Molecular typing: a key tool for the surveillance and control of nosocomial infection

Effects of laboratory capabilities on combating antimicrobial resistance, 2013-2016: A static model panel data analysis

OBJECTIVES

Antimicrobial resistance (AMR) has become a serious global public health problem. The World Health Organization (WHO) and European Union (EU) have taken actions to combat this issue, in which laboratory capability construction is a crucial part. This study aimed to explore the relationship between laboratory capabilities and antimicrobial resistance from a macro perspective.

METHODS

The study used annual national level penal data from the EU Laboratory Capability Monitoring System and Antimicrobial Resistance Surveillance Europe 2013-2016. A conventional static panel data analysis was constructed to establish the relationship between the antimicrobial resistance rates and laboratory capabilities.

RESULTS

Laboratory capability on antimicrobial drug resistance characterisation and monitoring (LC8) showed a positive effect on Escherichia coli (E. coli) combined resistance rate (Y5), E. coli resistant rate of aminoglycosides (Y4), and Klebsiella pneumoniae resistant rate of carbapenems (Y8) (OR=0.929, 0.957, and 0.861; P=0.035, 0.007, and 0.026, respectively). However, following the diagnostic testing guidelines (LC2) caused higher resistance rates of Klebsiella pneumoniae to fluoroquinolones (Y6), third-generation cephalosporins (Y7), and aminoglycosides (Y9) (OR=1.076, 1.093, and1.065; P=0.011, 0.032, and 0.002, respectively).

CONCLUSIONS

Antimicrobial drug resistance characterisation and monitoring by laboratories has contributed to minimising antimicrobial resistance, while the mechanism of laboratory capabilities to pose an ineffective or negative impact on AMR remains to be further studied.

Genetic stability of Brucella abortus isolates from an outbreak by multiple-locus variable-number tandem repeat analysis (MLVA16)

BACKGROUND

Brucellosis caused by Brucella abortus is one of the most important zoonoses in the world. Multiple-locus variable-number tandem repeat analysis (MLVA16) has been shown be a useful tool to epidemiological traceback studies in B. abortus infection. Thus, the present study aimed (i) to evaluate the genetic diversity of B. abortus isolates from a brucellosis outbreak, and (ii) to investigate the in vivo stability of the MLVA16 markers.

RESULTS

Three-hundred and seventy-five clinical samples, including 275 vaginal swabs and 100 milk samples, were cultured from a brucellosis outbreak in a cattle herd, which adopted RB51 vaccination and test-and-slaughter policies. Thirty-seven B. abortus isolates were obtained, eight from milk and twenty-nine from post-partum/abortion vaginal swabs, which were submitted to biotyping and genotyping by MLVA16. Twelve B. abortus isolates obtained from vaginal swabs were identified as RB51. Twenty four isolates, seven obtained from milk samples and seventeen from vaginal swabs, were identified as B. abortus biovar 3, while one isolate from vaginal swabs was identified as B. abortus biovar 1. Three distinct genotypes were observed during the brucellosis outbreak: RB observed in all isolates identified as RB51; W observed in all B. abortus biovar 3 isolates; and Z observed in the single B. abortus biovar 1 isolate. Epidemiological and molecular data show that the B. abortus biovar 1 genotype Z strain is not related to the B. abortus biovar 3 genotype W isolates, and represents a new introduction B. abortus during the outbreak.

CONCLUSIONS

The results of the present study on typing of multiple clinical B. abortus isolates from the same outbreak over a sixteen month period indicate the in vivo stability of MLVA16 markers, a low genetic diversity among B. abortus isolates and the usefulness of MLVA16 for epidemiological studies of bovine brucellosis.

Evaluation of ERIC-PCR as genotyping method for Corynebacterium pseudotuberculosis isolates

The aim of this study was to evaluate the Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR) as a tool for molecular typing of C. pseudotuberculosis isolates from eight different hosts in twelve countries. Ninety-nine C. pseudotuberculosis field strains, one type strain (ATCC 19410^T) and one vaccine strain (1002) were fingerprinted using the ERIC-1R and ERIC-2 primers, and the ERIC-1R+ERIC-2 primer pair. Twenty-nine different genotypes were generated by ERIC 1-PCR, 28 by ERIC 2-PCR and 35 by ERIC 1+2-PCR. The discriminatory index calculated for ERIC 1, ERIC 2, and ERIC 1+2-PCR was 0.89, 0.86, and 0.92, respectively. Epidemiological concordance was established for all ERIC-PCR assays. ERIC 1+2-PCR was defined as the best method based on suitability of the amplification patterns and discriminatory index. Minimal spanning tree for ERIC 1+2-PCR revealed three major clonal complexes and clustering around nitrate-positive (biovar Equi) and nitrate-negative (biovar Ovis) strains. Therefore, ERIC 1+2-PCR proved to be the best technique evaluated in this study for genotyping C. pseudotuberculosis strains, due to its usefulness for molecular epidemiology investigations.

Multilocus sequence typing of bacteria

Multilocus sequence typing (MLST) was proposed in 1998 as a portable, universal, and definitive method for characterizing bacteria, using the human pathogen Neisseria meningitidis as an example. In addition to providing a standardized approach to data collection, by examining the nucleotide sequences of multiple loci encoding housekeeping genes, or fragments of them, MLST data are made freely available over the Internet to ensure that a uniform nomenclature is readily available to all those interested in categorizing bacteria. At the time of writing, over thirty MLST schemes have been published and made available on the Internet, mostly for pathogenic bacteria, although there are schemes for pathogenic fungi and some nonpathogenic bacteria. MLST data have been employed in epidemiological investigations of various scales and in studies of the population biology, pathogenicity, and evolution of bacteria. The increasing speed and reduced cost of nucleotide sequence determination, together with improved web-based databases and analysis tools, present the prospect of increasingly wide application of MLST.

Les puces à ADN vont-elles révolutionner l’identification des bactéries ?

DNA-arrays are mainly known for their application in transcriptome analysis leading for instance to the discovery of new marker genes for diagnostics and prognostics in oncology. However, DNA arrays are also used for massively parallel analysis of DNA molecules allowing their quantification, the detection of single nucleotide polymorphisms and re-sequencing. This multi detection system is now applied to the << old >> problems of detecting and identifying bacteria in a biological sample and for the fine molecular characterization of a bacterial isolate. This new tool should serve for the diagnostic of an infection and for epidemiological studies such as those performed for the control of nosocomial infections or for the surveillance of bioterrorism attacks. DNA arrays carrying probes for 16S RNA specific of hundreds of bacterial species allow the identification of bacteria within a community by a single hybridization of amplified 16S rDNAs with universal primers and re-sequencing DNA arrays are used for multi locus sequence typing in a single step. Finally, the genome of an isolate could be characterized by DNA-arrays focused on a specific question like presence of toxin or antibiotic resistance genes. Up to now, DNA arrays are used in research laboratories for the rapid characterization at the genomic level of a strain collection, for evolutionary and population genetics studies and for the characterization of bacterial communities. Industrializing the process of DNA-array construction and hybridization is now needed in order to transfer this technology to hospitals and diagnostic laboratories.

Microbiology of nosocomial infections: progress and challenges

Technological advances have expanded the role of the clinical microbiology laboratory in supporting management and control of health-care-associated infections (HAI). Diagnostic capabilities have been complemented by new methods for characterisation of microbial antigens and nucleic acids. Genomic "fingerprinting" enables the study of transmission of nosocomial pathogens. Monitoring of their antimicrobial resistance patterns has gained critical importance. However, cost-effective application of microbiological testing for improved treatment and prevention of HAI requires further study.