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The faecal flora: a source of healthcare-associated infections and antibiotic resistance
Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Center for Health and Developmental Care, Department of Infection Control.
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Healthcare-associated infections (HAI) are important causes of mortality and morbidity, and antibiotic treatment is often necessary. Development and availability of new antibiotics are closely followed by development of resistance among microorganisms. During antibiotic therapy, a fraction of the antibiotic given is found in the gut. The human gut is an important reservoir of bacteria. Microorganisms residing or passing the gut is referred to as the gut flora or microbiota. The results of this thesis showed spread of Enterococcus spp between patients on a general intensive care unit, causing septicaemia. After improved hygiene, reorganisation of rooms and thorough cleaning of the unit, together with revision of antibiotic strategy, the incidence of septicaemia with Enterococcus spp fell. Investigation of patients treated for acute intra-abdominal infections showed a shift in the aerobic faecal flora from antibiotic-susceptible Enterobacteriaceae spp towards Enterococcus faecium, yeasts and species of Enterobacteriaceae more resistant to antibiotics, after antibiotic treatment and hospital care. Investigation of recurrent outbreaks of Serratia marcescens sepsis in patients admitted to a neonatal intensive care unit showed different clones with each outbreak. Multiple hygiene interventions and revision of antibiotic strategy subsequently obviated recurrent outbreaks of sepsis, but spread of S. marcescens was not reduced until compliance with basic hygiene guidelines remained stable above 80%. We also found that low gestational age at birth, ventilator treatment and central venous or umbilical catheters are independent risk factors for late onset sepsis. Investigation of the faecal microbiota in patients with acute appendicitis or diverticulitis revealed that disturbance of the faecal microbiota already existed on admission, with higher numbers of Enterobacteriaceae and less Bacteroides, Faecalibacterium, Ruminococcus and Prevotella prior to antibiotic treatment and hospitalisation, than the control population. After treatment and hospitalisation diversity increased significantly in the diverticulitis group, approaching the healthy controls in composition.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2013. , 82 p.
Series
Linköping University Medical Dissertations, ISSN 0345-0082 ; 1368
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:liu:diva-97709DOI: 10.3384/diss.diva-97709ISBN: 978-91-7519-591-9 (print)OAI: oai:DiVA.org:liu-97709DiVA: diva2:650229
Public defence
2013-10-11, Berzeliussalen, Campus US, Linköpings Universitet, Linköping, 13:00 (Swedish)
Opponent
Supervisors
Available from: 2013-09-20 Created: 2013-09-20 Last updated: 2013-12-03Bibliographically approved
List of papers
1. Clustering of enterococcal infections in a general intensive care unit
Open this publication in new window or tab >>Clustering of enterococcal infections in a general intensive care unit
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2003 (English)In: Journal of Hospital Infection, ISSN 0195-6701, E-ISSN 1532-2939, Vol. 54, no 3, 188-195 p.Article in journal (Refereed) Published
Abstract [en]

This is a retrospective study comparing patients' characteristics, antibiotic consumption and environmental contamination before the impact of a new regimen of intensified infection control measures in a general intensive care unit (ICU) at a university-affiliated tertiary-care teaching hospital. The new regimen consisted of (1) reorganization of patient rooms (2) improved hygienic measures including strict hygiene barrier nursing (3) more isolated patient care and (4) more restrictive use of antibiotics. The regimen was introduced after a cluster of enterococcal infections. All patients admitted to the ICU from 1 March 1995 to 28 february 1997 were included. A study period of 12 months after reorganization of the ward was compared with the 12 months immediately before it. The antibiotic consumption, the individual patient's severity of disease (APACHE score), and the extent of therapeutic interventions (TISS score) were recorded. Enterococci were typed biochemically, antibiograms were established and the relation between the isolates was investigated with pulsed-field gel electrophoresis. The bacteriological results and the patient data suggested a hospital-acquired spread as the cause of the ICU enterococcal outbreak. After implementation of the new regimen, we observed a reduction in the rate of enterococcal bloodstream infections from 3.1 to 1.8%. The consumption of antibiotics fell from 6.11 to 4.24 defined daily doses per patient.The introduction of strict hygiene and barrier nursing, more restrictive use of antibiotics, isolation of infected patients, thorough cleaning and disinfection of the unit was followed by an absence of enterococcal infection clustering and reduction in incidence of enterococcal bacteraemia. We were not able to determine whether the reduction in antibiotic consumption was due to the intervention programme. ⌐ 2003 The Hospital Infection Society. Published by Elsevier Science Ltd. All rights reserved.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:liu:diva-26498 (URN)10.1016/S0195-6701(03)00122-1 (DOI)11054 (Local ID)11054 (Archive number)11054 (OAI)
Available from: 2009-10-08 Created: 2009-10-08 Last updated: 2017-12-13
2. Changes in the aerobic faecal flora of patients treated with antibiotics for acute intra-abdominal infection
Open this publication in new window or tab >>Changes in the aerobic faecal flora of patients treated with antibiotics for acute intra-abdominal infection
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2012 (English)In: Scandinavian Journal of Infectious Diseases, ISSN 0036-5548, E-ISSN 1651-1980, Vol. 44, no 11, 820-827 p.Article in journal (Refereed) Published
Abstract [en]

Background: An open observational study was performed to investigate changes in the rectal flora and antibiotic susceptibility among faecal bacteria in patients treated with antibiotics for acute intra-abdominal infection. Methods: One hundred and forty patients with acute intra-abdominal infection requiring antibiotic treatment and hospitalization were included. Eight surgical units from the southern part of Sweden participated, between January 2006 and November 2007. Antibiotic treatments were according to local guidelines. Rectal swabs were obtained on admission (sample 1) and 2-14 days after the end of antibiotic treatment (sample 2). Aerobic bacteria and yeasts were analysed. The material was divided into 2 groups: 1 group with Enterobacteriaceae and 1 group with non-fermentative Gram-negative bacteria. The susceptibility to antibiotics in each group was compared between samples 1 and 2. Results: The main finding of this study on patients with severe intra-abdominal infections was a shift in the aerobic faecal flora following antibiotic treatment, from Escherichia coli to other more resistant Enterobacteriaceae, Enterococcus faecium, and yeasts. The susceptibility to cephalosporins and piperacillin-tazobactam decreased in Enterobacteriaceae. Conclusions: Following antibiotic treatment, a shift in the aerobic rectal flora to species with intrinsic antibiotic resistance was observed. This indicates that the emergence of resistance is not due to new mutations, but rather to selection of more resistant species. This should be taken into account when designing treatments for secondary intra-abdominal infections.

Place, publisher, year, edition, pages
Informa Healthcare, 2012
Keyword
Antibiotic resistance; faecal flora; intra-abdominal infection
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:liu:diva-86555 (URN)10.3109/00365548.2012.695455 (DOI)000310008900003 ()
Available from: 2012-12-19 Created: 2012-12-19 Last updated: 2017-12-06
3. Late onset neonatal sepsis, risk factors and interventions: an analysis of recurrent outbreaks of Serratia marcescens 2006-2011
Open this publication in new window or tab >>Late onset neonatal sepsis, risk factors and interventions: an analysis of recurrent outbreaks of Serratia marcescens 2006-2011
2014 (English)In: Journal of Hospital Infection, ISSN 0195-6701, E-ISSN 1532-2939, Vol. 86, no 1, 57-63 p.Article in journal (Refereed) Published
Abstract [en]

Background: during the period 2006 to 2011 we observed 11 patients with Serratia marcescens sepsis, a total of 47 patients were colonised due to spread of different clones. These recurrent clusters brought about interventions to reduce spread between patients.

Aim: to evaluate the effect of stepwise introduced interventions to prevent S marcescens colonisation/sepsis and to analyse risk factors for late onset sepsis (LOS).

Methods: to evaluate the interventions an open retrospective observational study was performed. A retrospective case-control study was performed to analyse risk factors for LOS.

Findings: main findings of this study were the decrease in S marcescens sepsis and colonisation after the stepwise adoption of hygiene interventions, as well as identifying low gestational age, low birth weight, indwelling central venous or umbilical catheter and ventilator treatment as risk factors for LOS. Compliance to basic hygiene guidelines was the only intervention continuously monitored from late 2007. Compliance increased gradually to a steady high level early 2009. There was a decrease in LOS with S marcescens (LOS-Ser) clustering after the second quarter of 2008. After the first quarter of 2009 we saw a decrease in S marcescens colonisation.

Conclusion: We were not able to isolate specific effects of each intervention, but an update of our antibiotic policy probably had effect on the occurrence of LOS-ser. The delayed effect of interventions on S marcescens colonisation was probably due to the time it takes for new routines to have impact, illustrated by the gradual increase in compliance to basic hygiene guidelines.

Place, publisher, year, edition, pages
Elsevier, 2014
Keyword
Serratia marcescens, outbreak, neonatal, late onset sepsis
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:liu:diva-97707 (URN)10.1016/j.jhin.2013.09.017 (DOI)000328481500009 ()
Available from: 2013-09-20 Created: 2013-09-20 Last updated: 2017-12-06Bibliographically approved
4. Disturbed intestinal microbiota (dysbiosis) and micro dynamics in patients treated for appendicitis and diverticulitis
Open this publication in new window or tab >>Disturbed intestinal microbiota (dysbiosis) and micro dynamics in patients treated for appendicitis and diverticulitis
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Introduction: The human gut microbiota is a large dynamic bacterial community, which is influenced by for instance antibiotic treatment and hospitalization. In patients with inflammatory bowel disease the diversity of gut microbiota is thought to be less diverse. The role of the gut microbiota in acute appendicitis and diverticulitis is still unclear. To investigate the microbial diversity in patients suffering from appendicitis or diverticulitis, and the microbiota dynamics after antibiotic therapy and hospitalization we performed an open observation study.

Methods and population: We have performed 16S rRNA sequence analysis on 42 individuals diagnosed with appendicitis and 18 individuals with diverticulitis as well as 33 healthy controls. Cultivation of the aerobic bacterial flora was performed as a complement to sequence analysis.

Results: In sequencing data at genus level, there are distinctive differences when comparing healthy controls to patients diagnosed with appendicitis. Healthy controls have a flora dominated by Bacteroides, and Faecalibacterium, Ruminococcus and Prevotella while appendicitis patients show an intestinal flora with a higher abundance of Escherichia/Shigella and unclassified Enterobacteriaceae. The same pattern, however not quite as distinct could be seen for the diverticulitis patients. The microbial diversity increases after treatment with antibiotics and hospitalization.

In the cultivated aerobic flora there was a significant loss of Escherichia coli and a significant gain of Citrobacter species, in the appendicitis group. In the appendicitis group as well as in the diverticulitis group there was a significant gain of Enterococcus faecium and Yeasts.

Conclusion: The main findings of this study are that patients arriving at the emergency department with acute appendicitis or diverticulitis have an already significant disturbed fecal microbiota previous to antibiotic treatment and hospitalization.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:liu:diva-97708 (URN)
Available from: 2013-09-20 Created: 2013-09-20 Last updated: 2013-09-20Bibliographically approved

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