Identification and Typing Methods for theStudy of Bacterial Infections: a Brief Reviewand Mycobacterial as Case of Study

Several techniques based on molecular biology and analytical chemistry has been developed to reduce some of the bacterial characterization limitations. Molecular methods represent the best alternative to identify bacterial strains isolated from diverse origins and to improve research in the context of molecular epidemiology. However, these methodologies are laborious and costly compared to phenotypic or classical techniques, and there are no reliable routine laboratories. This review shall provide basic elements for the understanding of these methodologies and raise interest in their collaborative use among analytical laboratories where bacterial identification and typing are priorities, because molecular methods are not universally implemented but are available in research and reference laboratories.

[1]  E. Basım.  Pulsed-Field Gel Electrophoresis (PFGE) Technique and its use in Molecular Biology , 2001 .

[2]  D. Ammons,et al.  In-house polymerase chain reaction for affordable and sustainable Chlamydia trachomatis detection in Trinidad and Tobago. , 2007, Revista panamericana de salud publica = Pan American journal of public health.

[3]  M. Maiden,et al.  Multi-locus sequence typing: a tool for global epidemiology. , 2003, Trends in microbiology.

[4]  M. Zervos,et al.  The application of molecular techniques to the study of hospital infection. , 2006, Archives of pathology & laboratory medicine.

[5]  D van Soolingen,et al.  Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology , 1997, Journal of clinical microbiology.

[6]  P. Sharp,et al.  ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. , 1991, Molecular microbiology.

[7]  J R Johnson,et al.  Development of polymerase chain reaction-based assays for bacterial gene detection. , 2000, Journal of microbiological methods.

[8]  B. V. Joseph,et al.  Combined use of Amplified Fragment Length Polymorphism and IS6110-RFLP in fingerprinting clinical isolates of Mycobacterium tuberculosis from Kerala, South India , 2007, BMC infectious diseases.

[9]  A. Ibekwe,et al.  Potential Human Pathogenic Bacteria in a Mixed Urban Watershed as Revealed by Pyrosequencing , 2013, PloS one.

[10]  P. Demirev,et al.  Characterization of intact microorganisms by MALDI mass spectrometry. , 2001, Mass spectrometry reviews.

[11]  Cecilia Hernández-Cortez,et al.  Aetiology and frequency of cervico-vaginal infections among Mexican women , 2013 .

[12]  Elena Jordana-Lluch,et al.  La espectrometría de masas en el laboratorio de microbiología clínica , 2012, Enfermedades Infecciosas y Microbiología Clínica.

[13]  E. Castro-Nallar,et al.  Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. , 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[14]  Nalin Rastogi,et al.  Current Methods in the Molecular Typing of Mycobacterium tuberculosis and Other Mycobacteria , 2014, BioMed research international.

[15]  H. Lambie,et al.  Characterization of Chlamydiaceae species using PCR and high resolution melt curve analysis of the 16S rRNA gene , 2009, Journal of applied microbiology.

[16]  M L Sammarco,et al.  [Molecular epidemiology of infectious diseases: analytical methods and results interpretation]. , 2014, Annali di igiene : medicina preventiva e di comunita.

[17]  D. Minnikin,et al.  Development and optimization of a gas chromatography/mass spectrometry method for the analysis of thermochemolytic degradation products of phthiocerol dimycocerosate waxes found in Mycobacterium tuberculosis , 2013, Rapid communications in mass spectrometry : RCM.

[18]  D. Young,et al.  Differentiation of Mycobacterium tuberculosis isolates by spoligotyping and IS6110 restriction fragment length polymorphism , 1997, Journal of clinical microbiology.

[19]  R. Wallace,,et al.  PCR amplification and restriction endonuclease analysis of a 65-kilodalton heat shock protein gene sequence for taxonomic separation of rapidly growing mycobacteria , 1995, Journal of clinical microbiology.

[20]  L. Otero,et al.  Actualización en infecciones de transmisión sexual: epidemiología, diagnóstico y tratamiento , 2004 .

[21]  H. Hernández,et al.  Métodos inmunológicos utilizados en la identificación rápida de bacterias y protozoarios en aguas , 2013 .

[22]  K. Jolley,et al.  Using multilocus sequence typing to study bacterial variation: prospects in the genomic era. , 2014, Future microbiology.

[23]  E. Hofer,et al.  Genotypic Characterization of Yersinia enterocolitica Biotype 4/O:3 Isolates from Pigs and Slaughterhouses Using SE-AFLP, ERIC-PCR, and PFGE , 2013, Journal of pathogens.

[24]  M. Domingo,et al.  Spacer oligonucleotide typing of Mycobacterium bovis strains from cattle and other animals: a tool for studying epidemiology of tuberculosis , 1996, Journal of clinical microbiology.

[25]  Highly specific and efficient primers for in-house multiplex PCR detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma hominis and Ureaplasma urealyticum , 2014, BMC Research Notes.

[26]  Germán Bou,et al.  Métodos de identificación bacteriana en el laboratorio de microbiología , 2011 .

[27]  J. Lupski,et al.  Molecular epidemiology of infections due to Enterobacter aerogenes: identification of hospital outbreak-associated strains by molecular techniques. , 1995, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[28]  S. Bolotin,et al.  The Ontario universal typing of tuberculosis (OUT-TB) surveillance program--what it means to you. , 2010, Canadian respiratory journal.

[29]  F. Sharif,et al.  Detection of Chlamydia trachomatis and Mycoplasma hominis, genitalium and Ureaplasma urealyticum by polymerase chain reaction in patients with sterile pyuria. , 2008, Advances in medical sciences.

[30]  D. Michael Olive,et al.  Principles and Applications of Methods for DNA-Based Typing of Microbial Organisms , 1999, Journal of Clinical Microbiology.

[31]  M. Hirata,et al.  Evaluation of hsp65 Nested PCR-Restriction Analysis (PRA) for Diagnosing Tuberculosis in a High Burden Country , 2013, BioMed research international.

[32]  Y. Wang,et al.  Comparison of Heat Inactivation and Cell Disruption Protocols for Identification of Mycobacteria from Solid Culture Media by Use of Vitek Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry , 2013, Journal of Clinical Microbiology.

[33]  P. Musoke,et al.  Species and genotypic diversity of non-tuberculous mycobacteria isolated from children investigated for pulmonary tuberculosis in rural Uganda , 2013, BMC Infectious Diseases.

[34]  J. Wolfe,et al.  Comparison of repetitive-sequence-based polymerase chain reaction with random amplified polymorphic DNA analysis for rapid genotyping of nontuberculosis mycobacteria. , 2012, Canadian journal of microbiology.

[35]  J. Lupski,et al.  Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction , 1994 .

[36]  Guadalupe Rodríguez-Angeles.  Principales características y diagnóstico de los grupos patógenos de Escherichia coli , 2002 .

[37]  K. Thompson,et al.  Comparative evaluation of Polymerase Chain Reaction-Restriction Enzyme Analysis (PRA) and sequencing of heat shock protein 65 (hsp65) gene for identification of aquatic mycobacteria. , 2009, Journal of microbiological methods.

[38]  M. Feizabadi,et al.  Application of Pulsed Field Gel Electrophoresis for Study of Genetic Diversity in Mycobacterium tuberculosis Strains Isolated From Tuberculosis Patients , 2014, Jundishapur journal of microbiology.

[39]  F. Fernández-Cuenca.  Aplicaciones de las técnicas de PCR a la epidemiología molecular de las enfermedades infecciosas , 2004 .

[40]  Nalin Rastogi,et al.  Molecular Characterization and Drug Resistance Patterns of Strains of Mycobacterium tuberculosis Isolated from Patients in an AIDS Counseling Center in Port-au-Prince, Haiti: a 1-Year Study , 2003, Journal of Clinical Microbiology.

[41]  J. Rolain,et al.  Use of MALDI-TOF mass spectrometry for identification of bacteria that are difficult to culture. , 2013, Journal of microbiological methods.