Comparison of three molecular subtyping techniques for Listeria monocytogenes

Distribution and phenotypic and genotypic characterization of Listeria monocytogenes isolated from food, Colombia, 2010-2018

Introduction: Listeria monocytogenes is a food-borne pathogen that may cause infections in humans such as meningitis, meningoencephalitis, and septicemia, as well as abortions. By serological typing 13 serotypes have been identified of which 4b is responsible for most of the outbreaks in the world. Objective: To determine the frequency and distribution of serotypes and molecular subtypes of L. monocytogenes isolated in Colombia from food from 2010 to 2018. Materials and methods: We conducted a retrospective and descriptive study based on the analysis of 2,420 isolates confirmed as L. monocytogenes and other species using biochemical and serological tests, and pulsed-field gel electrophoresis (PFGE) for molecular subtyping. Results: Of the 2,420 isolates received, 2,326 were confirmed as L. monocytogenes. The serotypes found were 4b (52%), 4d-4e (14.5%), 1/2a (11%), 1/2c (9.4%), 1/2b (9%), and 3a, 3b, 3c, 4c, 4d, 4e and 7 (less than 2%). The isolates came from Bogotá (43%), Antioquia (25%), Valle (10%), Nariño (9%), and other departments (7%). The genotypic characterization grouped the isolates in 167 PFGE patterns. The most frequent patterns were identified in various dairy and meat products, and in prepared foods. Conclusion: A 96.1% of the isolates corresponded to L. monocytogenes showing good agreement between isolates and identification. Serotype 4b, highly virulent, was the most frequent. The molecular analysis showed the possible dissemination and permanence over time of several serotypes, which highlights the importance of including this pathogen in epidemiological food surveillance programs.

Molecular typing, biofilm production, and detection of carbapenemase genes in multidrug-resistant Acinetobacter baumannii isolated from different infection sites using ERIC-PCR in Hamadan, west of Iran

BACKGROUND

Acinetobacter baumannii is an opportunistic pathogen that can cause several kinds of nosocomial infections. Increasing antibiotic resistance as well as identifying genetic diversity and factors associated with pathogenicity and prevalence of this bacterium is important. The aim of this study was the investigation of molecular typing, biofilm production, and detection of carbapenemase genes in multidrug-resistant Acinetobacter baumannii isolated from different infection sites using ERIC-PCR in Iran.

METHODS

Forty isolates of A. baumannii were obtained from various wards of the central hospital, in the west of Iran. Phenotypic identification and genetic diversity, biofilm production assay, and detection of Carbapenemase genes carried out.

RESULTS

Tracheal samples 26 (61.9 %) are the most frequent isolates, and 95 % of isolates were identified as MDR. 32.5 % of all A. baumannii strains were capable to form a strong biofilm. It was founded that antimicrobial resistance patterns had a significant relationship with strong biofilm formation (P = 0.001). Most frequencies of the studied genes were in the order of VIM (81 %), SPM (45.2 %), and IMP (35.7 %) genes. The VIM gene was the most frequent in all isolates which were significant (P = 0.006). 14 different ERIC-types were observed including 7 common types and 7 unique or single types. F type is the largest common type consisting of nine isolates and B, D, and E types contain two isolates separately.

CONCLUSIONS

ERIC-PCR technique was used to genetically classify A. baumannii isolates as one of the most common microorganisms in nosocomial infections.

Genotypic diversity in multi-drug-resistant E. coli isolated from animal feces and Yamuna River water, India, using rep-PCR fingerprinting

Genotypic diversity among multi-drug-resistant (MDR) aquatic E. coli isolated from different sites of Yamuna River was analyzed using repetitive element PCR (rep-PCR) methods viz. ERIC-PCR and (GTG)₅-PCR and compared with the MDR animal fecal isolates. The 97 E. coli isolates belonging to different serotypes, phylogroups, and multi-drug resistance patterns were analyzed. High genetic diversity was observed by both the methods; however, (GTG)₅ typing showed higher discriminating potential. Combination of ERIC types (E1-E32) and (GTG)₅ types (G1-G46) generated 77 genotypes. The frequency of genotypes ranged from 0.013 to 0.065. The genotype composition of E. coli isolates was highly diverse at all the sampling sites across Yamuna River except at its entry site in Delhi. The sampling sites under the influence of high anthropogenic activities showed an increase in number of unique genotype isolates. These sites also exhibited high multiple antibiotic resistance (MAR) indexes (above 0.25) suggesting high risk of contamination. Principal coordinate analysis (PCoA) showed limited clustering of genotypes based on the sampling sites. The most frequent genotypes were grouped in the positive zone of both the principal coordinates (PC1 and PC2). The genotypes of most of the animal fecal isolates were unique and occupied a common space in the negative PC1 area forming a separate cluster. High genotypic diversity among the aquatic E. coli and the drain isolates, discharging the untreated municipal waste in the river, was observed, suggesting that the sewage effluents contribute substantially to contamination of this river system than animal feces. The presence of such a high diversity among the MDR E. coli isolates in the natural river systems is of great public health significance and highlights the need of an efficient surveillance system for better management of Indian natural water bodies.

Genetic relatedness in carbapenem-resistant isolates from clinical specimens in Ghana using ERIC-PCR technique

AIM

Enterobacterial repetitive intergenic consensus (ERIC) sequence analysis is a powerful tool for epidemiological analysis of bacterial species. This study aimed to determine the genetic relatedness or variability in carbapenem-resistant isolates by species using this technique.

METHODS

A total of 111 non-duplicated carbapenem-resistant (CR) Gram-negative bacilli isolates from a three-year collection period (2012-2014) were investigated by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) in four selected hospital laboratories in Ghana. The isolates were also screened for carbapenemase and extended spectrum β-lactamase genes by PCR.

RESULTS

A proportion of 23.4% (26/111) of the genomic DNA extracts were carriers of PCR-positive carbapenemase genes, including 14.4% blaNDM-1, 7.2% blaVIM-1 and 1.8% blaOXA-48. The highest prevalence of carbapenemase genes was from non-fermenters, Acinetobacter baumannii and Pseudomonas aeruginosa. For the ESBL genes tested, 96.4% (107/111) of the CR isolates co-harboured both TEM-1 and SHV-1 genes. The ERIC-PCR gel analysis exhibited 1 to 8 bands ranging from 50 to 800 bp. Band patterns of 93 complex dissimilarities were visually distinguished from the 111 CR isolates studied, while the remaining 18 showed band similarities in pairs.

CONCLUSION

Overall, ERIC-PCR fingerprints have shown a high level of diversity among the species of Gram-negative bacterial pathogens and specimen collection sites in this study. ERIC-PCR optimisation assays may serve as a suitable genotyping tool for the assessment of genetic diversity or close relatedness of isolates that are found in clinical settings.