Old bugs - new tricksMicrobiology of UTIs

in 2010

Dr Tim Collyns

Consultant Microbiologist

Leeds Teaching Hospitals NHS Trust

Microbiological aetiology of UTIs

“Collateral” damage associated with antibiotics

Available therapeutic options in an era of

increasing resistance

Urinary tract infections (UTI):

“Simple” vs “complicated”

Lower vs upper

Community acquired vs hospital acquired

Healthcare associated.

Initial episode vs recurrent

Species distribution not changed

(antimicrobial resistance pattern increasing)

Symptomatic UTI vs asymptomatic bacteriuria

Urinary catheters WILL become colonised

Uncomplicated UTIs (cystitis)

ARESC Study:

Antimicrobial Resistance Epidemiological

Survey on Cystitis.

Female patients, 18 – 64

Nine European countries and Brazil,

2003 – 2006.

> 4200 enrolled.

Schito 2009.

Organism %

Escherichia coli 76.7

Klebsiella pneumoniae 3.5

Proteus mirabilis 3.4

Staphylococcus saprophyticus 3.6

Other uropathogens 7.6

Enterobacteriaceae

(Enterobacter, Citrobacter, Serratia, Klebsiella, Pantoea, Salmonella spp, M morganii)

Other Gram negatives (incl. Pseudomonas aeruginosa 0.2%)

Enterococci

Others 5.1

S aureus, coagulase negative staphylococci, streptococci

Pathogen distribution by country (W Europe)

after Schito 2009

Country Total (%) E coli K pneu P mira S sapr Uropath Others

France 488 (16.2) 409

(83.8)

5 (1.0) 15 (3.1) 21 (4.3) 21 (4.3) 17 (3.5)

N/lands 36 (1.2) 29

(80.6)

1 (2.8) 0 (0) 2 (5.6) 2 (5.6) 2 (5.6)

Spain 650 (21.5) 515

(79.2)

15 (2.3) 28 (4.3) 29 (4.5) 38 (5.9) 25 (3.8)

Germany 317 (10.5) 243

(76.7)

8 (2.5) 15 (4.7) 9 (2.8) 19 (6.0) 23 (7.3)

Italy 329 (10.9) 239

(72.6)

18 (5.5) 10 (3.0) 0 (0) 44 (13.4) 18 (5.5)

Austria 91 (3.0) 62

(68.1)

5 (5.5) 3 (3.3) 2 (2.2) 12 (13.2) 7 (7.7)

Western

Europe

1911 1497

(78.3)

52

(2.7)

71

(3.7)

63

(3.3)

136

(7.1)

92

(4.8)

E coli.....Know thine enemy

E coli

E coli, Blood Agar plate

E coli, MacConkey plate (Lactose fermenter)

E coli

Certain serogroups predominate

O1, O2, O4, O6, O7, O8, O75, O150, O18ab

Uropathogenic E coli clones

Certain serotypes more virulent

Cystitis or pyelonephritis

Adhesins – epithelial cell receptors

P fimbriae: globoseries glycosphingolipids

type I fimbriae

S/FIC fimbriae

G, M fimbriae

Sobel, Kaye 2010

Recurrent / structural abnormalities

Hospital / longterm healthcare facilties:

Increased proportion due to

Proteus, Pseudomonas, Klebsiella, Enterobacter

Enterococci, staphylococci (non S saprophyticus)

Historically – greater antibiotic resistance

Intrinsic (enterococci, staphylococci, Pseudomonas)

Cross-infections with resistant isolates

(catheter associated)

Treatment

Usually only if symptomatic

(Nonspecific therapy – hydration)

Antimicrobials:

Serum / tissue / urine concentration of agent

Site of infection

Lower (cystitis) – upper (pyelonephritis) - bacteraemia

(Renal insufficiency – urine concentration)

Organism in vitro susceptibility

Available classes (for Gram negative bacteria)

β-lactams:

Penicillins (e.g. ampicillin, amoxicillin, piperacillin;

+/- β-lactamase inhibitor)

Cephalosporins (oral / intravenous)

Monobactam - aztreonam

Carbapenems (intravenous, currently)

Quinolones

Aminoglycosides (intravenous / intramuscular)

Trimethoprim / co-trimoxazole

Nitrofurantoin

Tetracyclines

Susceptibilities of E coli isolates

Schito 2009

Antimicrobial % Sensitive (No.) Intermediate Resistant

Ampicillin 45.1 (1045) 6.6 (153) 48.3 (1117)

Co-amoxiclav 82.5 (1910) 13.7 (316) 3.8 (89)

Mecillinam 95.8 (2215) 1.5 (34) 2.8 (6.4)

Cefuroxime 82.4 (1907) 15.2 (353) 2.4 (55)

Ciprofloxacin 91.7 (2120) 0.2 (5) 8.1 (187)

Co-trimoxazole 70.6 (1633) 3.1 (72) 1.6 (38)

Nitrofurantoin 98.1 (2272) 1.3 (30) 0.6 (13)

Susceptibilities of E coli isolates

Schito 2009

Country AMP CO-A MEC CXM CIP COT NIT

Austria 43.5 93.5 100 77.4 98.4 71.0 100

France 60.9 90.9 97.1 89.3 98.4 87.8 97.3

Germany 59.2 88.6 97.6 93.0 96.3 74.1 92.5

Italy 43.1 71.5 94.1 77.7 87.5 71.2 97.5

Spain 35.3 80.9 94.1 78.6 89.3 66.2 94.1

N/lands 65.5 82.8 96.6 89.7 96.6 79.3 100

Brazil 37.7 79.8 94.8 74.5 89.2 54.5 94.3

E coli bacteraemias, 2008,

United Kingdom

Health Protection Agency

Agent Susceptible

%

Intermediate Resistant 95% CI

Non-sus

95% CI

Amoxicillin 30.9 0 69.1 64.4 73.4

Co-amoxiclav 66.0 0 34.0 29.5 38.7

Ciprofloxacin 81.7 0.5 17.8 14.8 22.3

Cefotaxime 89.9 0.5 9.6 7.5 13.4

Gentamicin 91.8 1.9 6.3 5.9 11.3

Meropenem 100 0 0 0 1.1

Piperacillin-

Tazobactam

89.2 6.3 4.4 8.1 14.2

Figure 3 Antibiotic susceptibility for E. coli bacteraemia reports, England, Wales and Northern Ireland, 2002-

2006*

Table 2. Antibiotic susceptibility data for reports of E. coli bacteraemia, England, Wales and Northern

Ireland: 20052009*

E. coli 2005 2006 2007 2008 2009

Total reports:

18,593 19,987 22,128 23,971 25,532

% Nonsusceptible

Cefotaxime

9% 11% 12% 11% 10%

Ceftazidime

% Nonsusceptible

9% 12% 12% 11% 10%

Ciprofloxacin

% Nonsusceptible

19% 23% 23% 21% 20%

Gentamicin

% Nonsusceptible

8% 9% 9% 8% 8%

Imipenem

% Nonsusceptible

0% 0% 0% 0% 0%

Meropenem

% Nonsusceptible

0% 0% 0% 0% 0%

β-lactam resistance in Enterobacteriaceae:

Enzyme mediated: β-lactamases

(Ancient heritage: > 2 billion years old)

Serine residue active site; or metalloenzymes (Zinc ion)

Inherent – gene carried on bacterial chromosome

“De-repressed”: e.g. Enterobacter, Citrobacter species

Acquired – transmissible genetic elements: plasmids

E.g. Klebsiella pneumoniae, E coli

Vary in ability to hydrolyse different β-lactams:

Some drug structures more resilient than others.

Some blocked by β-lactamase inhibitors

clavulanic acid (co-amoxiclav), tazobactam (with piperacillin)

Various classifications / name derivations

3 letter monikers for families:

SHV (>50): Variable response to sulfhydryl

inhibitors

TEM (>130): After patient (Temoneira)

CTX-M (>40), OXA, IMP:

Ability to hydrolyse cefotaxime, oxacillin, imipenem

VIM: Verona integron encoded metallo-β-lactamase

KPC: Klebsiella pneumoniae carbapenemase

NDM: New Delhi metallo-β-lactamase

Jacoby 2005;

NDM-1:

First detected United Kingdom January 2008.

Now predominant carbapenem-hydrolysing enzyme

in Enterobacteriaceae in UK (44% 2009)

2008 – 2009: 37 isolates

K pneumoniae (21), E coli (7), Enterobacter spp (5), Citrobacter

freundii (2), Morganella (1), Providencia (1)

29 patients – 15 in urine

ESBLs widespread in India,

NDM-1 also in isolates in north & south India

Links between many of the UK patients and India

Kumaraswamy 2010; HPA

37 isolates; % susceptible

Imipenem 0

Meropenem 3

Piperacillin-tazobactam 0

Cefotaxime 0

Aztreonam 11

Ciprofloxacin 8

Gentamicin 3

Amikacin 0

Minocycline 0

Tigecycline 64

Colistin 89 (Morganella, Providencia: Intrinsic R)

Antibiotics – downsides include

Allergic reactions – “penicillin”

Intolerance / GI side-effects.

Other adverse effects:

Aminoglycosides: nephrotoxicity, ototoxicity

Administration – e.g. if intravenous only.

Cost

“Collateral damage”

Secondary infections

Meticillin resistant S aureus, C difficile, GREs, Candida

“Induction” of resistance

Individual infecting organism

Circulating bacterial flora

MRSA

Fluoroquinolones (e.g. Ciprofloxacin).

MRSA usually resistant to fluoroquinolones

Good skin tissue penetration / excreted in human

sweat:

Loss of colonisation resistance by normal skin flora

In vitro:

Induction of fibronectin – binding proteins

Increased adhesion by quinolone resistant S aureus

Bisognano 2000, Paterson 2004,

Univariate analysis, antimicrobials pre MRSA / MSSA

infection

Graffunder 2002

Preceding

Antimicrobial

MRSA (%) MSSA (%) OR (95% CI) P value

β-l / β-LI 37.2 16.3 2.3 (1.4, 3.6) <0.001

Levofloxacin 41.3 5.7 7.3 (3.4, 15.4) <0.001

Aminoglycoside 19 2.4 7.8 (2.4, 25.3) <0.001

1st gen ceph 40.5 33.3 1.2 (0.87,1.7) 0.29

3rd gen ceph 6.6 3.3 2.0 (0.63,6.6) 0.25

Carbapenems 5.8 0.8 7.1 (0.89,5.7) 0.04

Co-trimoxazole 10.7 2.4 4.4 (1.3, 15.1) 0.01

Multiple logistic regression analysis, factors associated with

MRSA infection

Graffunder 2002

Risk factor OR 95% CIs P value

Levofloxacin 8.01 3.15, 20.3 <0.001

Macrolides 4.06 1.15, 14.4 0.03

Enteral feeding 2.55 1.37, 4.72 0.003

Surgery 2.24 1.19, 4.22 0.01

Previous

hospitalisation

1.95 1.02, 3.76 0.04

LOS before culture 1.03 1.0, 1.07 0.05

Clostridium difficile

Antibacterials: Loss of normal colonic microflora

“colonisation resistance”:

C difficile spore germination, multiplication, toxin

production – diarrhoea / worse sequelae

2nd & 3rd generation cephalosporins

(cefuroxime, cefotaxime, ceftazidime)

Clindamycin

Fluoroquinolones:

Certain strains: e.g. PCR ribotype 027.

Choice of treatment

Paradox

Severe sepsis: “Getting it right first time”

Preserving antimicrobial efficacy

“De-escalation”

Improve diagnostic speed

Aetiology; in vitro susceptibilities

Bacteriological methods long-standing, but:

Direct to specimens: PCR / NAAT

blood, sterile sites

Organism identification: MALDI-TOF

Matrix-Assisted Laser Desorption Ionisation Time

of Flight Mass Spectroscopy: bacteria / yeasts

Rapid automated sensitivity testing (< 12 hours)

Less familiar agents (...in United Kingdom)

Mecillinam

Beta lactam (6-β-amidinopenicillanic acid)

Pivmecillinam Pivaloyloxymethyl ester:

Much more active vs Gram negatives (binds to PBP2) (Enterococci resistant, S saprophyticus may be inhibited)

Enterobacteriaceae

Usual suspects more tricky:

P aeruginosa, Acinetobacter spp, anaerobes: resistant

Serratia marcescens: usually resistant

M morganii, Providencia spp may be sensitive

(Paradoxical effect with P stuartii)

P mirabilis, P vulgaris: usually sensitive

Uses: Urinary tract infections

Lower

(Upper – step down oral therapy).

((Other MDR coliforms: e.g. Biliary))

Advantages:

High % still susceptible (> 90% global)

Widely used in Scandinavia, >20 years, still high susceptibility

Low C difficile propensity

(Baines 2009: low risk in in vitro human gut model)

“Avoid” if penicillin allergy

(tho’ hypersensitivity reactions uncommon)Kahlmeter 2003, Wootton 2010

E coli, 3rd generation cephalosporin resistant:

% susceptible (Wootton 2010)

Mecillinam 100 (93.5% local CPD R)

Meropenem 100

Cefotaxime 13.3

Amoxicillin 0

Co-amoxiclav 0

Piperacillin-tazobactam 53.3

Ciprofloxacin 40

Nitrofurantoin 76.7

Trimethoprim 30

Gentamicin 53.3

Mastascan plate evaluation (LTHT)

Breakpoint plate, 8 mg/l [BSAC cut-off].

+/- testing by current disc method:

All if resistant, subset of those sensitive.

1192 Gram negative isolates tested.

Overall susceptible: 1147 (96%)

Norris (unpubd)

Temocillin

6-α-methoxy derivative of ticarcillin

Active vs Gram negative bacilli (excl P aeruginosa)

Stable vs many β-lactamases: SHV, TEM, CTX-M

families, also AmpC

Stable to some carbapenemases

Carbapenem-sparing agent, intravenous:

UTIs due to ESBL producing Enterobacteriaceae

“Ecologically benign”: Low propensity for C difficile

Livermore 2009.

E coli, Gram negative

Other “old” drugs:

Colistin

Iv fosfomycin

Conclusions:

E coli remains predominant UTI pathogen.

Increasing problems of resistance, globally

Recognition of collateral damage of antibiotics

Fluoroquinolones & MRSA

Severe sepsis: “Getting it right first time”...but de-

escalation

Carbapenem sparing agents

“Old” drugs being revived / re-visited

Mecillinam, temocillin.

Shortage of new antibiotics for Gram-negatives:

....avoid antibiotics unless clear clinical indication