals A long-term epigenetic memory switch controls bacterial virulence bimodality

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Irine Ronin ◽  
Naama Katsowich ◽  
Ilan Rosenshine ◽  
Nathalie Q Balaban
Keyword(s):  
Mathematical Modeling ◽  
Virulence Genes ◽  
Phenotypic Variability ◽  
Bacterial Virulence ◽  
Environmental Cues ◽  
Human Pathogen ◽  
Epigenetic Memory ◽  
E Coli

When pathogens enter the host, sensing of environmental cues activates the expression of virulence genes. Opposite transition of pathogens from activating to non-activating conditions is poorly understood. Interestingly, variability in the expression of virulence genes upon infection enhances colonization. In order to systematically detect the role of phenotypic variability in enteropathogenic E. coli (EPEC), an important human pathogen, both in virulence activating and non-activating conditions, we employed the ScanLag methodology. The analysis revealed a bimodal growth rate. Mathematical modeling combined with experimental analysis showed that this bimodality is mediated by a hysteretic memory-switch that results in the stable co-existence of non-virulent and hyper-virulent subpopulations, even after many generations of growth in non-activating conditions. We identified the per operon as the key component of the hysteretic switch. This unique hysteretic memory switch may result in persistent infection and enhanced host-to-host spreading.

scholarly journals Evolutionary epidemiology of a zoonosis

2021 ◽  
Author(s):  
Giulia I Corsi ◽  
Swapnil Tichkule ◽  
Anna Rosa Sannella ◽  
Paolo Vatta ◽  
Francesco Asnicar ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Virulence Genes ◽  
Population Admixture ◽  
Genome Sequences ◽  
Host Parasite Interactions ◽  
Geographic Origins ◽  
Evolutionary Epidemiology ◽  
Evolutionary Consequences ◽  
Host Parasite

Cryptosporidium parvum is a global zoonoses and a major cause of diarrhoea in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human- and ruminant-derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and all are likely recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long-term evolutionary consequences of these events. Our results suggest that increased globalisation and close human-animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host-parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race.

scholarly journals Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing

2020 ◽  
Vol 21 (23) ◽  
pp. 9161
Author(s):  
Zhao Chen ◽  
David L. Erickson ◽  
Jianghong Meng
Keyword(s):  
Virulence Genes ◽  
Bacterial Pathogens ◽  
Error Rates ◽  
Nanopore Sequencing ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Genomic Analyses ◽  
Long Read ◽  
Genome Analyses ◽  
Assembly Algorithms

Oxford Nanopore sequencing can be used to achieve complete bacterial genomes. However, the error rates of Oxford Nanopore long reads are greater compared to Illumina short reads. Long-read assemblers using a variety of assembly algorithms have been developed to overcome this deficiency, which have not been benchmarked for genomic analyses of bacterial pathogens using Oxford Nanopore long reads. In this study, long-read assemblers, namely Canu, Flye, Miniasm/Racon, Raven, Redbean, and Shasta, were thus benchmarked using Oxford Nanopore long reads of bacterial pathogens. Ten species were tested for mediocre- and low-quality simulated reads, and 10 species were tested for real reads. Raven was the most robust assembler, obtaining complete and accurate genomes. All Miniasm/Racon and Raven assemblies of mediocre-quality reads provided accurate antimicrobial resistance (AMR) profiles, while the Raven assembly of Klebsiella variicola with low-quality reads was the only assembly with an accurate AMR profile among all assemblers and species. All assemblers functioned well for predicting virulence genes using mediocre-quality and real reads, whereas only the Raven assemblies of low-quality reads had accurate numbers of virulence genes. Regarding multilocus sequence typing (MLST), Miniasm/Racon was the most effective assembler for mediocre-quality reads, while only the Raven assemblies of Escherichia coli O157:H7 and K. variicola with low-quality reads showed positive MLST results. Miniasm/Racon and Raven were the best performers for MLST using real reads. The Miniasm/Racon and Raven assemblies showed accurate phylogenetic inference. For the pan-genome analyses, Raven was the strongest assembler for simulated reads, whereas Miniasm/Racon and Raven performed the best for real reads. Overall, the most robust and accurate assembler was Raven, closely followed by Miniasm/Racon.

scholarly journals Within-Host Evolution of Burkholderia pseudomallei over a Twelve-Year Chronic Carriage Infection

mBio ◽  
2013 ◽  
Vol 4 (4) ◽  
Author(s):  
Erin P. Price ◽  
Derek S. Sarovich ◽  
Mark Mayo ◽  
Apichai Tuanyok ◽  
Kevin P. Drees ◽  
...  
Keyword(s):  
Burkholderia Pseudomallei ◽  
Bacterial Pathogens ◽  
Bacterial Persistence ◽  
Content Type ◽  
Human Host ◽  
Environmental Survival ◽  
Virulence Attenuation ◽  
Chronic Carriage ◽  
Host Evolution

ABSTRACT Burkholderia pseudomallei causes the potentially fatal disease melioidosis. It is generally accepted that B. pseudomallei is a noncommensal bacterium and that any culture-positive clinical specimen denotes disease requiring treatment. Over a 23-year study of melioidosis cases in Darwin, Australia, just one patient from 707 survivors has developed persistent asymptomatic B. pseudomallei carriage. To better understand the mechanisms behind this unique scenario, we performed whole-genome analysis of two strains isolated 139 months apart. During this period, B. pseudomallei underwent several adaptive changes. Of 23 point mutations, 78% were nonsynonymous and 43% were predicted to be deleterious to gene function, demonstrating a strong propensity for positive selection. Notably, a nonsense mutation inactivated the universal stress response sigma factor RpoS, with pleiotropic implications. The genome underwent substantial reduction, with four deletions in chromosome 2 resulting in the loss of 221 genes. The deleted loci included genes involved in secondary metabolism, environmental survival, and pathogenesis. Of 14 indels, 11 occurred in coding regions and 9 resulted in frameshift mutations that dramatically affected predicted gene products. Disproportionately, four indels affected lipopolysaccharide biosynthesis and modification. Finally, we identified a frameshift mutation in both P314 isolates within wcbR, an important component of the capsular polysaccharide I locus, suggesting virulence attenuation early in infection. Our study illustrates a unique clinical case that contrasts a high-consequence infectious agent with a long-term commensal infection and provides further insights into bacterial evolution within the human host. IMPORTANCE Some bacterial pathogens establish long-term infections that are difficult or impossible to eradicate with current treatments. Rapid advances in genome sequencing technologies provide a powerful tool for understanding bacterial persistence within the human host. Burkholderia pseudomallei is considered a highly pathogenic bacterium because infection is commonly fatal. Here, we document within-host evolution of B. pseudomallei in a unique case of human infection with ongoing chronic carriage. Genomic comparison of isolates obtained 139 months (11.5 years) apart showed a strong signal of adaptation within the human host, including inactivation of virulence and immunogenic factors, and deletion of pathways involved in environmental survival. Two global regulatory genes were mutated in the 139-month isolate, indicating extensive regulatory changes favoring bacterial persistence. Our study provides insights into B. pseudomallei pathogenesis and, more broadly, identifies parallel evolutionary mechanisms that underlie chronic persistence of all bacterial pathogens.

scholarly journals An Increased Risk of School-Aged Children with Viral Infection among Diarrhea Clusters in Taiwan during 2011–2019

Children ◽  
2021 ◽  
Vol 8 (9) ◽  
pp. 807
Author(s):  
Fu-Huang Lin ◽  
Yu-Ching Chou ◽  
Bao-Chung Chen ◽  
Jui-Cheng Lu ◽  
Chung-Jung Liu ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Bacterial Infections ◽  
Bacterial Pathogens ◽  
Single Infection ◽  
Public Places ◽  
The Public ◽  
School Aged Children ◽  
Increased Risk ◽  
Epidemiological Characteristics

Acute diarrhea is mainly caused by norovirus and rotavirus. Numerous factors modify the risk of diarrhea cluster infections and outbreaks. The purpose of this study was to explore the epidemiological characteristics, differences, and trends in the distribution of viral and bacterial pathogens that cause diarrhea cluster events as well as the public places where diarrhea cluster events took place in Taiwan from 2011 to 2019. We examined publicly available, annual summary data on 2865 diarrhea clusters confirmed by the Taiwan Centers for Disease Control (CDC) from 2011 to 2019. There were statistically significant differences (p < 0.001) in event numbers of diarrhea clusters among viral and bacterial pathogens, and statistically significant differences (p < 0.001) in event numbers of diarrhea clusters among bacterial pathogens. There were also statistically significant differences (p < 0.001) in the event numbers of diarrhea clusters among public places. Norovirus infections were the first most numerous (77.1%, 1810/2347) diarrhea clusters among viral and bacterial infections. Among bacterial infections, Staphylococcus aureus infections accounted for the greatest number of diarrhea clusters (35.5%, 104/293). Schools were the places with the greatest number of diarrhea clusters (49.1%, 1406/2865) among various institutions. Norovirus single infection (odds ratio, OR = 4.423), Staphylococcus aureus single infection (OR = 2.238), and school (OR = 1.983) were identified as risk factors. This is the first report of confirmed events of diarrhea clusters taken from surveillance data compiled by Taiwan’s CDC (2011–2019). This study highlights the importance of long-term and geographically extended studies, particularly for highly fluctuating pathogens, to understand the implications of the transmission of diarrhea clusters in Taiwan’s populations. Importantly, big data have been identified that can inform future surveillance and research efforts in Taiwan.

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