Top

European Journal of Clinical Microbiology & Infectious Diseases

Published in:

01-08-2014 | Article

MALDI-TOF mass spectrometry as a tool for the discrimination of high-risk Escherichia coli clones from phylogenetic groups B2 (ST131) and D (ST69, ST405, ST393)

Authors: Â. Novais, C. Sousa, J. de Dios Caballero, A. Fernandez-Olmos, J. Lopes, H. Ramos, T. M. Coque, R. Cantón, L. Peixe

Published in: European Journal of Clinical Microbiology & Infectious Diseases | Issue 8/2014

Abstract

Reliable, quick and low-cost methods are needed for the early detection of multidrug-resistant and highly virulent high-risk B2 and D Escherichia coli clones or clonal complexes (HiRCC). Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) seems to have a good discriminatory potential at different subspecies levels, but it was never evaluated for the discrimination of E. coli clones. We assessed the potential of MALDI-TOF MS coupled to multivariate data analysis to discriminate representative E. coli B2 and D HiRCC. Seventy-three E. coli isolates from B2 (including ST131 and B2 non-ST131 clones) and D (ST69, ST393, ST405) with variable pulsed-field gel electrophoresis (PFGE) patterns, origins and dates (1980–2010) were tested. MS spectra were acquired from independent extracts obtained from different plate cultures in two different Microflex LT MALDI-TOF devices (Bruker) after a standard extraction procedure. MALDI-TOF MS fingerprinting analysis revealed a good discriminatory ability between the four HiRCC analysed (ST131, ST69, ST405, ST393) and between B2 ST131 and other B2 non-ST131 isolates. Clusters defined by MALDI-TOF MS were consistent with the clonal complexes assigned by multilocus sequence typing (MLST), although differences were detected regarding the composition of clusters obtained by the comparison of PFGE profiles. We demonstrate, for the first time, that characteristic mass fingerprints of different E. coli HiRCC are sufficiently discriminatory and robust to enable their differentiation by MALDI-TOF MS, which might represent a promising tool for the optimisation of infection control, individual patient management and large-scale epidemiological studies of public health relevance. The good correlation between phenotypic and genotypic features further corroborates phylogenetic relationships delineated by MLST.

Baquero F, Coque TM (2011) Multilevel population genetics in antibiotic resistance. FEMS Microbiol Rev 35(5):705–706PubMedCrossRef

Woodford N, Turton JF, Livermore DM (2011) Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance. FEMS Microbiol Rev 35(5):736–755PubMedCrossRef

Johnson JR, Johnston B, Clabots C, Kuskowski MA, Castanheira M (2010) Escherichia coli sequence type ST131 as the major cause of serious multidrug-resistant E. coli infections in the United States. Clin Infect Dis 51(3):286–294PubMedCrossRef

Johnson JR, Tchesnokova V, Johnston B, Clabots C, Roberts PL, Billig M, Riddell K, Rogers P, Qin X, Butler-Wu S, Price LB, Aziz M, Nicolas-Chanoine MH, Debroy C, Robicsek A, Hansen G, Urban C, Platell J, Trott DJ, Zhanel G, Weissman SJ, Cookson BT, Fang FC, Limaye AP, Scholes D, Chattopadhyay S, Hooper DC, Sokurenko EV (2013) Abrupt emergence of a single dominant multidrug-resistant strain of Escherichia coli. J Infect Dis 207(6):919–928PubMedCentralPubMedCrossRef

Centers for Disease Control and Prevention (CDC) (2013) Antibiotic resistance threats in the United States, 2013. Available online at: http://www.cdc.gov/drugresistance/threat-report-2013/. Last accessed 13 December 2013

Novais A, Pires J, Ferreira H, Costa L, Montenegro C, Vuotto C, Donelli G, Coque TM, Peixe L (2012) Characterization of globally spread Escherichia coli ST131 isolates (1991 to 2010). Antimicrob Agents Chemother 56(7):3973–3976PubMedCentralPubMedCrossRef

Novais Â, Vuotto C, Pires J, Montenegro C, Donelli G, Coque TM, Peixe L (2013) Diversity and biofilm-production ability among isolates of Escherichia coli phylogroup D belonging to ST69, ST393 and ST405 clonal groups. BMC Microbiol 13:144PubMedCentralPubMedCrossRef

Blanco J, Mora A, Mamani R, López C, Blanco M, Dahbi G, Herrera A, Blanco JE, Alonso MP, García-Garrote F, Chaves F, Orellana MÁ, Martínez-Martínez L, Calvo J, Prats G, Larrosa MN, González-López JJ, López-Cerero L, Rodríguez-Baño J, Pascual A (2011) National survey of Escherichia coli causing extraintestinal infections reveals the spread of drug-resistant clonal groups O25b:H4-B2-ST131, O15:H1-D-ST393 and CGA-D-ST69 with high virulence gene content in Spain. J Antimicrob Chemother 66(9):2011–2021PubMedCrossRef

Blanco J, Mora A, Mamani R, López C, Blanco M, Dahbi G, Herrera A, Marzoa J, Fernández V, de la Cruz F, Martínez-Martínez L, Alonso MP, Nicolas-Chanoine MH, Johnson JR, Johnston B, López-Cerero L, Pascual A, Rodríguez-Baño J; Spanish Group for Nosocomial Infections (GEIH) (2013) Four main virotypes among extended-spectrum-beta-lactamase-producing isolates of Escherichia coli O25b:H4-B2-ST131: bacterial, epidemiological, and clinical characteristics. J Clin Microbiol 51(10):3358–3367PubMedCentralPubMedCrossRef

10.

Dahbi G, Mora A, López C, Alonso MP, Mamani R, Marzoa J, Coira A, García-Garrote F, Pita JM, Velasco D, Herrera A, Viso S, Blanco JE, Blanco M, Blanco J (2013) Emergence of new variants of ST131 clonal group among extraintestinal pathogenic Escherichia coli producing extended-spectrum beta-lactamases. Int J Antimicrob Agents 42(4):347–351PubMedCrossRef

11.

Clark AE, Kaleta EJ, Arora A, Wolk DM (2013) Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 26(3):547–603PubMedCrossRef

12.

Fenselau C, Demirev PA (2001) Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom Rev 20(4):157–171PubMedCrossRef

13.

Lartigue MF (2013) Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for bacterial strain characterization. Infect Genet Evol 13:230–235PubMedCrossRef

14.

Clark CG, Kruczkiewicz P, Guan C, McCorrister SJ, Chong P, Wylie J, van Caeseele P, Tabor HA, Snarr P, Gilmour MW, Taboada EN, Westmacott GR (2013) Evaluation of MALDI-TOF mass spectroscopy methods for determination of Escherichia coli pathotypes. J Microbiol Methods 94(3):180–191PubMedCrossRef

15.

Hrabák J, Chudácková E, Walková R (2013) Matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry for detection of antibiotic resistance mechanisms: from research to routine diagnosis. Clin Microbiol Rev 26(1):103–114PubMedCentralPubMedCrossRef

16.

Momo RA, Povey JF, Smales CM, O’Malley CJ, Montague GA, Martin EB (2013) MALDI-ToF mass spectrometry coupled with multivariate pattern recognition analysis for the rapid biomarker profiling of Escherichia coli in different growth phases. Anal Bioanal Chem 405(25):8251–8265PubMedCrossRef

17.

Kuehl B, Marten SM, Bischoff Y, Brenner-Weiss G, Obst U (2011) MALDI-ToF mass spectrometry-multivariate data analysis as a tool for classification of reactivation and non-culturable states of bacteria. Anal Bioanal Chem 401(5):1593–1600PubMedCrossRef

18.

Dieckmann R, Malorny B (2011) Rapid screening of epidemiologically important Salmonella enterica subsp. enterica serovars by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 77(12):4136–4146PubMedCentralPubMedCrossRef

19.

Barbuddhe SB, Maier T, Schwarz G, Kostrzewa M, Hof H, Domann E, Chakraborty T, Hain T (2008) Rapid identification and typing of Listeria species by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 74(17):5402–5407PubMedCentralPubMedCrossRef

20.

Wolters M, Rohde H, Maier T, Belmar-Campos C, Franke G, Scherpe S, Aepfelbacher M, Christner M (2011) MALDI-TOF MS fingerprinting allows for discrimination of major methicillin-resistant Staphylococcus aureus lineages. Int J Med Microbiol 301(1):64–68PubMedCrossRef

21.

Böhme K, Fernández-No IC, Pazos M, Gallardo JM, Barros-Velázquez J, Cañas B, Calo-Mata P (2013) Identification and classification of seafood-borne pathogenic and spoilage bacteria: 16S rRNA sequencing versus MALDI-TOF MS fingerprinting. Electrophoresis 34(6):877–887PubMedCrossRef

22.

Bernaschi P, Del Chierico F, Petrucca A, Argentieri A, Ciofi Degli Atti M, Ciliento G, Carletti M, Muraca M, Locatelli F, Putignani L (2013) Microbial tracking of multidrug-resistant Klebsiella pneumoniae isolates in a pediatric hospital setting. Int J Immunopathol Pharmacol 26(2):463–472PubMed

23.

Berrazeg M, Diene SM, Drissi M, Kempf M, Richet H, Landraud L, Rolain JM (2013) Biotyping of multidrug-resistant Klebsiella pneumoniae clinical isolates from France and Algeria using MALDI-TOF MS. PLoS One 8(4):e61428PubMedCentralPubMedCrossRef

24.

Welker M (2011) Proteomics for routine identification of microorganisms. Proteomics 11(15):3143–3153PubMedCrossRef

25.

Croxatto A, Prod’hom G, Greub G (2012) Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 36(2):380–407PubMedCrossRef

26.

Vlek AL, Bonten MJ, Boel CH (2012) Direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry improves appropriateness of antibiotic treatment of bacteremia. PLoS One 7(3):e32589PubMedCentralPubMedCrossRef

27.

Del Chierico F, Petrucca A, Vernocchi P, Bracaglia G, Fiscarelli E, Bernaschi P, Muraca M, Urbani A, Putignani L (2014) Proteomics boosts translational and clinical microbiology. J Proteomics 97:69–87PubMedCrossRef

28.

Clerc O, Prod’hom G, Vogne C, Bizzini A, Calandra T, Greub G (2013) Impact of matrix-assisted laser desorption ionization time-of-flight mass spectrometry on the clinical management of patients with Gram-negative bacteremia: a prospective observational study. Clin Infect Dis 56(8):1101–1107PubMedCrossRef

29.

Naes T, Isaksson T, Fearn T, Davis T (2002) A user-friendly guide to multivariate calibration and classification. NIR Publications, Chichester

30.

Geladi P, Kowalsky BR (1986) Partial least-squares regression: a tutorial. Anal Chim Acta 185:1–17CrossRef

31.

Alsberg BK, Kell DB, Goodacre R (1998) Variable selection in discriminant partial least-squares analysis. Anal Chem 70:4126–4133PubMedCrossRef

32.

De Maesschalck R, Candolfi A, Massart DL, Heuerding S (1999) Decision criteria for soft independent modeling of class analogy applied to near infrared data. Chemom Intell Lab Syst 47:65–77CrossRef

33.

Wold S (1976) Pattern recognition by means of disjoint principal components models. Pattern Recog 8:127–139CrossRef

34.

Hunter PR (1990) Reproducibility and indices of discriminatory power of microbial typing methods. J Clin Microbiol 28(9):1903–1905PubMedCentralPubMed

35.

Josten M, Reif M, Szekat C, Al-Sabti N, Roemer T, Sparbier K, Kostrzewa M, Rohde H, Sahl HG, Bierbaum G (2013) Analysis of the matrix-assisted laser desorption ionization-time of flight mass spectrum of Staphylococcus aureus identifies mutations that allow differentiation of the main clonal lineages. J Clin Microbiol 51(6):1809–1817PubMedCentralPubMedCrossRef

36.

Sandrin TR, Goldstein JE, Schumaker S (2013) MALDI TOF MS profiling of bacteria at the strain level: a review. Mass Spectrom Rev 32(3):188–217PubMedCrossRef

37.

Lasch P, Drevinek M, Nattermann H, Grunow R, Stämmler M, Dieckmann R, Schwecke T, Naumann D (2010) Characterization of Yersinia using MALDI-TOF mass spectrometry and chemometrics. Anal Chem 82(20):8464–8475PubMedCrossRef

38.

Dworzanski JP, Deshpande SV, Chen R, Jabbour RE, Snyder AP, Wick CH, Li L (2006) Mass spectrometry-based proteomics combined with bioinformatic tools for bacterial classification. J Proteome Res 5(1):76–87PubMedCrossRef

39.

Williams TL, Andrzejewski D, Lay JO, Musser SM (2003) Experimental factors affecting the quality and reproducibility of MALDI TOF mass spectra obtained from whole bacteria cells. J Am Soc Mass Spectrom 14(4):342–351PubMedCrossRef

40.

Dieckmann R, Helmuth R, Erhard M, Malorny B (2008) Rapid classification and identification of salmonellae at the species and subspecies levels by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 74(24):7767–7778PubMedCentralPubMedCrossRef

41.

Mellmann A, Bimet F, Bizet C, Borovskaya AD, Drake RR, Eigner U, Fahr AM, He Y, Ilina EN, Kostrzewa M, Maier T, Mancinelli L, Moussaoui W, Prévost G, Putignani L, Seachord CL, Tang YW, Harmsen D (2009) High interlaboratory reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry-based species identification of nonfermenting bacteria. J Clin Microbiol 47(11):3732–3734PubMedCentralPubMedCrossRef

42.

Wunschel SC, Jarman KH, Petersen CE, Valentine NB, Wahl KL, Schauki D, Jackman J, Nelson CP, White E 5th (2005) Bacterial analysis by MALDI-TOF mass spectrometry: an inter-laboratory comparison. J Am Soc Mass Spectrom 16(4):456–462PubMedCrossRef

43.

Suarez S, Ferroni A, Lotz A, Jolley KA, Guérin P, Leto J, Dauphin B, Jamet A, Maiden MC, Nassif X, Armengaud J (2013) Ribosomal proteins as biomarkers for bacterial identification by mass spectrometry in the clinical microbiology laboratory. J Microbiol Methods 94(3):390–396PubMedCentralPubMedCrossRef

44.

Rodrigues C, Machado E, Peixe L, Novais A (2013) IncI1/ST3 and IncN/ST1 plasmids drive the spread of bla _TEM-52 and bla _CTX-M-1/-32 in diverse Escherichia coli clones from different piggeries. J Antimicrob Chemother 68(10):2245–2248PubMed

Title: MALDI-TOF mass spectrometry as a tool for the discrimination of high-risk Escherichia coli clones from phylogenetic groups B2 (ST131) and D (ST69, ST405, ST393)
Authors: Â. Novais
C. Sousa
J. de Dios Caballero
A. Fernandez-Olmos
J. Lopes
H. Ramos
T. M. Coque
R. Cantón
L. Peixe
Publication date: 01-08-2014
Publisher: Springer Berlin Heidelberg
Published in: European Journal of Clinical Microbiology & Infectious Diseases / Issue 8/2014
Print ISSN: 0934-9723
Electronic ISSN: 1435-4373
DOI: https://doi.org/10.1007/s10096-014-2071-5

Live Webinar | 27-06-2024 | 18:00 (CEST)

Keynote webinar | Spotlight on medication adherence

Reserve your place

Live: Thursday 27th June 2024, 18:00-19:30 (CEST)

WHO estimates that half of all patients worldwide are non-adherent to their prescribed medication. The consequences of poor adherence can be catastrophic, on both the individual and population level.

Join our expert panel to discover why you need to understand the drivers of non-adherence in your patients, and how you can optimize medication adherence in your clinics to drastically improve patient outcomes.

Prof. Kevin Dolgin

Prof. Florian Limbourg

Prof. Anoop Chauhan

Developed by: Springer Medicine

Obesity Clinical Trial Summary

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.

Developed by: Springer Medicine

2024 ASCO Annual Meeting

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 8/2014

Seasonal trend and clinical presentation of Bacillus cereus bloodstream infection: association with summer and indwelling catheter

Comparison of flucytosine and fluconazole combined with amphotericin B for the treatment of HIV-associated cryptococcal meningitis: a systematic review and meta-analysis

Are hip hemiarthroplasty and total hip arthroplasty infections different entities? The importance of hip fractures

Scalp eschar and neck lymphadenopathy after tick bite: an emerging syndrome with multiple causes

Serological follow-up in patients with aorto-iliac disease and evidence of Q fever infection

Significantly higher occurrence of Cryptosporidium infection in Roma children compared with non-Roma children in Slovakia

Keynote webinar | Spotlight on medication adherence

Live: Thursday 27th June 2024, 18:00-19:30 (CEST)

At a glance: The STEP trials