A 21-Year Survey of Escherichia coli from Bloodstream Infections (BSI) in a Tertiary Hospital Reveals How Community-Hospital Dynamics of B2 Phylogroup Clones Influence Local BSI Rates

Sepsis is the third leading cause of mortality in Western countries and one of the Global Health Threats recognized by the WHO since 2017. Despite Escherichia coli constituting the most common cause of bloodstream infections (BSI), its epidemiology is not fully understood, in part due to the scarcity of local and longitudinal studies.

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Clinical Characteristics of Patients and Whole Genome Sequencing-Based Surveillance of Escherichia coli Community-Onset Bloodstream Infections at a Non-tertiary Hospital in CHINA

Frontiers in Microbiology ◽

10.3389/fmicb.2021.748471 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fenghong Chen ◽

Tao Lv ◽

Yupeng Xiao ◽

Aizhi Chen ◽

Yonghong Xiao ◽

...

Keyword(s):

Escherichia Coli ◽

Mortality Rate ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Antimicrobial Agents ◽

Bloodstream Infections ◽

Tertiary Hospital ◽

Living Environment ◽

Whole Genome ◽

Community Onset

Background:Escherichia coli is the most common pathogens in patients with community-onset blood stream infections (COBSI). Knowledge of the epidemiology of this disease is crucial to improve allocation of health resources, formulate isolation strategies that prevent transmission, and guide empirical antibiotic therapy.Methods: This retrospective observational study examined patients with E. coli COBSI (EC-COBSI) at a non-tertiary hospital in China. Whole-genome sequencing and analysis of the isolates was performed. The relationships of clinical variables with antimicrobial resistance and the genetic background of the isolates were examined.Results: There were 148 isolates in patients with EC-COBSI. All isolates were susceptible to ceftazidime/avibactam, carbapenems, and tigecycline; 35.1% were positive for extended spectrum β-lactamase (ESBL+); and blaCTX–M–14 was the most common ESBL gene. Patients with ESBL- isolates were more likely to receive appropriate empiric treatment than those with ESBL+ isolates (61.5% vs. 91.4%, p < 0.001), but these two groups had similar mortality rates. The overall 30-day mortality rate was 9.5%. Phylogenetic analysis showed that the isolates were diverse, and that the main sequence types (STs) were ST95, ST131, and ST69. Intra-abdominal infection was the primary source of disease, and isolates from these patients had lower frequencies of virulence genes.Conclusion: The mortality rate of patients with EC-COBSI was unrelated to ESBL status of the isolates. Most isolates had low resistance to most of the tested antimicrobial agents. The isolates were diverse, and multiple strains were related. Prevention and control of EC-COBSI should target prevention of patient colonization and the living environment.

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Extended-Spectrum-β-Lactamase- and Plasmid AmpC-Producing Escherichia coli Causing Community-Onset Bloodstream Infection: Association of Bacterial Clones and Virulence Genes with Septic Shock, Source of Infection, and Recurrence

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02351-19 ◽

2020 ◽

Vol 64 (8) ◽

Author(s):

Inga Fröding ◽

Badrul Hasan ◽

Isak Sylvin ◽

Maarten Coorens ◽

Pontus Nauclér ◽

...

Keyword(s):

Escherichia Coli ◽

Septic Shock ◽

Prostate Biopsy ◽

Virulence Genes ◽

Multivariable Analysis ◽

Bloodstream Infections ◽

Content Type ◽

E Coli ◽

Extended Spectrum ◽

Community Onset

ABSTRACT Invasive infections due to extended-spectrum-β-lactamase- and pAmpC-producing Escherichia coli (ESBL/pAmpC-EC) are an important cause of morbidity, often caused by the high-risk clone sequence type (ST131) and isolates classified as extraintestinal pathogenic E. coli (ExPEC). The relative influence of host immunocompetence versus microbiological virulence factors in the acquisition and outcome of bloodstream infections (BSI) is poorly understood. Herein, we used whole-genome sequencing on 278 blood culture isolates of ESBL/pAmpC-EC from 260 patients with community-onset BSI collected from 2012 to 2015 in Stockholm to study the association of virulence genes, sequence types, and antimicrobial resistance with severity of disease, infection source, ESBL/pAmpC-EC BSI low-risk patients, and patients with repeated episodes. ST131 subclade C2 comprised 29% of all patients. Factors associated with septic shock in multivariable analysis were patient host factors (hematologic cancer or transplantation and reduced daily living activity), presence of the E. coli virulence factor iss (increased serum survival), absence of phenotypic multidrug resistance, and absence of the genes pap and hsp. Adhesins, particularly pap, were associated with urinary tract infection (UTI) source, while isolates from post-prostate biopsy sepsis had a low overall number of virulence operons, including adhesins, and commonly belonged to ST131 clades A, B, and subclade C1, ST1193, and ST648. ST131 was associated with recurrent episodes. In conclusion, the most interesting finding is the association of iss with septic shock. Adhesins are important for UTI pathogenesis, while otherwise low-pathogenic isolates from the microbiota can cause post-prostate biopsy sepsis.

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The Establishment and Diversification of Epidemic-Associated Serogroup W Meningococcus in the African Meningitis Belt, 1994 to 2012

mSphere ◽

10.1128/msphere.00201-16 ◽

2016 ◽

Vol 1 (6) ◽

Cited By ~ 23

Author(s):

Adam C. Retchless ◽

Fang Hu ◽

Abdoul-Salam Ouédraogo ◽

Seydou Diarra ◽

Kristen Knipe ◽

...

Keyword(s):

Burkina Faso ◽

Meningococcal Disease ◽

Disease Surveillance ◽

Bloodstream Infections ◽

Rapid Identification ◽

Sub Saharan Africa ◽

Common Cause ◽

Content Type ◽

Meningitis Belt ◽

Sub Saharan

ABSTRACT Meningococcal disease (meningitis and bloodstream infections) threatens millions of people across the meningitis belt of sub-Saharan Africa. A vaccine introduced in 2010 protects against Africa’s then-most common cause of meningococcal disease, N. meningitidis serogroup A. However, other serogroups continue to cause epidemics in the region—including serogroup W. The rapid identification of strains that have been associated with prior outbreaks can improve the assessment of outbreak risk and enable timely preparation of public health responses, including vaccination. Phylogenetic analysis of newly sequenced serogroup W strains isolated from 1994 to 2012 identified two groups of strains linked to large epidemics in Burkina Faso, one being descended from a strain that caused an outbreak during the Hajj pilgrimage in 2000. We find that applying whole-genome sequencing to meningococcal disease surveillance collections improves the discrimination among strains, even within a single nation-wide epidemic, which can be used to better understand pathogen spread. Epidemics of invasive meningococcal disease (IMD) caused by meningococcal serogroup A have been eliminated from the sub-Saharan African so-called “meningitis belt” by the meningococcal A conjugate vaccine (MACV), and yet, other serogroups continue to cause epidemics. Neisseria meningitidis serogroup W remains a major cause of disease in the region, with most isolates belonging to clonal complex 11 (CC11). Here, the genetic variation within and between epidemic-associated strains was assessed by sequencing the genomes of 92 N. meningitidis serogroup W isolates collected between 1994 and 2012 from both sporadic and epidemic IMD cases, 85 being from selected meningitis belt countries. The sequenced isolates belonged to either CC175 (n = 9) or CC11 (n = 83). The CC11 N. meningitidis serogroup W isolates belonged to a single lineage comprising four major phylogenetic subclades. Separate CC11 N. meningitidis serogroup W subclades were associated with the 2002 and 2012 Burkina Faso epidemics. The subclade associated with the 2012 epidemic included isolates found in Burkina Faso and Mali during 2011 and 2012, which descended from a strain very similar to the Hajj (Islamic pilgrimage to Mecca)-related Saudi Arabian outbreak strain from 2000. The phylogeny of isolates from 2012 reflected their geographic origin within Burkina Faso, with isolates from the Malian border region being closely related to the isolates from Mali. Evidence of ongoing evolution, international transmission, and strain replacement stresses the importance of maintaining N. meningitidis surveillance in Africa following the MACV implementation. IMPORTANCE Meningococcal disease (meningitis and bloodstream infections) threatens millions of people across the meningitis belt of sub-Saharan Africa. A vaccine introduced in 2010 protects against Africa’s then-most common cause of meningococcal disease, N. meningitidis serogroup A. However, other serogroups continue to cause epidemics in the region—including serogroup W. The rapid identification of strains that have been associated with prior outbreaks can improve the assessment of outbreak risk and enable timely preparation of public health responses, including vaccination. Phylogenetic analysis of newly sequenced serogroup W strains isolated from 1994 to 2012 identified two groups of strains linked to large epidemics in Burkina Faso, one being descended from a strain that caused an outbreak during the Hajj pilgrimage in 2000. We find that applying whole-genome sequencing to meningococcal disease surveillance collections improves the discrimination among strains, even within a single nation-wide epidemic, which can be used to better understand pathogen spread.

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An ST131 clade and a Phylogroup A clade bearing a novel Escherichia coli O-antigen cluster predominate among bloodstream E. coli isolates from southwest Nigeria hospitals

10.1101/2021.11.07.21265989 ◽

2021 ◽

Author(s):

Ayorinde O. Afolayan ◽

Aaron O. Aboderin ◽

Anderson O. Oaikhena ◽

Erkison Ewomazino Odih ◽

Veronica O. Ogunleye ◽

...

Keyword(s):

Escherichia Coli ◽

High Risk ◽

Antimicrobial Resistance ◽

Bloodstream Infections ◽

Whole Genome ◽

Southwestern Nigeria ◽

Common Cause ◽

E Coli ◽

Factors Associated ◽

Southwest Nigeria

Escherichia coli bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasion and, in recent years, are increasingly multiply antimicrobial resistant. In Nigeria, E. coli is a common cause of bloodstream infections but the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified, susceptibility-tested and whole genome-sequenced 68 bloodstream E. coli isolates recovered between 2016 and 2018 at three sentinel sites in southwestern Nigeria. Resistance to antimicrobials commonly used in Nigeria was high, reaching 100 % (n = 67) for trimethoprim, 92.5 % (n = 62) for ampicillin, 79.1 % (n = 53) for ciprofloxacin, and 55.2 % (n = 37) for aminoglycosides. All the isolates were susceptible to carbapenems and colistin. The strain set included isolates from globally disseminated high-risk clones including those belonging to ST12 (n=2), ST131 (n=12), and ST648 (n = 4). Twenty-three (33.82%) of the isolates clustered within two clades. The first of these consisted of ST131 strains, comprised of O16:H5 and O25:H4 sub-lineages. The second was an ST10-ST167 complex clade comprised of strains carrying capsular genes that may have originated in Klebsiella. We additionally determined that four ST90 strains from one sentinel represented a retrospectively detected outbreak. Our data demonstrate that a broad repertoire of invasive E. coli isolates cause bloodstream infections in southwest Nigeria. In addition to pandemic lineages, particularly ST131, these include a previously undescribed lineage. Genomic surveillance is valuable for tracking these and other clones and for outbreak identification.

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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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Three cases of mcr-1-positive colistin-resistant Escherichia coli bloodstream infections in Italy, August 2016 to January 2017

Eurosurveillance ◽

10.2807/1560-7917.es.2017.22.16.30517 ◽

2017 ◽

Vol 22 (16) ◽

Cited By ~ 17

Author(s):

Marta Corbella ◽

Bianca Mariani ◽

Carolina Ferrari ◽

Francesco Comandatore ◽

Erika Scaltriti ◽

...

Keyword(s):

Escherichia Coli ◽

Multidrug Resistance ◽

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Genome Sequencing ◽

Bloodstream Infections ◽

Tertiary Hospital ◽

Whole Genome ◽

E Coli ◽

Sequence Types

We describe three cases of bloodstream infection caused by colistin-resistant Escherichia coli in patients in a tertiary hospital in Italy, between August 2016 and January 2017. Whole genome sequencing detected the mcr-1 gene in three isolated strains belonging to different sequence types (STs). This occurrence of three cases with mcr-1-positive E. coli belonging to different STs in six months suggests a widespread problem in settings where high multidrug resistance is endemic such as in Italy.

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Response of Extraintestinal Pathogenic Escherichia coli to Human Serum Reveals a Protective Role for Rcs-Regulated Exopolysaccharide Colanic Acid

Infection and Immunity ◽

10.1128/iai.00800-13 ◽

2013 ◽

Vol 82 (1) ◽

pp. 298-305 ◽

Cited By ~ 33

Author(s):

Helen Miajlovic ◽

Niamh M. Cooke ◽

Gary P. Moran ◽

Thomas R. F. Rogers ◽

Stephen G. Smith

Keyword(s):

Escherichia Coli ◽

Cell Wall ◽

Human Serum ◽

Transcriptional Response ◽

Bloodstream Infections ◽

Protective Role ◽

Content Type ◽

Colanic Acid ◽

Envelope Stress ◽

Strain Cft073

ABSTRACTExtraintestinalEscherichia coli(ExPEC) organisms are the leading cause of Gram-negative bacterial bloodstream infections. These bacteria adapt to survival in the bloodstream through expression of factors involved in scavenging of nutrients and resisting the killing activity of serum. In this study, the transcriptional response of a prototypic ExPEC strain (CFT073) to human serum was investigated. Resistance of CFT073 to the bactericidal properties of serum involved increased expression of envelope stress regulators, including CpxR, σE, and RcsB. Many of the upregulated genes induced by active serum were regulated by the Rcs two-component system. This system is triggered by envelope stress such as changes to cell wall integrity. RcsB-mediated serum resistance was conferred through induction of the exopolysaccharide colanic acid. Production of this exopolysaccharide may be protective while cell wall damage caused by serum components is repaired.

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In VitroAnalyses of Ethanol Activity against Candida albicans Biofilms

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00263-12 ◽

2012 ◽

Vol 56 (8) ◽

pp. 4487-4489 ◽

Cited By ~ 18

Author(s):

Hallie S. Rane ◽

Stella M. Bernardo ◽

Carla J. Walraven ◽

Samuel A. Lee

Keyword(s):

Candida Albicans ◽

Biofilm Formation ◽

Bloodstream Infections ◽

Optimal Dose ◽

Limited Data ◽

Common Cause ◽

Content Type ◽

Treatment And Prevention ◽

Lock Therapy ◽

Candida Albicans Biofilms

ABSTRACTCandida albicansis a common cause of catheter-related bloodstream infections (CR-BSI). Ethanol (EtOH) lock therapy has been attempted despite limited data on optimal dose and duration. Concentrations of 35% EtOH or higher for a minimum of 4 h demonstrated a >99% reduction in matureC. albicansbiofilm metabolic activity and prevented regrowth. Concentrations of 10% EtOH or higher reducedC. albicansbiofilm formation by >99%. Further investigation of EtOH lock therapy for treatment and prevention ofC. albicansCR-BSI is warranted.

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Acute Pyelonephritis with Bacteremia Caused byEnterococcus hirae: A Rare Infection in Humans

Case Reports in Infectious Diseases ◽

10.1155/2016/4698462 ◽

2016 ◽

Vol 2016 ◽

pp. 1-3 ◽

Cited By ~ 3

Author(s):

Ana Pãosinho ◽

Telma Azevedo ◽

João V. Alves ◽

Isabel A. Costa ◽

Gustavo Carvalho ◽

...

Keyword(s):

Escherichia Coli ◽

Clinical Practice ◽

Emergency Room ◽

Acute Pyelonephritis ◽

Enterococcus Hirae ◽

Common Cause ◽

The Third ◽

Enterococcal Species

Enterococci are one of the usual residents of the microflora in humans. In the last decade this genus has been reported as the third most common cause of bacteremia. We present the case of a 78-year-old female who was admitted to the emergency room because of nausea, lipothymia, and weakness. She was diagnosed with a pyelonephritis with bacteremia, with the isolation in blood and urine cultures ofEscherichia coliandEnterococcus hirae. This last microorganism is a rarely isolated pathogen in humans. Currently it is estimated to represent 1–3% of all enterococcal species isolated in clinical practice.

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Characterization of Multiple NDM-1-Producing Enterobacteriaceae Isolates from the Same Patient

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.04862-14 ◽

2015 ◽

Vol 59 (6) ◽

pp. 3648-3651 ◽

Cited By ~ 21

Author(s):

Nathalie Tijet ◽

David Richardson ◽

Gregory MacMullin ◽

Samir N. Patel ◽

Roberto G. Melano

Keyword(s):

Escherichia Coli ◽

Male Patient ◽

Community Hospital ◽

Enterobacter Cloacae ◽

Blood Cultures ◽

Content Type ◽

Carbapenem Resistant ◽

Plasmid Analysis ◽

Providencia Stuartii

ABSTRACTA male patient was admitted to a community hospital in Ontario, Canada, with an infected sacral ulcer after returning from India, where he was hospitalized. Carbapenem-resistantEscherichia coli(isolated from blood cultures),Enterobacter cloacae, andProvidencia stuartii(from urine samples), all positive forblaNDM-1, were recovered. Comparative NDM-1 plasmid analysis suggests both lateral plasmid transfer and independent acquisition of theblaNDM-1gene in these clinical isolates.

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