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Figure 1. Minimum spanning trees showing ST distribution by;. ST117. ST69. ST393. ST415. ST59. ST131. ST73. ST14. ST95. ST357. ST404. 1a) year 152 isolates from 2001 (white) 116 isolates from 2010 (black). ST12. ST80. ST127. ST10. ST88. ST131. - PowerPoint PPT Presentation
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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 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References1 www.bsacsurv.org 2Doumith M., Williams M.J. and Woodford N. unpublished, 3Clermont O, Bonacorsi S, Bingen E. Appl Environ Microbiol. 2000 Oct;66(10):4555-8. 4http://mlst.ucc.ie/mlst/dbs/Ecoli 5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
0%
20%
40%
60%
80%
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