On the evolution and biogeography of Apple stem grooving capillovirus.

Apple stem grooving Capillovirus (ASGV) has a wide host range, notably apples, pears and citrus. It is found worldwide. In this study, the published nucleotide sequences of the genomes of 60 isolates and of over 200 coat protein (CP) genes, including those of seven newly determined Iranian isolates, were analyzed. The non-recombinant genomes showed that sequences concatenated from the replicase genes (minus a short variable region), together with the movement and CP genes gave the best supported ML phylogenies, and these also correlated best with CP phylogenies, so that information from phylogenies of the genomic sequences could be augmented, with caution, by that from CP phylogenies. The basal ASGV population was only isolated from CP samples from Himachal Pradesh of northern India. Its progeny lineages diverged into populations in south and east Asia, especially China. The ASVG population in the USA probably came from a Chinese lineage, and the Eurasian one, including seven Iranian isolates, from Indian lineages. The analyses suggests that trade, negative selection and founder effects were the most important factors affecting the genetic evolution of ASGV.

Genetic Diversity of Campylobacter on Broiler Carcasses Collected Preevisceration and Postchill in 17 U.S. Poultry Processing Plants†

Campylobacter jejuni and Campylobacter coli are the most important human enteropathogens among the campylobacters. The objective of this study was to determine how diversity in Campylobacter populations found on chicken carcasses collected from 17 broiler processing plants in the United States is impacted by processing. Genetic diversity was determined for up to four isolates per carcass by sequencing the short variable region (SVR) of the flaA locus. On 70% of Campylobacter-positive carcasses, all isolates were indistinguishable by flaA SVR typing. The genetic diversity of Campylobacter decreased as carcasses proceeded through processing; Campylobacter populations obtained early in processing where carcasses are moved from the kill line to the evisceration line (rehang) were significantly more genetically diverse (P < 0.05) than those from carcasses sampled postchill (diversity indices of 0.9472 and 0.9235, respectively). Certain Campylobacter subtypes were found only at rehang and not at postchill. Other subtypes were found at postchill and not at rehang. These data suggest that some subtypes may not be able to survive processing, whereas others may persist on the carcass or within the equipment despite stressors encountered in the processing environment.

Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and fla Short Variable Region Typing of Clonal Complexes of Campylobacter jejuni Strains of Human, Bovine, and Poultry Origins in Luxembourg

ABSTRACT Campylobacter jejuni is the most common cause of bacterial gastroenteritis in Luxembourg, with a marked seasonal peak during summer. The majority of these infections are thought to be sporadic, and the relative contribution of potential sources and reservoirs is still poorly understood. We monitored human cases from June to September 2006 (n = 124) by molecular characterization of isolates with the aim of rapidly detecting temporally related cases. In addition, isolates from poultry meat (n = 36) and cattle cecal contents (n = 48) were genotyped for comparison and identification of common clusters between veterinary and human C. jejuni populations. A total of 208 isolates were typed by sequencing the fla short variable region, macrorestriction analysis resolved by pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). We observed a high diversity of human strains during a given summer season. Poultry and human isolates had a higher diversity of sequence types than isolates of bovine origin, for which clonal complexes CC21 (41.6%) and CC61 (18.7%) were predominant. CC21 was also the most common complex found among human isolates (21.8%). The substantial concordance between PFGE and MLST results for this last group of strains suggests that they are clonally related. Our study indicates that while poultry remains an important source, cattle could be an underestimated reservoir of human C. jejuni cases. Transmission mechanisms of cattle-specific strains warrant further investigation.

Broiler Campylobacter Contamination and Human Campylobacteriosis in Iceland

ABSTRACT To examine whether there is a relationship between the degree of Campylobacter contamination observed in product lots of retail Icelandic broiler chicken carcasses and the incidence of human disease, 1,617 isolates from 327 individual product lots were genetically matched (using the flaA short variable region [SVR[) to 289 isolates from cases of human campylobacteriosis whose onset was within approximately 2 weeks from the date of processing. When there was genetic identity between broiler isolates and human isolates within the appropriate time frame, a retail product lot was classified as implicated in human disease. According to the results of this analysis, there were multiple clusters of human disease linked to the same process lot or lots. Implicated and nonimplicated retail product lots were compared for four lot descriptors: lot size, prevalence, mean contamination, and maximum contamination (as characterized by direct rinse plating). For retail product distributed fresh, Mann-Whitney U tests showed that implicated product lots had significantly (P = 0.0055) higher mean contamination than nonimplicated lots. The corresponding median values were 3.56 log CFU/carcass for implicated lots and 2.72 log CFU/carcass for nonimplicated lots. For frozen retail product, implicated lots were significantly (P = 0.0281) larger than nonimplicated lots. When the time frame was removed, retail product lots containing Campylobacter flaA SVR genotypes also seen in human disease had significantly higher mean and maximum contamination numbers than lots containing no genotypes seen in human disease for both fresh and frozen product. Our results suggest that cases of broiler-borne campylobacteriosis may occur in clusters and that the differences in mean contamination levels may provide a basis for regulatory action that is more specific than a presence-absence standard.