Meta-analysis of Pandemic Escherichia coli ST131 Plasmidome Proves Restricted Plasmid-clade Associations

AbstractExtraintestinal multidrug resistant Escherichia coli sequence type (ST) 131 is a worldwide pandemic pathogen and a major cause of urinary tract and bloodstream infections. The role of this pandemic lineage in multidrug resistance plasmid dissemination is still scarce. We herein performed a meta-analysis on E. coli ST131 whole-genome sequence (WGS) databases to unravel ST131 plasmidome and specifically to decipher CTX-M encoding plasmids-clade associations. We mined 880 ST131 WGS data and proved that CTX-M-27-encoding IncF[F1:A2:B20] (Group1) plasmids are strictly found in clade C1, whereas CTX-M-15-encoding IncF[F2:A1:B-] (Group2) plasmids exist only in clade C2 suggesting strong plasmid-clade adaptations. Specific Col-like replicons (Col156, Col(MG828), and Col8282) were also found to be clade C1-associated. BLAST-based search revealed that Group1 and Group2 plasmids are narrow-host-range and restricted to E.coli. Among a collection of 20 newly sequenced Israeli ST131 CTX-M-encoding plasmids (2003–2016), Group1 and Group2 plasmids were dominant and associated with the expected clades. We found, for the first time in ST131, a CTX-M-15-encoding phage-like plasmid group (Group3) and followed its spread in the WGS data. This study offers a comprehensive way to decipher plasmid-bacterium associations and demonstrates that the CTX-M-encoding ST131 Group1 and Group2 plasmids are clade-restricted and presumably less transmissible, potentially contributing to ST131 clonal superiority.

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Draft Genomic Sequences of Three Escherichia coli Sequence Type 131 Isolates (H45, H43ii, and H43iii) from Patients in Lagos, Nigeria

Microbiology Resource Announcements ◽

10.1128/mra.00076-20 ◽

2020 ◽

Vol 9 (17) ◽

Author(s):

Yishan Yang ◽

Christopher H. Sommers ◽

Eyitayo O. Adenipekun ◽

Marina Ceruso ◽

Charlene R. Jackson ◽

...

Keyword(s):

Escherichia Coli ◽

Urinary Tract ◽

Bloodstream Infections ◽

Multidrug Resistant ◽

Sequence Type ◽

Urine Samples ◽

Genomic Sequences ◽

Content Type ◽

E Coli

Escherichia coli sequence type 131 (ST131) has recently emerged as a leading multidrug-resistant pathogen that causes urinary tract and bloodstream infections in humans. Here, we report the draft genomic sequences of three E. coli ST131 isolates, H45, H43ii, and H43iii, from urine samples of patients in Lagos, Nigeria.

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1054. Biofilm Formation Among Escherichia coli Bloodstream Infection Isolates Is Associated With Source of Bacteremia and Bacterial Sequence Type

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy210.891 ◽

2018 ◽

Vol 5 (suppl_1) ◽

pp. S315-S315

Author(s):

Carolyn Chang ◽

Felicia Ruffin ◽

Vance G Fowler ◽

Joshua T Thaden

Keyword(s):

Escherichia Coli ◽

Biofilm Formation ◽

Bloodstream Infections ◽

Multidrug Resistant ◽

Clinical Impact ◽

Sequence Type ◽

Apache Ii Score ◽

E Coli ◽

Biofilm Production ◽

Bacterial Sequence

Abstract Background The clinical impact of Escherichia coli biofilm formation is unknown. Methods Adults with E. coli bloodstream infections (BSI) were prospectively enrolled from 2002 to 2015. All E. coli isolates were genotyped using Multilocus sequence typing (MLST) and underwent crystal violet biofilm formation assay quantified by absorbance at 540 nm (OD540) in triplicate. Associations between biofilm formation and patient/bacterial characteristics were characterized by t-tests and ANOVA tests. Results Ninety-eight percent (186) of the 189 isolates formed detectable biofilms. Bacterial sequence type (ST) was associated with biofilm formation (P < 0.001), as ST73 (average OD540 = 0.017) and ST393 (average OD540 = 0.016) had higher average biofilm formation while ST69 (average OD540 = 0.007) and ST405 (average OD540 = 0.002) had lower biofilm formation. E. coli isolates with non-multidrug-resistant (non-MDR) phenotype were associated with increased biofilm formation (MDR: average OD540 = 0.006; average non-MDR: OD540 = 0.01; P = 0.003). BSI isolates arising from pneumonia or urine/pyelonephritis were associated with the highest biofilm production (P = 0.04). No associations were identified between biofilm formation and route of infection, APACHE-II score, mortality, or complications of BSI. Conclusion In this prospective study of E. coli BSI isolates, biofilm formation was associated with ST, non-MDR phenotype, and BSI source. Disclosures All authors: No reported disclosures.

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Molecular survey of mcr1 and mcr2 plasmid mediated colistin resistance genes in Escherichia coli isolates of animal origin in Iran

BMC Research Notes ◽

10.1186/s13104-021-05519-6 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Kayhan Ilbeigi ◽

Mahdi Askari Badouei ◽

Hossein Vaezi ◽

Hassan Zaheri ◽

Sina Aghasharif ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Genes ◽

Companion Animals ◽

Multidrug Resistant ◽

Animal Origin ◽

Colistin Resistance ◽

E Coli ◽

High Level ◽

Farming Industry

Abstract Objectives The emergence of colistin-resistant Enterobacteriaceae from human and animal sources is one of the major public health concerns as colistin is the last-resort antibiotic for treating infections caused by multidrug-resistant Gram-negative bacteria. We aimed to determine the prevalence of the prototype widespread colistin resistance genes (mcr-1 and mcr-2) among commensal and pathogenic Escherichia coli strains isolated from food-producing and companion animals in Iran. Results A total of 607 E. coli isolates which were previously collected from different animal sources between 2008 and 2016 used to uncover the possible presence of plasmid-mediated colistin resistance genes (mcr-1 and mcr-2) by PCR. Overall, our results could not confirm the presence of any mcr-1 or mcr-2 positive E. coli among the studied isolates. It is concluded that despite the important role of food-producing animals in transferring the antibiotic resistance, they were not the main source for carriage of mcr-1 and mcr-2 in Iran until 2016. This study suggests that the other mcr variants (mcr-3 to mcr-9) might be responsible for conferring colistin resistance in animal isolates in Iran. The possible linkage between pig farming industry and high level of mcr carriage in some countries needs to be clarified in future prospective studies.

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Bacterial genotypic and patient risk factors for adverse outcomes in Escherichia coli bloodstream infections: a prospective molecular-epidemiological study

10.1101/2021.06.18.21258557 ◽

2021 ◽

Author(s):

Elita Jauneikaite ◽

Kate Honeyford ◽

Oliver Blandy ◽

Mia Mosavie ◽

Max Pearson ◽

...

Keyword(s):

Escherichia Coli ◽

Length Of Stay ◽

Single Agent ◽

Bloodstream Infections ◽

Outcome Data ◽

Sequence Type ◽

Adverse Outcomes ◽

Beta Lactam ◽

E Coli ◽

Sequence Types

Background Escherichia coli bloodstream infections have increased rapidly in the UK, for reasons that are unclear. The relevance of highly fit, or multi-drug resistant lineages such as ST131 to overall E. coli disease burden remains to be fully determined. We set out to characterise the prevalence of E. coli multi-locus sequence types (MLST) and determine if these were associated with adverse outcomes in an urban population of E. coli bacteraemia patients. Methods We undertook whole genome sequencing of E. coli blood isolates from all patients with diagnosed E. coli bacteraemia in north-west London from July 2015 to August 2016 and assigned multi-locus sequence types to all isolates. Isolate sequence types were linked to routinely collected antimicrobial susceptibility, patient demographic, and clinical outcome data to explore relationships between the E. coli sequence types, patient factors, and outcomes. Findings A total of 551 E. coli genomes were available for analysis. More than half of these cases were caused by four E. coli sequence types: ST131 (21%), ST73 (15%), ST69 (9%) and ST95 (8%). E. coli genotype ST131-C2 was associated with non-susceptibility to quinolones and third-generation cephalosporins, and also to amoxicillin, augmentin, gentamicin and trimethoprim. An association between the ST131-C2 lineage and longer length-of-stay was detected, although multivariable regression modelling did not demonstrate an association between E. coli sequence type and mortality. However, a number of unexpected associations were identified, including gentamicin non-susceptibility, ethnicity, and sex that might influence mortality and length-of-stay, requiring further research. Interpretation Although E. coli sequence type was associated with antimicrobial non-susceptibility patterns and length-of-stay, we did not find that E. coli sequence type was associated with increased mortality. Where ST131 is prevalent, caution is required when pairing beta-lactam agents with gentamicin or using single agent aminoglycosides.

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Escherichia coli Sequence Type 131 (ST131) Subclone H30 as an Emergent Multidrug-Resistant Pathogen Among US Veterans

Clinical Infectious Diseases ◽

10.1093/cid/cit503 ◽

2013 ◽

Vol 57 (9) ◽

pp. 1256-1265 ◽

Cited By ~ 124

Author(s):

Aylin Colpan ◽

Brian Johnston ◽

Stephen Porter ◽

Connie Clabots ◽

Ruth Anway ◽

...

Keyword(s):

Escherichia Coli ◽

Multidrug Resistant ◽

Sequence Type ◽

Us Veterans

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Spread of NDM-5 and OXA-181 Carbapenemase-Producing Escherichia coli in Chad

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00646-19 ◽

2019 ◽

Vol 63 (11) ◽

Cited By ~ 2

Author(s):

Oumar Ouchar Mahamat ◽

Manon Lounnas ◽

Mallorie Hide ◽

Abelsalam Tidjani ◽

Julio Benavides ◽

...

Keyword(s):

Escherichia Coli ◽

Healthy Volunteers ◽

Resistance Genes ◽

Sequence Type ◽

Hospitalized Patients ◽

Content Type ◽

E Coli ◽

First Time

ABSTRACT We detected for the first time blaNDM-5 and blaOXA-181 in Escherichia coli isolates from hospitalized patients and healthy volunteers in Chad. These resistance genes were located on IncX3 and IncF plasmids. Despite the large diversity of E. coli clones, the identified resistant intestinal isolates belonged mainly to the same sequence type.

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Occurrence of blaKPC-2, blaCTX-M, and mcr-1 in Enterobacteriaceae from Well Water in Rural China

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02569-16 ◽

2017 ◽

Vol 61 (4) ◽

Cited By ~ 31

Author(s):

Pan Sun ◽

Zhenwang Bi ◽

Maud Nilsson ◽

Beiwen Zheng ◽

Björn Berglund ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Rural China ◽

Multidrug Resistant ◽

Sequence Type ◽

Well Water ◽

Content Type ◽

Potential Source ◽

Extended Spectrum

ABSTRACT We report on the coexistence of mcr-1 and bla CTX-M in multidrug-resistant, extended-spectrum β-lactamase-producing Escherichia coli belonging to the sequence type 10 complex isolated from well water in rural China. Raoultella ornithinolytica with bla KPC-2 was also detected in well water from the same area. This study shows that genes coding for resistance to last-resort antibiotics are present in wells in rural China, indicating a potential source of antibiotic resistance.

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Escherichia coli Sequence Type ST131 as an Emerging Fluoroquinolone-Resistant Uropathogen among Renal Transplant Recipients

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01089-09 ◽

2009 ◽

Vol 54 (1) ◽

pp. 546-550 ◽

Cited By ~ 52

Author(s):

James R. Johnson ◽

Brian Johnston ◽

Connie Clabots ◽

Michael A. Kuskowski ◽

Swaroop Pendyala ◽

...

Keyword(s):

Escherichia Coli ◽

Renal Transplant ◽

Multidrug Resistant ◽

Sequence Type ◽

Renal Transplant Recipients ◽

Transplant Recipients ◽

Black Race ◽

E Coli ◽

Extended Spectrum

ABSTRACT Among 40 Escherichia coli urine isolates from renal transplant recipients (Galveston, TX, 2003 to 2005), sequence type ST131 (O25:H4) was highly prevalent (representing 35% of isolates overall and 60% of fluoroquinolone-resistant isolates), virulent appearing, antimicrobial resistant (but extended-spectrum-cephalosporin susceptible), and associated with black race. Pulsotypes were diverse; some were linked to other locales. ST131 emerged significantly during the study period. These findings suggest that E. coli ST131 may constitute an important new multidrug-resistant threat to renal transplant recipients.

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The Behavioral Immune System Shapes Political Intuitions: Why and How Individual Differences in Disgust Sensitivity Underlie Opposition to Immigration

American Political Science Review ◽

10.1017/s0003055416000770 ◽

2017 ◽

Vol 111 (2) ◽

pp. 277-294 ◽

Cited By ~ 55

Author(s):

LENE AARØE ◽

MICHAEL BANG PETERSEN ◽

KEVIN ARCENEAUX

Keyword(s):

Immune System ◽

Emotional Processing ◽

Meta Analysis ◽

The United States ◽

Behavioral Immune System ◽

Psychological Mechanisms ◽

Nationally Representative ◽

First Time ◽

Representative Samples

We present, test, and extend a theoretical framework that connects disgust, a powerful basic human emotion, to political attitudes through psychological mechanisms designed to protect humans from disease. These mechanisms work outside of conscious awareness, and in modern environments, they can motivate individuals to avoid intergroup contact by opposing immigration. We report a meta-analysis of previous tests in the psychological sciences and conduct, for the first time, a series of tests in nationally representative samples collected in the United States and Denmark that integrate the role of disgust and the behavioral immune system into established models of emotional processing and political attitude formation. In doing so, we offer an explanation for why peaceful integration and interaction between ethnic majority and minorities is so hard to achieve.

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Evidence of Sharing ofKlebsiella pneumoniaeStrains between Healthy Companion Animals and Cohabiting Humans

Journal of Clinical Microbiology ◽

10.1128/jcm.01537-18 ◽

2019 ◽

Vol 57 (6) ◽

Cited By ~ 10

Author(s):

Cátia Marques ◽

Adriana Belas ◽

Catarina Aboim ◽

Patrícia Cavaco-Silva ◽

Graça Trigueiro ◽

...

Keyword(s):

Antimicrobial Susceptibility ◽

Close Contact ◽

Companion Animals ◽

Multidrug Resistant ◽

Sequence Type ◽

Content Type ◽

Healthy Humans ◽

Tract Infections ◽

Healthy Participants

ABSTRACTThis study aimed to characterize the fecal colonization and sharing ofKlebsiella pneumoniaestrains between companion animals and humans living in close contact. Fecal samples were collected from 50 healthy participants (24 humans, 18 dogs, and 8 cats) belonging to 18 households. Samples were plated onto MacConkey agar (MCK) plates with and without cefotaxime or meropenem supplementation. Up to fiveK. pneumoniaecolonies per participant were compared by pulsed-field gel electrophoresis (PFGE) after XbaI restriction.K. pneumoniaestrains with unique pulse types from each participant were characterized for antimicrobial susceptibility, virulence genes, and multilocus sequence type (MLST). FecalK. pneumoniaepulse types were compared to those of clinicalK. pneumoniaestrains from animal and human patients with urinary tract infections (n = 104).K. pneumoniaecolonization was detected in nonsupplemented MCK in around 38% of dogs (n = 7) and humans (n = 9).K. pneumoniaestrains isolated from dogs belonged to sequence type 17 (ST17), ST188, ST252, ST281, ST423, ST1093, ST1241, ST3398, and ST3399. None of theK. pneumoniaestrains were multidrug resistant or hypervirulent. Two households included multiple colonized participants. Notably, two colonized dogs within household 15 (H15) shared a strain each (ST252 and ST1241) with one coliving human. One dog from H16 shared one PFGE-undistinguishableK. pneumoniaeST17 strain with two humans from different households; however, the antimicrobial susceptibility phenotypes of these three strains differed. Two main virulence genotypes were detected, namelyfimH-1 mrkD ycfM entB kfuandfimH-1 mrkD ycfM entB kpn. These results highlight the potential role of dogs as a reservoir ofK. pneumoniaeto humans and vice versa. Furthermore, to our best knowledge, this is the first report of healthy humans and dogs sharingK. pneumoniaestrains that were undistinguishable by PFGE/MLST.

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