To identify traits that predict avian pathogenic Escherichia coli (APEC) virulence, 124 avian E. coli isolates of known pathogenicity and serogroup were subjected to virulence genotyping and phylogenetic typing. The results were analyzed by multiple-correspondence analysis. From this analysis, five genes carried by plasmids were identified as being the most significantly associated with highly pathogenic APEC strains: iutA, hlyF, iss, iroN, and ompT. A multiplex PCR panel targeting these five genes was used to screen a collection of 994 avian E. coli isolates. APEC isolates were clearly distinguished from the avian fecal E. coli isolates by their possession of these genes, suggesting that this pentaplex panel has diagnostic applications and underscoring the close association between avian E. coli virulence and the possession of ColV plasmids. Also, the sharp demarcation between APEC isolates and avian fecal E. coli isolates in their plasmid-associated virulence gene content suggests that APEC isolates are well equipped for a pathogenic lifestyle, which is contrary to the widely held belief that most APEC isolates are opportunistic pathogens. Regardless, APEC isolates remain an important problem for poultry producers and a potential concern for public health professionals, as growing evidence suggests a possible role for APEC in human disease. Thus, the pentaplex panel described here may be useful in detecting APEC-like strains occurring in poultry production, along the food chain, and in human disease. This panel may be helpful toward clarifying potential roles of APEC in human disease, ascertaining the source of APEC in animal outbreaks, and identifying effective targets of avian colibacillosis control.

Emerging evidence indicates a central role for the microbiome in immunity. However, causal evidence in humans is sparse. Here, we administered broad-spectrum antibiotics to healthy adults prior and subsequent to seasonal influenza vaccination. Despite a 10,000-fold reduction in gut bacterial load and long-lasting diminution in bacterial diversity, antibody responses were not significantly affected. However, in a second trial of subjects with low pre-existing antibody titers, there was significant impairment in H1N1-specific neutralization and binding IgG1 and IgA responses. In addition, in both studies antibiotics treatment resulted in (1) enhanced inflammatory signatures (including AP-1/NR4A expression), observed previously in the elderly, and increased dendritic cell activation;(2) divergent metabolic trajectories, with a 1,000-fold reduction in serum secondary bile acids, which was highly correlated with AP-1/NR4A signaling and inflammasome activation. Multiomics integration revealed significant associations between bacterial species and metabolic phenotypes, highlighting a key role for the microbiome in modulating human immunity.

ColV plasmids have long been associated with the virulence of Escherichia coli, despite the fact that their namesake trait, ColV production, does not appear to contribute to virulence. Such plasmids or their associated sequences appear to be quite common among avian pathogenic E. coli (APEC) and are strongly linked to the virulence of these organisms. In the present study, a 180-kb ColV plasmid was sequenced and analyzed. This plasmid, pAPEC-O2-ColV, possesses a 93-kb region containing several putative virulence traits, including iss, tsh, and four putative iron acquisition and transport systems. The iron acquisition and transport systems include those encoding aerobactin and salmochelin, the sit ABC iron transport system, and a putative iron transport system novel to APEC, eit. In order to determine the prevalence of the virulence-associated genes within this region among avian E. coli strains, 595 APEC and 199 avian commensal E. coli isolates were examined for genes of this region using PCR. Results indicate that genes contained within a portion of this putative virulence region are highly conserved among APEC and that the genes of this region occur significantly more often in APEC than in avian commensal E. coli. The region of pAPEC-O2-ColV containing genes that are highly prevalent among APEC appears to be a distinguishing trait of APEC strains.Avian pathogenic Escherichia coli (APEC) strains are the etiologic agents of colibacillosis in birds, an important problem in the poultry industry (7). Along with uropathogenic E. coli (UPEC) and the E. coli strain causing neonatal meningitis or septicemias, APEC strains fall under the category of extraintestinal pathogenic E. coli (ExPEC) (39). ExPEC strains are characterized by the possession of virulence factors that enable their extraintestinal lifestyle and make them distinct from commensal and diarrheagenic E. coli strains (39). Among APEC strains, the iroBCDEN locus (11), shown to encode the siderophore salmochelin in Salmonella enterica (16), the aerobactin operon (51), and the yersiniabactin operon (21) are iron acquisition systems thought to contribute to virulence. Other putative APEC virulence factors include those contributing to complement resistance, such as the increased serum survival gene (iss) (31,33,37); tsh, the temperature-sensitive hemagglutinin gene (34); and the presence of ColV plasmids (37). In fact, it appears that large virulence plasmids, including ColV plasmids, are a defining feature of the APEC pathotype (37, 44).ColV and ColV plasmids have interested scientists for many years, with Gratia first describing ColV as "principle V" in 1925 (53). ColV plasmids, which encode ColV production, typically range in size from 80 to 180 kb (53) and encode traits such as aerobactin production (51) and complement resistance (31). Unlike other colicins, ColV itself is a small protein that is exported from the cell and behaves more like a microcin, disrupting the formation of cell membrane potential required for energy production (53). The ColV operon ...

Since extraintestinal pathogenic Escherichia coli (ExPEC) strains from human and avian hosts encounter similar challenges in establishing infection in extraintestinal locations, they may share similar contents of virulence genes and capacities to cause disease. In the present study, 1,074 ExPEC isolates were classified by phylogenetic group and possession of 67 other traits, including virulence-associated genes and plasmid replicon types. These ExPEC isolates included 452 avian pathogenic E. coli strains from avian colibacillosis, 91 neonatal meningitis E. coli (NMEC) strains causing human neonatal meningitis, and 531 uropathogenic E. coli strains from human urinary tract infections. Cluster analysis of the data revealed that most members of each subpathotype represent a genetically distinct group and have distinguishing characteristics. However, a genotyping cluster containing 108 ExPEC isolates was identified, heavily mixed with regard to subpathotype, in which there was substantial trait overlap. Many of the isolates within this cluster belonged to the O1, O2, or O18 serogroup. Also, 58% belonged to the ST95 multilocus sequence typing group, and over 90% of them were assigned to the B2 phylogenetic group typical of human ExPEC strains. This cluster contained strains with a high number of both chromosome-and plasmid-associated ExPEC genes. Further characterization of this ExPEC subset with zoonotic potential urges future studies exploring the potential for the transmission of certain ExPEC strains between humans and animals. Also, the widespread occurrence of plasmids among NMEC strains and members of the mixed cluster suggests that plasmid-mediated virulence in these pathotypes warrants further attention. Speculation has long existed regarding a food-borne origin for extraintestinal pathogenic Escherichia coli (ExPEC) strains (28,33,42) and has spawned recent work investigating E. coli contaminants of food and the ExPEC strains of food-producing animals (15,18,24,40). Of particular interest in this regard are avian pathogenic E. coli (APEC) strains that cause colibacillosis in poultry (3,9,35,36,38). Although it has been widely assumed that most APEC strains do not possess zoonotic potential, recent reports have suggested otherwise for certain groups of strains (2,9,29,30,35,36), and some researchers have demonstrated that APEC strains and their plasmids may be transmitted to human hosts (27,38). Recently, APEC isolates have been compared to ExPEC isolates from human urinary tract infections (UTIs) and neonatal meningitis, revealing that these "subpathotypes" have some overlap in serogroups, phylogenetic groups, virulence genotypes, and abilities to cause disease in certain animal models (9,30,31,35,36). The validity of these observations was sustained by comparison of the first APEC genome sequence with sequenced ExPEC isolates of humans (25), which revealed that few differences existed between the sequenced APEC strain (APEC O1) and human strains. In fact, results of an in silico multilocus sequence typing ...