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Phylogenetic analysis of E. coli causing bacteraemia in the UK and Ireland in 2001 and 2010

Williams, MJ.*, Doumith, M.*, Hope, R.*, Wain, J.*, Underwood, A.*, Turton, J.*, Reynolds, R.

#

, Livermore, DM.* and

Woodford, N.*

*HPA Colindale, London, UK, # BSAC, Bristol, UK

Introduction

E.coli

is one of the commonest agents of bacteraemia, gastrointestinal and urinary tract infections (UTIs) in the UK.

•While

E. coli lineages causing UTIs and gastrointestinal disease are well known, less is known about those from bacteraemias.

•We compared the phylogeny of

E. coli from bacteraemias in the

UK and Ireland in 2001 vs. 2010

Methods

•409 E.coli

isolates from 18 centres across the UK and Ireland from the BSAC Bacteraemia Surveillance

Programme 1

•172 from 2001

•237 from 2010

•Assigned to phylogroups (A, B1, B2 or D) by PCR using a modified method 2 based on the Clermont 3 scheme

•Multi-locus sequence typing was used to analyse 152 isolates from 2001 and 116 isolates from 2010 using the Achtman scheme 4

•Resistance testing performed by agar dilution 5

•ESBL presence confirmed by PCR 5

Results

1.MLST

• A total of 83 STs were detected (see figure 1a) of which:

•47 were only present in 2001

•19 were only present in 2010

•17 were present in both years

• ST73 was the most common ST in both years (20% of isolates in

2001 and 22% in 2010); it is also as a major ST in UTIs 6

• 42% of isolates in 2001, 59% in 2010 belonged to ST73, ST95,

ST131, ST12 and ST127

•Prevalent STs were distributed across multiple centres in both years (figure 1b)

Figure 1. Minimum spanning trees showing ST distribution by; ST117

2.Phylotyping

• The phylogroup distributions of the 2001 and 2010 isolates were similar, and resembled those reported for UTI isolates 7 , with B2 dominant (77% in 2001; 71% in 2010) (figure 2)

• Second most common was phylogroup D (11% 2001 and 14%

2010), followed by group B1 (6% vs 8%) then A (4% vs 6%)

Figure 2. Percentage phylogroups by year

100%

Percentage

90%

80%

70%

60%

50%

40%

30%

20%

10%

0%

D

B2

B1

A

2001 2010

Year

3. Antimicrobial resistance and bacteraemia origins

• UTIs were the commonest source of bacteraemias (figure 4) including those due to the 5 major STs (except ST127 in 2010, where many bacteraemias had unknown sources)

• There was a significant increase of resistance to gentamicin, ciprofloxacin and cephalosporins in 2010 mainly due to diverse ST types and ST131

• Amoxicillin resistance remained unchanged in both years (56%)

• Numbers of isolates belonging to the international ST131 clone rose from 5/152 in 2001 (4 centres) to 16/116 in 2010 (10 centres)

• None of the ST131 isolates in 2001 was ciprofloxacin-resistant or

ESBL-positive, but 11 were ciprofloxacin-resistant in 2010 and 5

(from multiple centres) had ESBLs. (see table 1)

Figure 4. Sources of bacteraemia by year and ST

100%

Other

80%

Not Known

60%

ST69 Percentage

40%

Rsesipiratory tract

ST393 ST415

ST59

ST131

20%

0%

Gastrointestinal tract

Genitourinary tract

ST73 ST14

ST95

ST404

ST357

2001 2010 2001 2010 2001 2010 2001 2010 2001 2010 2001 2010

ST/Year

ST10

ST88

ST12

ST127

ST80

1a) year

•152 isolates from 2001 (white)

•116 isolates from 2010 (black)

Table 1. Prevalence of resistance

Antimicrobial

Amoxicillin

Gentamicin

Ciprfloxacin

Imipenem

Ceftazdime

% Resistance in 2001

All STs

56%

4%

6%

Major STs Other STs

22%

0%

1%

34%

4%

6%

0%

0%

0%

0%

0%

0%

% Resistance in 2010

All STs

56%

8%

16%

0%

7%

Major STs

30%

4%*

1%*

0%

1% #

Other STs

26%

4%

15%

0%

6%

Percentage of resistant isolates in 2001vs 2010 in all STs, major STs (ST73,

ST95, ST131, ST12 and ST127) and in other non-major STs.

*Resistance in ST131 only #Resistance in ST131 and 1 isolate of ST12

ST95

ST12

ST73

ST127

ST131

1b) centre

•268 isolates coloured by centre

Conclusions

• Phylogroups B2 and D dominated in both years; these harbour virulence factors associated with extra-intestinal E. coli 8

• With the exception of ST131, the major STs in both years remained susceptible to most antimicrobials

• The major STs have been reported to be associated with UTIs 9

• There was a significant increase in cases of bacteraemia caused by the international ST131 clone, with more members of this clone found resistant in 2010 than 2001.

• Resistance to cephalosporins, aminoglycosides and quinolones rose from 2001 to 2010 largely due to diverse STs and ST131

• Carbapenem resistance was not seen

References

1 www.bsacsurv.org

2 Doumith M., Williams M.J. and Woodford N. unpublished

,

3 Clermont O, Bonacorsi S, Bingen E. Appl Environ Microbiol. 2000 Oct;66(10):4555-8.

4 http://mlst.ucc.ie/mlst/dbs/Ecoli 5 http://www.bsacsurv.org/uploads/protocols/publications/bacteraemia_v3.3_110207.pdf

6 Lau et al . J Clin Microbiol. 2008 March; 46(3): 1076

–1080 7 Jakobsen et al . Foodborne Pathog Dis.

2010 May;7(5):537-47 8 Picard et al . Infect Immun.

1999 Feb;67(2):546-53. 9 Croxall et al . J Antimicrob Chemother.

2011 Nov;66(11):2501-8

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