Characterizing the APEC pathotype

The purpose of this study was to compare avian pathogenic (APEC) isolates to fecal isolates of apparently healthy poultry (avian fecal or AFEC) by their possession of various traits in order to ascertain whether APEC and AFEC are distinct and if the APEC strains constitute a distinct pathotype. Four hundred and fifty-one APEC and one hundred and four AFEC isolates were examined for possession of traits associated with the virulence of human extraintestinal pathogenic (ExPEC) as well as APEC. Several of the genes occurred in the majority of APEC and only infrequently in AFEC, including ,, ,, , , , and. Of these genes, several have been found on large plasmids in APEC. Other genes occurred in significantly more APEC than AFEC but did not occur in the majority of APEC. Isolates were also evaluated by serogroup, lactose utilization, and hemolytic reaction. Twenty-nine and a half percent of the APEC and forty-two and three tenths percent of the AFEC were not serogrouped because they were not typeable with standard antisera, typed to multiple serogroups, were rough, autoagglutinated, or were not done. Around 65% of the typeable APEC (205 isolates) and AFEC (41 isolates) were classified into shared serogroups, and about a third of both fell into APEC- (113 isolates) or AFEC- (19 isolates) unique serogroups. Most were able to use lactose. No isolate was hemolytic. Overall, the majority of the APEC isolates surveyed shared a common set of putative virulence genes, many of which have been localized to an APEC plasmid known as pTJ100. This common set of genes may prove useful in defining an APEC pathotype

Spoilage Identification of Beef Using an Electronic Nose System

A commercially available Cyranose-320. conducting polymer-based electronic nose system was used to analyze the volatile organic compounds emanating from fresh beef strip loins (M. Longisimmus lumborum) stored at 4°C and 10°C. Two statistical techniques, i.e., linear discriminant analysis (LDA) and quadratic discriminant analysis (QDA), were used to develop classification models from the collected sensor signals. The performances of the developed models were validated by two different methods: leave-1-out cross-validation, and bootstrapping. The developed models classified meat samples based on the microbial population into “unspoiled” (microbial counts \u3c6.0 log10 cfu/g) and “spoiled” (microbial counts \u3e 6.0 log10 cfu/g). Overall, quadratic discriminant-based classification models performed better than linear discriminant analysis based models. For the meat samples stored at 10°C, the highest classification accuracies obtained by the LDA method with leave-1-out and bootstrapping validations were 87.10% and 85.87%, respectively. On the other hand, classification by QDA and subsequent validation by leave-1-out and bootstrapping provided highest accuracies of 87.5% and 97.38%, respectively. For samples stored at 4°C, the LDA method provided highest classification accuracies of 79.17% and 85.64% using leave-1-out and bootstrapping validation, respectively. When the QDA method was used, the highest classification accuracies obtained for the samples stored at 4°C were 87.50% and 98.48%, respectively, with leave-1-out and bootstrapping validations

Comparison of Extraintestinal Pathogenic Escherichia coli Strains from Human and Avian Sources Reveals a Mixed Subset Representing Potential Zoonotic Pathogens

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

Genotypic and Phenotypic Traits That Distinguish Neonatal Meningitis-Associated Escherichia coli from Fecal E. coli Isolates of Healthy Human Hosts

Neonatal meningitis Escherichia coli (NMEC) is one of the top causes of neonatal meningitis worldwide. Here, 85 NMEC and 204 fecal E. coli isolates from healthy humans (HFEC) were compared for possession of traits related to virulence, antimicrobial resistance, and plasmid content. This comparison was done to identify traits that typify NMEC and distinguish it from commensal strains to refine the definition of the NMEC subpathotype, identify traits that might contribute to NMEC pathogenesis, and facilitate choices of NMEC strains for future study. A large number of E. coli strains from both groups were untypeable, with the most common serogroups occurring among NMEC being O18, followed by O83, O7, O12, and O1. NMEC strains were more likely than HFEC strains to be assigned to the B2 phylogenetic group. Few NMEC or HFEC strains were resistant to antimicrobials. Genes that best discriminated between NMEC and HFEC strains and that were present in more than 50% of NMEC isolates were mainly from extraintestinal pathogenic E. coli genomic and plasmid pathogenicity islands. Several of these defining traits had not previously been associated with NMEC pathogenesis, are of unknown function, and are plasmid located. Several genes that had been previously associated with NMEC virulence did not dominate among the NMEC isolates. These data suggest that there is much about NMEC virulence that is unknown and that there are pitfalls to studying single NMEC isolates to represent the entire subpathotype

Comparative Analysis of Phylogenetic Assignment of Human and Avian ExPEC and Fecal Commensal Escherichia coli Using the (Previous and Revised) Clermont Phylogenetic Typing Methods and its Impact on Avian Pathogenic Escherichia coli (APEC) Classification

The Clermont scheme has been used for subtyping of Escherichia coli since it was initially described in early 2000. Since then, researchers have used the scheme to type and sub-type commensal E. coli and pathogenic E. coli, such as extraintestinal pathogenic E. coli (ExPEC), and compare their phylogenetic assignment by pathogenicity, serogroup, distribution among ExPEC of different host species and complement of virulence and resistance traits. Here, we compare assignments of human and avian ExPEC and commensal E. coli using the old and revised Clermont schemes to determine if the new scheme provides a refined snapshot of isolate classification. 1,996 E. coli from human hosts and poultry, including 84 human neonatal meningitis E. coli isolates, 88 human vaginal E. coli, 696 human uropathogenic E. coli, 197 healthy human fecal E. coli, 452 avian pathogenic E. coli (APEC), 200 retail poultry E. coli, 80 crop and gizzard E. coli from healthy poultry at slaughter and 199 fecal E. coli from healthy birds at slaughter. All isolates were subject to phylogenetic analysis using the Clermont et al. (2000, 2013) schemes and compared to determine the effect of the new classification on strain designation. Most of the isolates’ strain designation remained where they were originally assigned. Greatest designation change occurred in APEC where 53.8% of isolates were reclassified; while classification rates among human strains ranged from 8 to 14%. However, some significant changes were observed for UPEC associated strains with significant (P < 0.05) designation changes observed from A to C and D to E or F phylogenetic types; a similar designation change was noted among NMEC for D to F designation change. Among the APEC significant designation changes were observed from A to C and D to E and F. These studies suggest that the new scheme provides a tighter and more meaningful definition of some ExPEC; while the new typing scheme has a significant impact on APEC classification. A comparison of phylogenetic group assignment by content of virulence, resistance, replicon and pathogenicity island genes in APEC suggests that insertion of pathogenicity islands into the genome appears to correlate closely with revised phylogenetic assignment.This article is published as Logue, Catherine M., Yvonne Wannemuehler, Bryon A. Nicholson, Curt Doetkott, Nicolle L. Barbieri, and Lisa K. Nolan. "Comparative analysis of phylogenetic assignment of human and avian ExPEC and fecal commensal Escherichia coli using the (previous and revised) Clermont phylogenetic typing methods and its impact on avian pathogenic Escherichia coli (APEC) classification." Frontiers in Microbiology 8 (2017): 283. DOI: 10.3389/fmicb.2017.00283. Copyright 2017 Logue, Wannemuehler, Nicholson, Doetkott, Barbieri and Nolan. Attribution 4.0 International (CC BY 4.0). Posted with permission

Characterizing the APEC pathotype

The purpose of this study was to compare avian pathogenic (APEC) isolates to fecal isolates of apparently healthy poultry (avian fecal or AFEC) by their possession of various traits in order to ascertain whether APEC and AFEC are distinct and if the APEC strains constitute a distinct pathotype. Four hundred and fifty-one APEC and one hundred and four AFEC isolates were examined for possession of traits associated with the virulence of human extraintestinal pathogenic (ExPEC) as well as APEC. Several of the genes occurred in the majority of APEC and only infrequently in AFEC, including ,, ,, , , , and. Of these genes, several have been found on large plasmids in APEC. Other genes occurred in significantly more APEC than AFEC but did not occur in the majority of APEC. Isolates were also evaluated by serogroup, lactose utilization, and hemolytic reaction. Twenty-nine and a half percent of the APEC and forty-two and three tenths percent of the AFEC were not serogrouped because they were not typeable with standard antisera, typed to multiple serogroups, were rough, autoagglutinated, or were not done. Around 65% of the typeable APEC (205 isolates) and AFEC (41 isolates) were classified into shared serogroups, and about a third of both fell into APEC- (113 isolates) or AFEC- (19 isolates) unique serogroups. Most were able to use lactose. No isolate was hemolytic. Overall, the majority of the APEC isolates surveyed shared a common set of putative virulence genes, many of which have been localized to an APEC plasmid known as pTJ100. This common set of genes may prove useful in defining an APEC pathotype.This article is from Veterinary Research 36, no. 2 (2005): 241–256, doi:10.1051/vetres:2004057.</p

Identification of Minimal Predictors of Avian Pathogenic Escherichia coli Virulence for Use as a Rapid Diagnostic Tool

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. coliisolates. APEC isolates were clearly distinguished from the avian fecal E. coliisolates by their possession of these genes, suggesting that this pentaplex panel has diagnostic applications and underscoring the close association between avianE. 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.This article is from Journal of Clinical Microbiology 46, no. 12 (December 2008): 3987–3996, doi:10.1128/JCM.00816-08.</p