Antimicrobial Resistant Escherichia coli Clinical, Epidemiological and Molecular Characteristics in

306 Pages·2015·15.13 MB·English

Antimicrobial Resistant Escherichia coli
Clinical, Epidemiological and Molecular Characteristics in
the Australian Region
Dr. Benjamin Alexander Rogers
MBBS (Hons), FRACP
A thesis submitted for the degree of Doctor of Philosophy at
The University of Queensland in 2014
School of Medicine
A
BSTRACT

Background
Escherichia coli is the most common gram-negative bacteria to cause human infection. The pathological
manifestations range from minor disease to severe life threatening sepsis. Urinary tract infection, most often
caused by E. coli, is also the most common bacterial infection in humans. Since the inception of
antimicrobial therapy in the early 20th century, E. coli has systematically developed resistance to almost all
known antimicrobials, posing a challenge for the treatment of such infections.
From a global perspective, the first decade of the 21st century heralded a change in the epidemiology and
tempo of resistance amongst E. coli. Previously, resistance to third generation cephalosporins (3GC) was
primarily associated with current or previous healthcare exposure. In the past decade however, expanded-
spectrum cephalosporin resistant E. coli (ESC-R-EC), usually mediated by Extended Spectrum beta-
lactamase (ESBL) genes has spread widely within the communities of many regions, independent of
healthcare associated acquisition.
The latter half of this decade has led to the delineation of two further challenges amongst resistant E. coli.
The first is the identification of Sequence Type 131 E. coli (ST131), a global ‘pandemic’
 clone fine-tuned for
resistance and virulence. This clone is now implicated in a significant proportion of community ESBL E. coli
infections globally. The second challenge is the emergence of E. coli harbouring carbapenemase genes,
conferring resistance to carbapenem antimicrobials used to treat severe ESBL producing E. coli infection.
Methods
Through several studies we have aimed to better define global and local aspects of antimicrobial resistant E.
coli, in particular ESC-R-EC. The studies have included clinical and laboratory based research.
Clinical research included a multi-centre case-control study of community onset ESC-R-EC infection in
Australia and New Zealand, and a national survey of health services’
 infection control practices pertaining to
multi-resistant gram-negative bacilli and patients at risk of harbouring these.
Laboratory research included molecular epidemiological investigation of E. coli from two sources. The first
was isolates from the 182 participants in the case-control study, comprising a broad sample of community
onset 3GC resistant and susceptible E. coli from Australia and New Zealand. The second was a collection of
isolates from a previously conducted study on carriage of resistant E. coli in overseas travellers returning to
Australia.
Results 182 patients (91 cases and 91 controls) were recruited across six tertiary hospitals in Australia and
New Zealand for the case-control study. Multivariate logistic regression identified risk factors for 3GCR-EC

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including birth on the Indian subcontinent (OR=11.13, 2.17-56.98, p=0.003), urinary tract infection in the
past year (per infection OR=1.430, 1.13-1.82, p=0.003), travel to South East Asia, China, Indian
subcontinent, Africa and the Middle East (OR=3.089, 1.29-7.38, p=0.011), prior exposure to trimethoprim+/-
sulfamethoxazole &/or extended spectrum cephalosporins (OR=3.665, 1.30-10.35, p=0.014) and healthcare
exposure in the previous six months (OR=3.16, 1.54-6.46, p=0.02).
Molecular epidemiological analysis of isolates demonstrated a predominance of CTX-M type ESBL’s, as
now reported in most other regions of the world. From a global perspective, a unique distribution of ST131
E.coli was demonstrated, with a very low prevalence of ST131 amongst 3GC susceptible isolates compared
with resistant isolates (7% vs. 45%). Susceptible isolates showed diversity with six MLST defined clusters of
isolates. Amongst 3GCR isolates, ST131 dominated, comprising 40/89 isolates, with 88% (35/40) of ST131
being of the recently defined fimH 30 sub-clone variant. Whilst patients with ST131 were significantly more
likely to have an upper rather than lower urinary tract infection (relative risk 1.8, p=0.040), they were
otherwise relatively epidemiologically homogenous with other 3GCR-EC.
Analysis of isolates from returned travellers gave insight into the dynamics of carriage of antimicrobial
resistant E. coli in the bowel flora and supported a number of findings from the case control study. The risk
of prolonged carriage after travel was lower for 3GC-resistant than ciprofloxacin or gentamicin resistant
isolates and the duration of carriage was also longer for the latter resistance phenotypes (75th quartile 8 vs.
62 and 63 days respectively). In multivariate analysis, risks of prolonged carriage included antimicrobial use
whilst travelling (RR 3.3, 1.3–8.4) and phylogenetic group B2 (RR 9.3, 3.4–25.6) and D (RR 3.8, 1.6–8.8).
Clonality amongst longitudinal isolates from the same participant was demonstrated in 92% of participants
and most marked amongst 3GC resistant isolates. ST131 was surprisingly infrequent amongst participants
(3% of participants).
Conclusion
Within this thesis, study of a variety of aspects of antimicrobial resistant E. coli in Australia and New
Zealand has revealed unique insights into this pathogen locally and globally. These insights include the
delineation of risks within the community, temporality of risk and a unique molecular epidemiology.
Furthermore studies completed within this thesis highlight several key future directions of research including
clinical studies to investigate risk-factor modification and optimal therapy, economic impact analyses of
resistant E. coli infection, and further in-depth genetic studies.
III
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ECLARATION BY AUTHOR
This thesis is composed of my original work, and contains no material previously published
or written by another person except where due reference has been made in the text. I have clearly
stated the contribution by others to jointly-authored works that I have included in my thesis.
I have clearly stated the contribution of others to my thesis as a whole, including statistical
assistance, survey design, data analysis, significant technical procedures, professional editorial
advice, and any other original research work used or reported in my thesis. The content of my thesis
is the result of work I have carried out since the commencement of my research higher degree
candidature and does not include a substantial part of work that has been submitted to qualify for
the award of any other degree or diploma in any university or other tertiary institution. I have
clearly stated which parts of my thesis, if any, have been submitted to qualify for another award.
I acknowledge that an electronic copy of my thesis must be lodged with the University Library and,
subject to the General Award Rules of The University of Queensland, immediately made available
for research and study in accordance with the Copyright Act 1968.
I acknowledge that copyright of all material contained in my thesis resides with the copyright
holder(s) of that material. Where appropriate I have obtained copyright permission from the
copyright holder to reproduce material in this thesis.

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UBLICATIONS DURING CANDIDATURE
Peer-reviewed publications
Paterson DL, Rogers BA. How Soon is Now? The urgent need for randomized, controlled trials
evaluating multi-resistant bacterial infection. Clin Infect Dis. 2010 Dec 1;51(11):1245-7. Epub
2010 Oct 25.
Rogers BA, Sidjabat HE, Paterson DL. Escherichia coli O25b-ST131: a pandemic, multiresistant,
community-associated strain. J Antimicrob Chemother. 2011 Jan;66(1):1-14. PubMed PMID:
21081548. Epub 2010/11/18. Eng.
Rogers BA, Aminzadeh Z, Hayashi Y, Paterson DL. Country-to-country transfer of patients and the
risk of multi-resistant bacterial infection. Clin Infect Dis. 2011 Jul 1;53(1):49-56. PubMed PMID:
21653302. Epub 2011/06/10.
Avent ML, Rogers BA, Cheng AC, Paterson DL. Current use of aminoglycosides: indications,
pharmacokinetics and monitoring for toxicity. Intern Med J. 2011 Jun;41(6):441-9. PubMed PMID:
21309997. Epub 2011/02/12.
Totsika M, Moriel DG, Idris A, Rogers BA, Wurpel DJ, Phan MD, et al. Uropathogenic
Escherichia coli mediated urinary tract infection. Current drug targets. 2012 Oct;13(11):1386-99.
PubMed PMID: 22664092. Epub 2012/06/06.
Rogers BA, Kennedy KJ, Sidjabat HE, Jones M, Collignon P, Paterson DL. Prolonged carriage of
resistant E. coli by returned travellers: clonality, risk factors and bacterial characteristics. Eur J Clin
Microbiol Infect Dis. 2012 Sep;31(9):2413-20. PubMed PMID: 22391758. Epub 2012/03/07.
Rogers BA, Hayashi Y. An oral carbapenem, but only now intravenous penicillin: the paradox of
Japanese antimicrobials. International journal of infectious diseases : IJID : official publication of
the International Society for Infectious Diseases. 2012 Dec;16(12):e830-2. PubMed PMID:
23041363. Epub 2012/10/09.
Rogers BA, Sidjabat HE, Silvey A, Anderson TL, Perera S, Li J, et al. Treatment options for New
Delhi metallo-beta-lactamase-harboring enterobacteriaceae. Microb Drug Resist. 2013
Apr;19(2):100-3. PubMed PMID: 23330550. Epub 2013/01/22.
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Rogers BA, Doi Y. Who is leading this dance? Understanding the spread of Escherichia coli
sequence type 131. Infect Control Hosp Epidemiol. 2013 Apr;34(4):370-2. PubMed PMID:
23466909. Epub 2013/03/08.
Williamson DA, Barrett LK, Rogers BA, Freeman JT, Hadway P, Paterson DL. Infectious
complications following transrectal ultrasound-guided prostate biopsy: new challenges in the era of
multidrug-resistant Escherichia coli. Clin Infect Dis. 2013 Jul;57(2):267-74. PubMed PMID:
23532481. Epub 2013/03/28.
Williamson DA, Freeman JT, Roberts SA, Heffernan H, Dyet K, Paterson DL, Rogers BA et al.
Rectal colonization with New Delhi metallo-beta-lactamase-1-producing Escherichia coli prior to
transrectal ultrasound (TRUS)-guided prostate biopsy. J Antimicrob Chemother. 2013 Jul 3.
PubMed PMID: 23825384. Epub 2013/07/05.
Ingram PR, Rogers BA, Sidjabat HE, Gibson GS, Inglis TJJ. Co-selection may explain high rates
of ciprofloxacin non-susceptible Eschericia coli from retail poultry reared without prior
fluoroquinolone exposure, J Med Micro, 2013 62, 1743-1746.
Rogers BA, Ingram PR, Runnegar N, Pitman MC, Freeman JT, Athan E, Havers S, Sidjabat H,
Jones M, Gunning E, De Almeida M, Styles K, Paterson DL. Community onset Escherichia coli
infection resistant to expanded-spectrum cephalosporins in low-prevalence countries. Antimicrob
Agents Chemother, 2014, 58, 2126-2134
Petty NK, Ben Zakour NL, Stanton-Cook M, Skippington E, Totsika M, Forde BM, Phan MD,
Gomes Moriel D, Peters KM, Davies M, Rogers BA et al. Global dissemination of a multidrug
resistant Escherichia coli clone. Proc Natl Acad Sci. 2014;111, 5694-9. doi:
10.1073/pnas.1322678111.
Rogers BA, Havers SM, Brown TM, Paterson DL, Predictors of use of infection control
precautions for multi-resistant gram-negative bacilli in Australian hospitals: Analysis of a national
survey, Am Jour Infect Cont, 2014, 42, 963-9. doi: 10.1016/j.ajic.2014.05.035
Rogers BA, Ingram PR, Runnegar N, Pitman MC, Freeman JT, Athan E, Havers S, Sidjabat H,
Gunning E, De Almeida M, Styles K, Paterson DL. Sequence Type 131 fimH30 and fimH41 Sub-
clones Amongst Escherichia coli Isolates in Australia and New Zealand, In J Antimicrob Agents,
2015, 45; 351-8, doi: 10.1016/j.ijantimicag.2014.11.015
Conference Presentations
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Rogers BA, Silvey A, Sidjabat H, Perera S, Yam WC, Paterson D. Travelling With Friends: NDM-
1 and Other Resistance Genes. The Australasian Society for Infectious Diseases, Annual Scientific
Meeting 2011; Lorne, Vic, Australia: ASID; 2011. (Oral Presentation)
Sidjabat H, Silvey A, Yam WC, Rogers BA, Walsh TR, Vohra R, et al. C1-526 - Features of
Plasmids Carrying blaNDM-1 and blaNDM-3 in Australia. 51st Interscience Conference on
Antimicrobial Agents and Chemotherapy; Chicago, IL: American Society for Microbiology; 2011.
(Oral Presentation)
Rogers BA, Kennedy K, Sidjabat H, Collignon P, Paterson D. P-1587 - Prolonged Gastrointestinal
Carriage of Antimicrobial-Resistant Escherichia coli in International Travellers. 51st Interscience
Conference on Antimicrobial Agents and Chemotherapy; Chicago, IL, USA: American Society for
Microbiology; 2011. (Oral Presentation)
Rogers BA, Ingram PR, Runnegar N, Pitman MC, Freeman JT, Athan E, et al. Risk Factors for 3rd
Generation Cephalosporin Resistant Community Onset E. coli Infections from Six Centres in
Australia and New Zealand. Antimicrobials 2013, Australian Society for Antimcirobials Annual
Scientific Meeting; Sydney, NSW, Australia: ASA; 2013. (Oral Presentation)
Rogers BA, Ingram PR, Runnegar N, Freeman JT, Pitman MC, Athan E, et al. C2-689 - Risk
factors for 3rd Generation Cephalosporin Resistant Community Onset E. coli Infections from Seven
Centres in Low Prevalence Countries. 52nd Interscience Conference on Antimicrobial Agents and
Chemotherapy; San Francisco, CA, USA: American Society for Microbiology; 2012. (Poster
Presentations)
Rogers BA, Havers SM, Ingram PR, Runnegar N, Athan E, Korman TM, et al. Variation in
Infection Prevention Precautions for Patients Admittted to Hospital with Community Onset
Infection Due to 3rd Generation Cephalosporin Resistant E. coli. Australian College for Infection
Prevention and Control, National Conference; Sydney, NSW, Australia: ACIPC; 2012. (Poster
Presentations)
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UBLICATIONS INCLUDED IN THIS THESIS
(The contribution of individual authors is described under each publication)
Chapter 1.

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1) Rogers BA, Aminzadeh Z, Hayashi Y, Paterson DL. Country-to-country transfer of patients and
the risk of multi-resistant bacterial infection. Clin Infect Dis. 2011
• BAR – Design and concept 80%, interpretation of data 80%, drafting and writing
80%, editing and revision 70%. ZA – Writing 10%, YH – Writing 10%. DLP –
Design and concept 20%, interpretation of data 20%, editing and revision 30%.
Chapter 2.
1) Rogers BA, Sidjabat HE, Paterson DL. Escherichia coli O25b-ST131: a pandemic,
multiresistant, community-associated strain. J Antimicrob Chemother. 2011
• BAR – Design and concept 60%, interpretation of data 80%, drafting and writing
70%, editing and revision 70%. HES – Writing 20%. DLP – Design and concept
40%, interpretation of data 20%, drafting and writing 10%, editing and revision 30%.
Chapter 3.
1) Rogers BA, Ingram PR, Runnegar N, Pitman MC, Freeman JT, Athan E, et al. Community
onset Escherichia coli infection resistant to expanded-spectrum cephalosporins in low-
prevalence countries. Antimicrob Agents Chemother, 2014.
• BAR – Design and concept 90%, data collection 25%, data cleaning and entry 90%,
laboratory analysis 90%, interpretation of data 100%, statistical analysis 80%,
drafting and writing 100%, editing and revision 80%. DLP – Design and concept
10%, editing and revision 10%. MAJ - statistical analysis 20%. The remainder of the
authors in this study contributed to data collection editing and revision of the paper.
Chapter 4.
1) Rogers BA, Ingram PR, Runnegar N, Pitman MC, et al. Sequence Type 131 fimH30 and
fimH41 Sub-clones Amongst Escherichia coli Isolates in Australia and New Zealand, Int J
Antimicrob Agents, 2015.
• BAR – Design and concept 90%, data collection 25%, data cleaning and entry 90%,
laboratory analysis 70%, interpretation of data 100%, statistical analysis 100%,
drafting and writing 100%, editing and revision 80%. DLP – Design and concept
10%, editing and revision 10%. The remainder of the authors in this study
contributed to data collection editing and revision of the paper.

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Chapter 5.
1) Rogers BA, Kennedy KJ, Sidjabat HE, Jones M, Collignon P, Paterson DL. Prolonged carriage
of resistant E. coli by returned travellers: clonality, risk factors and bacterial characteristics. Eur
J Clin Microbiol Infect Dis. 2012
• BAR – Design and concept 80%, laboratory analysis 90%, interpretation of data
100%, statistical analysis 50%, drafting and writing 100%, editing and revision 70%.
KJK – design and concept 5%, editing and revision 5% Sidjabat HE – laboratory
analysis 10% MJ – statistical analysis 50%. PC design and concept 5%, editing and
revision 5%. DLP – Design and concept 10%, editing and revision 20%
Chapter 6.
1) Rogers BA, Havers SM, Brown TM, Paterson DL. Predictors of use of infection control
precautions for multi-resistant gram-negative bacilli in Australian hospitals: Analysis of a
national survey, Am J Infect Control, 2014
• BAR – Design and concept 80%, Survey construction 50% interpretation of data
100%, statistical analysis 90%, drafting and writing 90%, editing and revision 70%.
SMH – design and concept 10%, statistical analysis 10%, editing and revision 10%,
TMB – survey construction 50%. editing and revision 10%. DLP – Design and
concept 10%, editing and revision 10%
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C
ONTRIBUTIONS BY OTHERS TO THE THESIS
In addition to the contributions outlined above, Laurie Beechy assisted with data entry for the case
control study. Ms Tiffany Brown assisted with data collection for the case control study. Wan Keat
Yam and Dr Anna Sartor assisted with laboratory work, including genotypic and phenotypic
characterisation presented in chapters 3, 4 and 5. Diane Josey (English Language Business) and
Sarah Rogers assisted with proof reading of the final version of this thesis.

S
TATEMENT OF PARTS OF THE THESIS
SUBMITTED TO QUALIFY FOR THE AWARD OF

ANOTHER DEGREE
None.

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