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 Programme1

•172 from 2001•237 from 2010

•Assigned to phylogroups (A, B1, B2 or D) by PCR using a modified method 2 based on the Clermont3 scheme•Multi-locus sequence typing was used to analyse 152 isolates from 2001 and 116 isolates from 2010 using the Achtman scheme4

•Resistance testing performed by agar dilution 5

•ESBL presence confirmed by PCR5

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 UTIs9

• 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

References1 www.bsacsurv.org 2Doumith M., Williams M.J. and Woodford N. unpublished, 3Clermont O, Bonacorsi S, Bingen E. Appl Environ Microbiol. 2000 Oct;66(10):4555-8. 4http://mlst.ucc.ie/mlst/dbs/Ecoli 5 http://www.bsacsurv.org/uploads/protocols/publications/bacteraemia_v3.3_110207.pdf 6Lau et al. J Clin Microbiol. 2008 March; 46(3): 1076–1080 7Jakobsen et al. Foodborne Pathog Dis. 2010 May;7(5):537-47 8Picard et al. Infect Immun. 1999 Feb;67(2):546-53. 9Croxall et al. J Antimicrob Chemother. 2011 Nov;66(11):2501-8

Figure 2. Percentage phylogroups by year

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 UTIs6 • 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 4. Sources of bacteraemia by year and ST

Year

2.Phylotyping• The phylogroup distributions of the 2001 and 2010 isolates were similar, and resembled those reported for UTI isolates7, 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%)

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

2001 2010

DB2B1A

ST/Year

Percentage

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 1. Minimum spanning trees showing ST distribution by;

1a) year

•152 isolates from 2001 (white)

•116 isolates from 2010 (black)

1b) centre

•268 isolates coloured by centre

ST69

ST127

ST393

ST73 ST131

ST12

ST95

ST117

ST415

ST59

ST357

ST80

ST14

ST404

ST10

ST88

ST73

ST127

ST131

ST12

ST95

Table 1. Prevalence of resistance

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

Percentage

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100%

All

ST

s

All

ST

s

ST

73

ST

73

ST

95

ST

95

ST

13

1

ST

13

1

ST

12

ST

12

ST

12

7

ST

12

7

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

Other

Not Known

Rsesipiratory tract

GastrointestinaltractGenitourinary tract

All STs Major STs Other STs All STs Major STs Other STsAmoxicillin 56% 22% 34% 56% 30% 26%Gentamicin 4% 0% 4% 8% 4%* 4%Ciprfloxacin 6% 1% 6% 16% 1%* 15%Imipenem 0% 0% 0% 0% 0% 0%Ceftazdime 0% 0% 0% 7% 1%# 6%

Antimicrobial% Resistance in 2001 % Resistance in 2010