Identification of Yersinia species by the API 20E

Yersinia canariae sp. nov., isolated from a human yersiniosis case

A Gram-negative rod from the Yersinia genus was isolated from a clinical case of yersiniosis in the United Kingdom. Long read sequencing data from an Oxford Nanopore Technologies (ONT) MinION in conjunction with Illumina HiSeq reads were used to generate a finished quality genome of this strain. Overall Genome Related Index (OGRI) of the strain was used to determine that it was a novel species within Yersinia , despite biochemical similarities to Yersinia enterocolitica . The 16S ribosomal RNA gene accessions are MN434982-MN434987 and the accession number for the complete and closed chromosome is CP043727. The type strain is SRR7544370T (=NCTC 14382T/=LMG 31573T).

Salmonella, Shigella, and yersinia

Salmonella, Shigella, and Yersinia cause a well-characterized spectrum of disease in humans, ranging from asymptomatic carriage to hemorrhagic colitis and fatal typhoidal fever. These pathogens are responsible for millions of cases of food-borne illness in the United States each year, with substantial costs measured in hospitalizations and lost productivity. In the developing world, illness caused by these pathogens is not only more prevalent but also associated with a greater case-fatality rate. Classic methods for identification rely on selective media and serology, but newer methods based on mass spectrometry and polymerase chain reaction show great promise for routine clinical testing.

Yersinia massiliensis sp. nov., isolated from fresh water

Two bacterial organisms, 50640T and 823, were isolated from fresh water in Marseilles, France, and were further identified as members of the genus Yersinia on the basis of their phenotypic characteristics and 16S rRNA gene sequencing. Their unique phenotypic profile differed from that of closely related species of Yersinia bercovieri and Yersinia mollaretii by exhibiting positive indole and inositol tests, and from that of Yersinia frederiksenii by lacking the ability to ferment l-rhamnose. A polyphasic approach, including almost complete 16S rRNA gene sequencing (1461 bp) and partial sequencing of hsp60 (683 bp), gyrB (662 bp), sodA (624 bp) and rpoB (1049 bp) showed that isolates 50640T and 823 exhibited 98.5, 93.5, 90.4, 92.4 and 96.6 % similarity with Y. mollaretii, 98.7, 93.0, 90.1, 89.1 and 96.2 % with Y. bercovieri, and 98.4, 93.2, 89.8, 88.9 and 95.2 % with Y. frederiksenii, respectively. Both isolates exhibited an identical 16S rRNA gene sequence and differed by one to five point mutations in housekeeping gene sequences. Phylogenetic reconstructions based on the combination of these four housekeeping genes indicated that the two isolates formed a unique branch supported by a bootstrap value of 93 %. Their unique phenotypic traits, 16S rRNA gene sequence, together with housekeeping gene sequences exhibiting <97 % similarity with closely related species, and phylogenetic analyses suggested that the two isolates represent a so far undescribed Yersinia species. The name Yersinia massiliensis sp. nov. is proposed for this new taxon (type strain 50640T=CIP 109351T=CCUG 53443T; isolate 823=CIP 109352=CCUG 53444).

Current and developing technologies for monitoring agents of bioterrorism and biowarfare

Recent events have made public health officials acutely aware of the importance of rapidly and accurately detecting acts of bioterrorism. Because bioterrorism is difficult to predict or prevent, reliable platforms to rapidly detect and identify biothreat agents are important to minimize the spread of these agents and to protect the public health. These platforms must not only be sensitive and specific, but must also be able to accurately detect a variety of pathogens, including modified or previously uncharacterized agents, directly from complex sample matrices. Various commercial tests utilizing biochemical, immunological, nucleic acid, and bioluminescence procedures are currently available to identify biological threat agents. Newer tests have also been developed to identify such agents using aptamers, biochips, evanescent wave biosensors, cantilevers, living cells, and other innovative technologies. This review describes these current and developing technologies and considers challenges to rapid, accurate detection of biothreat agents. Although there is no ideal platform, many of these technologies have proved invaluable for the detection and identification of biothreat agents.

Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase β-subunit

The phylogeny of enterobacterial species commonly found in clinical samples was analysed by comparing partial sequences of their elongation factor Tu gene (tuf) and of their F-ATPase β-subunit gene (atpD). An 884 bp fragment for tuf and an 884 or 871 bp fragment for atpD were sequenced for 96 strains representing 78 species from 31 enterobacterial genera. The atpD sequence analysis exhibited an indel specific to Pantoea and Tatumella species, showing, for the first time, a tight phylogenetic affiliation between these two genera. Comprehensive tuf and atpD phylogenetic trees were constructed and are in agreement with each other. Monophyletic genera are Cedecea, Edwardsiella, Proteus, Providencia, Salmonella, Serratia, Raoultella and Yersinia. Analogous trees based on 16S rRNA gene sequences available from databases were also reconstructed. The tuf and atpD phylogenies are in agreement with the 16S rRNA gene sequence analysis, and distance comparisons revealed that the tuf and atpD genes provide better discrimination for pairs of species belonging to the family Enterobacteriaceae. In conclusion, phylogeny based on tuf and atpD conserved genes allows discrimination between species of the Enterobacteriaceae.

Manual and automated instrumentation for identification of Enterobacteriaceae and other aerobic gram-negative bacilli

Identification of gram-negative bacilli, both enteric and nonenteric, by conventional methods is not realistic for clinical microbiology laboratories performing routine cultures in today's world. The use of commercial kits, either manual or automated, to identify these organisms is a common practice. The advent of rapid or "spot" testing has eliminated the need for some commonly isolated organisms to be identified with the systems approach. Commercially available systems provide more in-depth identification to the species level as well as detect new and unusual strains. The answers obtained from these systems may not always be correct and must be interpreted with caution. The patient demographics, laboratory workload and work flow, and technologist's skill levels should dictate the system of choice. Cost considerations introduce another variable into the equation affecting choice. Each system has its own strengths and weaknesses, and each laboratory must decide on the level of sophistication that fulfills its particular needs.

Low occurrence of pathogenic Yersinia enterocolitica in clinical, food, and environmental samples: a methodological problem

While Yersinia enterocolitica is an important pathogen, which can cause yersiniosis in humans and animals, its epidemiology remains obscure. The pig is the major reservoir of pathogenic Y. enterocolitica of bioserotype 4/O:3, the most common type found in humans. Y. enterocolitica is thought to be a significant food-borne pathogen, although pathogenic isolates have seldom been recovered from foods. The low isolation rate of this pathogenic bacterium in natural samples, including clinical, food, and environmental samples, may be due to the limited sensitivity of culture methods. During the last decade, numerous DNA-based methods, such as PCR and colony hybridization assays, have been designed to detect pathogenic Y. enterocolitica in natural samples more rapidly and with better sensitivity than can be achieved by culture methods. In addition, the occurrence of pathogenic Y. enterocolitica in natural samples is clearly higher with PCR than with culture methods. The methods available for detection of pathogenic Y. enterocolitica in natural samples are reviewed in this article.

Yersiniae other than Y. enterocolitica, Y. pseudotuberculosis, and Y. pestis: the ignored species

The genus Yersinia is composed of 11 species, of which three (Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica) have been exhaustively characterized. The remaining eight species (Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. bercovieri, Y. mollaretii, Y. rohdei, Y. ruckeri, and Y. aldovae) have not been studied extensively and, because of the absence of classical Yersinia virulence markers, are generally considered to be nonpathogenic. However, recent data suggest that some of these eight species may cause disease by virtue of their having virulence factors distinct from those of Y. enterocolitica. These data raise intriguing questions about the mechanisms by which these species interact with their host cells and elicit human disease.

Identification of Yersinia species by the Vitek GNI card

The Vitek GNI card was used to identify 212 isolates of 10 Yersinia species. Identification was correct for 96.3% of the isolates (156 of 162) to the genus level and for 57.4% of the isolates (93 of 162) to the species level for Yersinia spp. listed in the Vitek database. We recommend additional identification methods for isolates assigned to the genus Yersinia by the Vitek system.

Comparison of systems for identification and differentiation of species within the genus Yersinia

Of four tested identification systems (API 20E, API Rapid 32 IDE, Micronaut E, and the PCR-based Yersinia enterocolitica Amplification Set), API 20E is still the system of choice for identifying pathogenic Yersinia isolates. It provides the highest sensitivity both at the genus and at the species level and has the best cost-effectiveness correlation.

Application of Yersinia kristensenii bacteriocin as a specific marker for the rapid identification of suspected isolates of Yersinia enterocolitica

Out of 143 suspected foods and clinical isolates of the genus Yersinia, 77 isolates were bacteriocin-sensitive and 66 bacteriocin non-sensitive. Of the 77 bacteriocin-sensitive isolates, 72 (93.5%) were identified as Y. enterocolitica and 5 (6.49%) as Y. frederiksenii. Out of 66 bacteriocin non-sensitive suspected isolates, 22 (33.3%) were identified as Yersinia spp. other than Y. enterocolitica and 43 (65.1%) were other Gram-negative bacteria with the exception of one (1.5%) isolate identified as Y. enterocolitica.

In vitro characteristics of Yersinia pseudotuberculosis of nonhuman primate origin

Six strains of serotypes 1 or 2 of Y. pseudotuberculosis were isolated from dead squirrel monkeys, a cotton-top tamarin and a marmoset hybrid. All strains harboured a 71.6 kb plasmid, all were totally oxacillin-resistant and partially resistant to cephalosporins. Biochemically, serotypes 1 and 2 differed from each other in their beta-galactosidase production in a nonfermenter system, whereas the lack of rhamnose, maltose, salicin and trehalose fermentation seemed to be attributable to technical causes.