Typing

About: Typing is a research topic. Over the lifetime, 5010 publications have been published within this topic receiving 146539 citations.

Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages

Abstract: Third-generation cephalosporins are a class of β-lactam antibiotics that are often used for the treatment of human infections caused by Gram-negative bacteria, especially Escherichia coli. Worryingly, the incidence of human infections caused by third-generation cephalosporin-resistant E. coli is increasing worldwide. Recent studies have suggested that these E. coli strains, and their antibiotic resistance genes, can spread from food-producing animals, via the food-chain, to humans. However, these studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these strains. We therefore used whole-genome sequencing (WGS) to study the relatedness of cephalosporin-resistant E. coli from humans, chicken meat, poultry and pigs. One strain collection included pairs of human and poultry-associated strains that had previously been considered to be identical based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance gene sequencing. The second collection included isolates from farmers and their pigs. WGS analysis revealed considerable heterogeneity between human and poultry-associated isolates. The most closely related pairs of strains from both sources carried 1263 Single-Nucleotide Polymorphisms (SNPs) per Mbp core genome. In contrast, epidemiologically linked strains from humans and pigs differed by only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed three distinct plasmid lineages (IncI1- and IncK-type) that carried cephalosporin resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL)- and AmpC-types. The plasmid backbones within each lineage were virtually identical and were shared by genetically unrelated human and animal isolates. Plasmid reconstructions from short-read sequencing data were validated by long-read DNA sequencing for two strains. Our findings failed to demonstrate evidence for recent clonal transmission of cephalosporin-resistant E. coli strains from poultry to humans, as has been suggested based on traditional, low-resolution typing methods. Instead, our data suggest that cephalosporin resistance genes are mainly disseminated in animals and humans via distinct plasmids.

Bacteriophage typing of Staphylococcus aureus.

Abstract: The routine methods for propagation of staphylococcal typing bacteriophages, and for their use in identifying strains of staphylococci, are described.Most of the phages can be propagated in fluid media as well as on agar, and for some glucose-peptone-water is a better medium than nutrient or Todd-Hewitt broth.Many phage filtrates derived from broth or agar propagation contain, in addition to the phage, an agent that inhibits the growth of staphylococci.Investigations of variations in the routine typing technique showed that considerable latitude is permissible in the age of cultures used for typing and in the inoculation procedures. It is, however, important to test all phage filtrates after propagation for purity and freedom from the inhibitory agent; and to repeat the tests frequently during use to detect alterations in titre.About 40% of staphylococci are not lysed by the phages used at their test dilution; about half of these untypable strains are lysed by undiluted phage filtrates.An analysis was made of the results of typing 567 independent strains of staphylococci; 229 of these showed strong lysis by one or more phages, but there were no fewer than 82 distinct phage patterns represented, and only 118 strains were lysed strongly by a single phage. Certain phages tend to appear together in patterns and on the basis of such associations three main phage groups can be distinguished; they are known respectively as the ‘3A’, ‘6/47’ and ‘52’ groups.No method was discovered for segregating patterns into ‘types’, but conventions have been devised on the basis of the variation observed in sets of strains from various sources, for distinguishing between different patterns.We are deeply indebted to Dr V. D. Allison for teaching us the bacteriophage typing methods and for giving us the benefit of his wide experience.We are grateful to the following for sending us phages, and in some cases discussing their results with us: Dr Phyllis Rountree, Sydney; Dr R. Wahl, Paris; Dr G. Wallmark, Stockholm; Dr H. Williams Smith, Poultry Research Station, and Mr A. M. Hood, Birmingham.Our thanks are also due to Miss S. Mayo, Mrs E. Lyons and Mr D. Woodroof for technical assistance. The photographs for PI. 14 were taken by Mr W. Clifford.

Comparative Genotyping of Campylobacter jejuni by Amplified Fragment Length Polymorphism, Multilocus Sequence Typing, and Short Repeat Sequencing: Strain Diversity, Host Range, and Recombination

Abstract: Three molecular typing methods were used to study the relationships among 184 Campylobacter strains isolated from humans, cattle, and chickens. All strains were genotyped by amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), and sequence analysis of a genomic region with short tandem repeats designated clustered regularly interspaced short palindromic repeats (CRISPRs). MLST and AFLP analysis yielded more than 100 different profiles and patterns, respectively. These multiple-locus typing methods resulted in similar genetic clustering, indicating that both are useful in disclosing genetic relationships between Campylobacter jejuni isolates. Group separation analysis of the AFLP analysis and MLST data revealed an unexpected association between cattle and human strains, suggesting a common source of infection. Analysis of the polymorphic CRISPR region carrying short repeats allowed about two-thirds of the typeable strains to be distinguished, similar to AFLP analysis and MLST. The three methods proved to be equally powerful in identifying strains from outbreaks of human campylobacteriosis. Analysis of the MLST data showed that intra- and interspecies recombination occurs frequently and that the role of recombination in sequence variation is 50 times greater than that of mutation. Examination of strains cultured from cecum swabs revealed that individual chickens harbored multiple Campylobacter strain types and that some genotypes were found in more than one chicken. We conclude that typing of Campylobacter strains is useful for identification of outbreaks but is probably not useful for source tracing and global epidemiology because of carriage of strains of multiple types and an extremely high diversity of strains in animals.