Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during systemic infection

The dissemination of pathogens through blood and their establishment within organs lead to severe clinical outcomes. However, the within-host dynamics that underly pathogen spread to and clearance from systemic organs remain largely uncharacterized. In animal models of infection, the observed pathogen population results from the combined contributions of bacterial replication, persistence, death, and dissemination, each of which can vary across organs. Quantifying the contribution of each these processes is required to interpret and understand experimental phenotypes. Here, we leveraged STAMPR, a new barcoding framework, to investigate the population dynamics of extraintestinal pathogenic E. coli, a common cause of bacteremia, during murine systemic infection. We show that while bacteria are largely cleared by most organs, organ-specific clearance failures are pervasive and result from dramatic expansions of clones representing less than 0.0001% of the inoculum. Clonal expansion underlies the variability in bacterial burden between animals, and stochastic dissemination of clones profoundly alters the pathogen population structure within organs. Despite variable pathogen expansion events, host bottlenecks are consistent yet highly sensitive to infection variables, including inoculum size and macrophage depletion. We adapted our barcoding methodology to facilitate multiplexed validation of bacterial fitness determinants identified with transposon mutagenesis and confirmed the importance of bacterial hexose metabolism and cell envelope homeostasis pathways for organ-specific pathogen survival. Collectively our findings provide a comprehensive map of the population biology that underlies bacterial systemic infection and a framework for barcode-based high-resolution mapping of infection dynamics.

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Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains

mSphere ◽

10.1128/msphere.00390-16 ◽

2017 ◽

Vol 2 (2) ◽

Cited By ~ 11

Author(s):

Craig M. Stephens ◽

Sheila Adams-Sapper ◽

Manraj Sekhon ◽

James R. Johnson ◽

Lee W. Riley

Keyword(s):

Public Health ◽

Antibiotic Resistance ◽

Genetic Factors ◽

Health Concern ◽

Public Health Concern ◽

Antibiotic Resistant ◽

Content Type ◽

E Coli ◽

Bacterial Genetic ◽

Public Health Strategies

ABSTRACT Antibiotic resistance in bacterial pathogens is a major public health concern. This work was motivated by the observation that only a small proportion of ST95 isolates, a major pandemic lineage of extraintestinal pathogenic E. coli, have acquired antibiotic resistance, in contrast to many other pandemic lineages. Understanding bacterial genetic factors that may prevent acquisition of resistance could contribute to the development of new biological, medical, or public health strategies to reduce antibiotic-resistant infections. Extraintestinal pathogenic Escherichia coli (ExPEC) strains belonging to multilocus sequence type 95 (ST95) are globally distributed and a common cause of infections in humans and domestic fowl. ST95 isolates generally show a lower prevalence of acquired antimicrobial resistance than other pandemic ExPEC lineages. We took a genomic approach to identify factors that may underlie reduced resistance. We fully assembled genomes for four ST95 isolates representing the four major fimH-based lineages within ST95 and also analyzed draft-level genomes from another 82 ST95 isolates, largely from the western United States. The fully assembled genomes of antibiotic-resistant isolates carried resistance genes exclusively on large (>90-kb) IncFIB/IncFII plasmids. These replicons were common in the draft genomes as well, particularly in antibiotic-resistant isolates, but we also observed multiple instances of a smaller (8.3-kb) ampicillin resistance plasmid that had been previously identified in Salmonella enterica. Among ST95 isolates, pansusceptibility to antibiotics was significantly associated with the fimH6 lineage and the presence of homologs of the previously identified 114-kb IncFIB/IncFII plasmid pUTI89, both of which were also associated with reduced carriage of other plasmids. Potential mechanistic explanations for lineage- and plasmid-specific effects on the prevalence of antibiotic resistance within the ST95 group are discussed. IMPORTANCE Antibiotic resistance in bacterial pathogens is a major public health concern. This work was motivated by the observation that only a small proportion of ST95 isolates, a major pandemic lineage of extraintestinal pathogenic E. coli, have acquired antibiotic resistance, in contrast to many other pandemic lineages. Understanding bacterial genetic factors that may prevent acquisition of resistance could contribute to the development of new biological, medical, or public health strategies to reduce antibiotic-resistant infections.

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Genome evolution and the emergence of pathogenicity in avian Escherichia coli

Nature Communications ◽

10.1038/s41467-021-20988-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Leonardos Mageiros ◽

Guillaume Méric ◽

Sion C. Bayliss ◽

Johan Pensar ◽

Ben Pascoe ◽

...

Keyword(s):

Escherichia Coli ◽

Association Studies ◽

Virulence Gene ◽

Systemic Infection ◽

Disease Status ◽

Evolutionary Mechanisms ◽

Sustainable Food ◽

E Coli ◽

Common Birds ◽

Systemic Infections

AbstractChickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.

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Influence of Inoculation Method, Spot Inoculation Site, and Inoculation Size on the Efficacy of Acidic Electrolyzed Water against Pathogens on Lettuce

Journal of Food Protection ◽

10.4315/0362-028x-66.11.2010 ◽

2003 ◽

Vol 66 (11) ◽

pp. 2010-2016 ◽

Cited By ~ 45

Author(s):

SHIGENOBU KOSEKI ◽

KYOICHIRO YOSHIDA ◽

YOSHINORI KAMITANI ◽

KAZUHIKO ITOH

Keyword(s):

Population Size ◽

Room Temperature ◽

Escherichia Coli O157 ◽

Bacterial Inoculation ◽

Pathogen Population ◽

Salmonella Spp ◽

Electrolyzed Water ◽

Inoculation Methods ◽

E Coli ◽

Inoculation Site

The influence of bacterial inoculation methods on the efficacy of sanitizers against pathogens was examined. Dip and spot inoculation methods were employed in this study to evaluate the effectiveness of acidic electrolyzed water (AcEW) and chlorinated water (200 ppm free available chlorine) against Escherichia coli O157:H7 and Salmonella spp. Ten pieces of lettuce leaf (5 by 5 cm) were inoculated by each method then immersed in 1.5 liters of AcEW, chlorinated water, or sterile distilled water for 1 min with agitation (150 rpm) at room temperature. The outer (abaxial) and inner (adaxial) surfaces of the lettuce leaf were distinguished in the spot inoculation. Initial inoculated pathogen population was in the range 7.3 to 7.8 log CFU/g. Treatment with AcEW and chlorinated water resulted in a 1 log CFU/g or less reduction of E. coli O157:H7 and Salmonella populations inoculated with the dip method. Spot inoculation of the inner surface of the lettuce leaf with AcEW and chlorinated water reduced the number of E. coli O157:H7 and Salmonella by approximately 2.7 and 2.5 log CFU/g, respectively. Spot inoculation of the outer surface of the lettuce leaf with both sanitizers resulted in approximately 4.6 and 4.4 log CFU/g reductions of E. coli O157:H7 and Salmonella, respectively. The influence of inoculation population size was also examined. Each sanitizer could not completely eliminate the pathogens when E. coli O157:H7 and Salmonella cells inoculated on the lettuce were of low population size (103 to 104 CFU/g), regardless of the inoculation technique.

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Lactoferrin protects neonatal rats from gut-related systemic infection

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.2001.281.5.g1140 ◽

2001 ◽

Vol 281 (5) ◽

pp. G1140-G1150 ◽

Cited By ~ 88

Author(s):

Lynn Edde ◽

Ronaldo B. Hipolito ◽

Freda F. Y. Hwang ◽

Denis R. Headon ◽

Robert A. Shalwitz ◽

...

Keyword(s):

Systemic Infection ◽

In Vitro Studies ◽

Peptide Antibiotics ◽

Neonatal Rats ◽

Vitro Assay ◽

E Coli ◽

Severity Scores ◽

Factor Α

Lactoferrin is a milk protein that reportedly protects infants from gut-related, systemic infection. Proof for this concept is limited and was addressed during in vivo and in vitro studies. Neonatal rats pretreated orally with recombinant human lactoferrin (rh-LF) had less bacteremia and lower disease severity scores ( P < 0.001) after intestinal infection with Escherichia coli. Control animals had 1,000-fold more colony-forming units of E. coli per milliliter of blood than treated animals ( P < 0.001). Liver cultures from control animals had a twofold increase in bacterial counts compared with cultures from rh-LF-treated pups ( P < 0.02). Oral therapy with rh-LF + FeSO4did not alter the protective effect. In vitro studies confirmed that rh-LF interacted with the infecting bacterium and rat macrophages. An in vitro assay showed that rh-LF did not kill E. coli, but a combination of rh-LF + lysozyme was microbicidal. In vitro studies showed that rat macrophages released escalating amounts of nitric oxide and tumor necrosis factor-α when stimulated with increasing concentrations of rh-LF. The in vitro studies suggest that rh-LF may act with other “natural peptide antibiotics” or may prime macrophages to kill E. coli in vivo.

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Click-chemistry enabled directed evolution of glycosynthases for bespoke glycans synthesis

10.1101/2020.03.23.001982 ◽

2020 ◽

Cited By ~ 1

Author(s):

Ayushi Agrawal ◽

Chandra Kanth Bandi ◽

Tucker Burgin ◽

Youngwoo Woo ◽

Heather B. Mayes ◽

...

Keyword(s):

Single Cell ◽

Click Chemistry ◽

Directed Evolution ◽

Cell Sorting ◽

Screening Methods ◽

Carbohydrate Active Enzymes ◽

E Coli ◽

Highly Sensitive ◽

Increased Activity

AbstractEngineering of carbohydrate-active enzymes like glycosynthases for chemoenzymatic synthesis of bespoke oligosaccharides has been limited by the lack of suitable directed evolution based protein engineering methods. Currently there are no ultrahigh-throughput screening methods available for rapid and highly sensitive single cell-based screening of evolved glycosynthase enzymes employing azido sugars as substrates. Here, we report a fluorescence-based approach employing click-chemistry for the selective detection of glycosyl azides (versus free inorganic azides) that facilitated ultrahigh-throughput in-vivo single cell-based assay of glycosynthase activity. This discovery has led to the development of a directed evolution methodology for screening and sorting glycosynthase mutants for synthesis of desired fucosylated oligosaccharides. Our screening technique facilitated rapid fluorescence activated cell sorting of a large library of glycosynthase variants (>106 mutants) expressed in E. coli to identify several novel mutants with increased activity for β-fucosyl-azide activated donor sugars towards desired acceptor sugars, demonstrating the broader applicability of this methodology.

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Subdural false twins: concomitant appearance of subdural haematoma and spontaneous subdural empyema

BMJ Case Reports ◽

10.1136/bcr-2020-240110 ◽

2021 ◽

Vol 14 (6) ◽

pp. e240110

Author(s):

Rúben Santos Cardoso ◽

Sofia Tavares ◽

Inácio Reis ◽

José Luís Alves

Keyword(s):

Multidisciplinary Approach ◽

Systemic Infection ◽

Blood Analysis ◽

Surgical Drainage ◽

Subdural Collection ◽

E Coli ◽

History Of ◽

The Right ◽

Burr Holes ◽

Dural Opening

A 55-year-old man was taken to the emergency department due to right arm weakness for the past 3 days and fever (39.5°C). There was no impaired consciousness, no history of trauma and meningeal signs were absent on physical examination. Blood analysis and inflammatory markers were not evocative of a systemic infection. A cranial CT scan was requested, revealing hypodense bilateral hemispheric subdural collections, suggestive of chronic subdural haematomas. He was submitted to surgical drainage by burr holes, which confirmed the chronic subdural collection on the left side. Unexpectedly, after dural opening on the right side, a subdural purulent collection was found, which was later confirmed as an empyema due to Escherichia coli infection. A second surgical drainage was performed by craniotomy due to recurrence of the right subdural collection. Spontaneously appearing subdural empyemas due to E. coli are extremely rare and their treatment is not always straightforward. The reported case is an example of an apparently straightforward and frequent pathology that turned out to be a challenging case, requiring a multidisciplinary approach.

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Chemical and Irradiation Treatments for Killing Escherichia coli O157:H7 on Alfalfa, Radish, and Mung Bean Seeds

Journal of Food Protection ◽

10.4315/0362-028x-66.5.767 ◽

2003 ◽

Vol 66 (5) ◽

pp. 767-774 ◽

Cited By ~ 63

Author(s):

M. L. BARI ◽

E. NAZUKA ◽

Y. SABINA ◽

S. TODORIKI ◽

K. ISSHIKI

Keyword(s):

Escherichia Coli ◽

Heat Treatment ◽

Mung Bean ◽

Escherichia Coli O157 ◽

E Coli ◽

Chemical Treatments ◽

Dry Heat ◽

Pathogen Populations ◽

Dry Heat Treatment ◽

Alfalfa Seeds

In this study, the effectiveness of dry-heat treatment in combination with chemical treatments (electrolyzed oxidizing [EO] water, califresh-S, 200 ppm of active chlorinated water) with and without sonication in eliminating Escherichia coli O157:H7 on laboratory-inoculated alfalfa, radish, and mung bean seeds was compared with that of dry-heat treatment in combination with irradiation treatment. The treatment of mung bean seeds with EO water in combination with sonication followed by a rinse with sterile distilled water resulted in reductions of approximately 4.0 log10 CFU of E. coli O157:H7 per g, whereas reductions of ca. 1.52 and 2.64 log10 CFU/g were obtained for radish and alfalfa seeds. The maximum reduction (3.70 log10 CFU/g) for mung bean seeds was achieved by treatment with califresh-S and chlorinated water (200 ppm) in combination with sonication and a rinse. The combination of dry heat, hot EO water treatment, and sonication was able to eliminate pathogen populations on mung bean seeds but was unable to eliminate the pathogen on radish and alfalfa seeds. Other chemical treatments used were effective in greatly reducing pathogen populations on radish and alfalfa seeds without compromising the quality of the sprouts, but these treatments did not result in the elimination of pathogens from radish and alfalfa seeds. Moreover, a combination of dry-heat and irradiation treatments was effective in eliminating E. coli O157:H7 on laboratory-inoculated alfalfa, radish, and mung bean seeds. An irradiation dose of 2.0 kGy in combination with dry heat eliminated E. coli O157:H7 completely from alfalfa and mung bean seeds, whereas a 2.5-kGy dose of irradiation was required to eliminate the pathogen completely from radish seeds. Dry heat in combination with irradiation doses of up to 2.0 kGy did not unacceptably decrease the germination percentage for alfalfa seeds or the length of alfalfa sprouts but did decrease the lengths of radish and mung bean sprouts.

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Characterization and Antibiogram of Escherichia coli Associated with Mortality in Broilers and Ducklings in Bangladesh

Bangladesh Journal of Veterinary Medicine ◽

10.3329/bjvm.v2i1.1927 ◽

1970 ◽

Vol 2 (1) ◽

pp. 9-14 ◽

Cited By ~ 1

Author(s):

MT Islam ◽

MA Islam ◽

MA Samad ◽

SML Kabir

Keyword(s):

Escherichia Coli ◽

Antibiotic Sensitivity ◽

High Rate ◽

E Coli ◽

Sensitivity Pattern ◽

Highly Sensitive ◽

Biochemical Studies ◽

Increasing Trend ◽

Escherichia Coli Infection ◽

Hemorrhagic Enteritis

Mortality in broilers (6.56%) and growing ducks (11.0%) caused by Escherichia coli was recorded in the experimental flocks study during the period from May to August 2003. E. coli organisms isolated from broiler birds affected with characteristic lesions of omphalitis and yolk sac infection, fibrinous pericarditis and peri-hepatitis , hemorrhagic enteritis, and accumulation of excessive pericardial and peritoneal fluid, whereas from ducks with lesions of hemorrhagic enteritis and extensive epicardial hemorrhages. Each of the 21 isolates collected from broilers and 11 isolates from ducks was characterized by cultural and biochemical studies, of which 8 isolates from broilers and 5 isolates from ducks were tested for antibiotic sensitivity with 9 different antibiotics. The antibiotic sensitivity pattern showed that the isolates were highly sensitive to ciprofloxacin but an increasing trend of resistance was recorded in broilers (7 / 9) than duck (4 / 9) isolates. It may be concluded from the results of this study that the high rate of E. coli infection in broilers and ducks along with the high resistance of isolates to antibiotics constitute a threat to the poultry industry in Bangladesh. Key words: Escherichia coli infection; mortality; broilers; ducks; characterization; antibiogram doi: 10.3329/bjvm.v2i1.1927 Bangl. J. Vet. Med. (2004). 2 (1) : 09-14

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