Naola Ferguson-Noel

Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum

Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches. Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house finches (Carpodacus mexicanus), a common North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG, as well as in poultry outgroups. Using whole-genome sequences of 12 House Finch isolates across a 13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House Finch isolates of only ∼2% of ancestral poultry strains and a nucleotide substitution rate of 0.8−1.2×10−5 per site per year both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for bacteria. We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to the House Finch host, but after the invasion of House Finches there is progressive loss of CRISPR repeat diversity, and recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG strains retain only ∼50% of the CRISPR repertoire founding (1994–95) strains and have lost the CRISPR–associated genes required for CRISPR function. Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs.

The Mycoplasma gallisepticum 16S–23S rRNA Intergenic Spacer Region Sequence as a Novel Tool for Epizootiological Studies

Abstract Mycoplasma gallisepticum (MG) contains two sets of rRNA genes (5S, 16S and 23S) in its genome, but only one of the two is organized in an operon cluster and contains a unique 660-nucleotide intergenic spacer region (IGSR) between the 16S and the 23S rRNA genes. We designed a polymerase chain reaction (PCR) for the specific amplification of the complete MG IGSR segment. The MG IGSR PCR was tested on 18 avian mollicute species and was confirmed as MG specific. The reaction sensitivity was demonstrated by comparing it to the well-established MG mgc2 PCR. The MG IGSR sequence was found to be highly variable (discrimination [D] index of 0.950) among a variety of MG laboratory strains, vaccine strains, and field isolates. The sequencing of the MG IGSR appears to be a valuable single-locus sequence typing (SLST) tool for MG isolate differentiation in diagnostic cases and epizootiological studies.

Detection and Differentiation of Avian Mycoplasmas by Surface-Enhanced Raman Spectroscopy Based on a Silver Nanorod Array

ABSTRACT Mycoplasma gallisepticum is a bacterial pathogen of poultry that is estimated to cause annual losses exceeding

Role of Mycoplasma synoviae in Commercial Layer Escherichia coli Peritonitis Syndrome

780 million. The National Poultry Improvement Plan guidelines recommend regular surveillance and intervention strategies to contain M. gallisepticum infections and ensure mycoplasma-free avian stocks, but several factors make detection of M. gallisepticum and diagnosis of M. gallisepticum infection a major challenge. Current techniques are laborious, require special expertise, and are typically plagued by false results. In this study, we describe a novel detection strategy which uses silver nanorod array–surface-enhanced Raman spectroscopy (NA-SERS) for direct detection of avian mycoplasmas. As a proof of concept for use in avian diagnostics, we used NA-SERS to detect and differentiate multiple strains of avian mycoplasma species, including Acholeplasma laidlawii, Mycoplasma gallinarum, Mycoplasma gallinaceum, Mycoplasma synoviae, and M. gallisepticum, including vaccine strains 6/85, F, and ts-11. Chemometric multivariate analysis of spectral data was used to classify these species rapidly and accurately, with >93% sensitivity and specificity. Furthermore, NA-SERS had a lower limit of detection that was 100-fold greater than that of standard PCR and comparable to that of real-time quantitative PCR. Detection of M. gallisepticum in choanal cleft swabs from experimentally infected birds yielded good sensitivity and specificity, suggesting that NA-SERS is applicable for clinical detection.

Influence of Swab Material on the Detection of Mycoplasma gallisepticum and Mycoplasma synoviae by Real-Time PCR

Abstract Mycoplasma synoviae (MS) is an important pathogen of domestic poultry and is prevalent in commercial layers. During the last decade Escherichia coli peritonitis became a major cause of layer mortality. The possible role of MS in the E. coli peritonitis syndrome of laying hens was studied. Four groups of 64 mycoplasma-free commercial layers at the onset of lay (about 80% daily production) were challenged with a virulent MS strain or a virulent avian E. coli strain or both. The four experimental groups were identified as follows: negative control, E. coli, MS, and MS plus E. coli. A typical E. coli peritonitis mortality was reproduced and included one, three, zero, and five birds in the negative control, E. coli, MS, and MS plus E. coli groups, respectively. Only the increased mortality in the MS plus E. coli group had statistical significance. Four weeks postchallenge 10 clinically normal birds from each of the four experimental groups were necropsied. All of the examined birds in the two MS-challenged groups demonstrated severe tracheal lesions. Body cavity lesions were detected in two and four birds in the MS and MS plus E. coli groups, respectively. The results demonstrate a possible pathogenesis mechanism of respiratory origin with regard to the layer E. coli peritonitis syndrome, show the MS pathological effect in layers, and indicate that a virulent MS strain can act as a complicating factor in the layer E. coli peritonitis syndrome.

The Efficacy of Three Commercial Mycoplasma gallisepticum Vaccines in Laying Hens

SUMMARY. Recent reports have shown an increased recovery of cells from flocked nylon swabs which may improve the specimen quality and the real sensitivity of diagnostic tests in a clinical setting. In this study, the detection of Mycoplasma gallisepticum (MG) and M. synoviae (MS), using dry swabs of different materials (nylon flocked, cotton, and polyester), was investigated using real-time TaqMan® PCR protocols. Different types of samples, including dilutions of pure broth cultures of MG and MS as well as swabs from tracheas of experimentally infected chickens and field cases of infection, were analyzed. There were no statistical differences in real-time PCR results among the different swab types (P < 0.05), indicating that this is not likely to be a significant factor in MG and MS detection by this method. RESUMEN. Influencia de material del hisopo en la detección de Mycoplasma gallisepticum y Mycoplasma synoviae por PCR en tiempo real. Informes recientes han demostrado un aumento de la recuperación de las células a partir de hisopos de nylon agrupados lo que puede mejorar la calidad de la muestra y la sensibilidad real de las pruebas de diagnóstico en un entorno clínico. En este estudio, se analizó la detección de Mycoplasma gallisepticum y de M. synoviae, utilizando hisopos secos de diferentes materiales (nylon agrupados, algodón y poliéster), y mediante un protocolo de PCR en tiempo real con la tecnología TaqMan®. Se analizaron los diferentes tipos de muestras, incluyendo las diluciones de cultivos puros en caldo de M. gallisepticum y de M. synoviae, así como hisopos de tráquea de pollos infectados experimentalmente y los casos de infecciones en el campo. No se observaron diferencias estadísticas en los resultados de PCR en tiempo real entre los diferentes tipos de hisopo (P < 0.05), indicando que no es probable que el tipo de material de hisopo sea un factor significativo en la detección de M. gallisepticum y de M. synoviae por este método.

Comparison of multiple genes and 16S–23S rRNA intergenic space region for their capacity in high resolution melt curve analysis to differentiate Mycoplasma gallisepticum vaccine strain ts-11 from field strains

SUMMARY. The efficacy of three commercial Mycoplasma gallisepticum (MG) immunizing agents—a bacterin, a recombinant fowlpox-MG vaccine, and a live F-strain vaccine—was compared in specific-pathogen-free hens in egg production. Three groups of 25 chickens were vaccinated with one of the vaccines at 10 wk of age and 25 birds were not vaccinated. At 25 wk of age (and approximately 50% egg production), 20 birds from each of the three vaccinated groups and 15 nonvaccinated controls were challenged with virulent R-strain via aerosol; the birds were necropsied and evaluated at 10 days post-challenge. The MG bacterin and live F-strain vaccinations were both protective and resulted in significant differences in air sac lesions, tracheal lesions, and ovarian regression compared to the nonvaccinated controls and the recombinant fowlpox-MG vaccine (P ≤ 0.05). The evaluation of ovarian regression is a useful method of testing the efficacy of MG vaccines in laying hens. RESUMEN. Eficacia de tres vacunas comerciales contra Mycoplasma gallisepticum en gallinas ponedoras. La eficacia de tres agentes inmunizantes comerciales de Mycoplasma gallisepticum: una bacterina, una vacuna recombinante de viruela aviar/M. gallisepticum, y una vacuna viva con la cepa F, se compararon en gallinas libres de patógenos específicos que estaban en la etapa de producción de huevos. Tres grupos de 25 pollos fueron vacunados con una de las vacunas a las 10 semanas de edad y se dejaron 25 aves no vacunadas. A las 25 semanas de edad (y aproximadamente alrededor del 50% de la producción de huevo), 20 aves de cada uno de los tres grupos vacunados y 15 controles no vacunados se desafiaron con la cepa virulenta R, a través de aerosoles, se evaluaron las aves y se les practicó la necropsia a los 10 días después del desafío. La bacterina de M. gallisepticum y la vacuna viva con la cepa F, confirieron protección y mostraron diferencias significativas en las lesiones en los sacos aéreos, en las lesiones traqueales, y la regresión del ovario en comparación con los controles no vacunados y con las aves vacunadas con la vacuna recombinante de viruela aviar/M. gallisepticum (P ≤ 0.05). La evaluación de la regresión de ovario es un método útil para probar la eficacia de las vacunas contra M. gallisepticum en las gallinas ponedoras.

The development and application of a Mycoplasma gallisepticum sequence database

Mycoplasma gallisepticum (MG) is an important avian pathogen causing significant economic losses in the global poultry industry. In an attempt to compare and evaluate existing genotyping methods for differentiation of MG strains/isolates, high resolution melt (HRM) curve analysis was applied to 5 different PCR methods targeting vlhA, pvpA, gapA, mgc2 genes and 16S-23S rRNA intergenic space region (IGSR). To assess the discriminatory power of PCR-HRM of examined genes and IGSR, MG strains ts-11, F, 6/85 and S6, and, initially, 8 field isolates were tested. All MG strains/isolates were differentiated using PCR-HRM curve analysis and genotype confidence percentage (GCP) values of vlhA and pvpA genes, while only 0, 3 and 4 out of 12 MG strains/isolates were differentiated using gapA, mgc2 genes and IGSR, respectively. The HRM curve analysis of vlhA and pvpA genes was found to be highly correlated with the genetic diversity of the targeted genes confirmed by sequence analysis of amplicons generated from MG strains. The potential of the vlhA and pvpA genes was also demonstrated for genotyping of 12 additional MG strains from Europe and the USA. Results from this study provide a direct comparison between genes previously used in sequencing-based genotyping methods for MG strain identification and highlight the usefulness of vlhA and pvpA HRM curve analyses as rapid and reliable tools specially for diagnosis and differentiation of MG strains used here.

Evaluation of Mycoplasma gallisepticum K-Strain as a Live Vaccine in Chickens

Molecular analysis was conducted on 36 Mycoplasma gallisepticum DNA extracts from tracheal swab samples of commercial poultry in seven South African provinces between 2009 and 2012. Twelve unique M. gallisepticum genotypes were identified by polymerase chain reaction and sequence analysis of the 16S-23S rRNA intergenic spacer region (IGSR), M. gallisepticum cytadhesin 2 (mgc2), MGA_0319 and gapA genetic regions. The DNA sequences of these genotypes were distinct from those of M. gallisepticum isolates in a database composed of sequences from other countries, vaccine and reference strains. The most prevalent genotype (SA-WT#7) was detected in samples from commercial broilers, broiler breeders and layers in five provinces. South African M. gallisepticum sequences were more similar to those of the live vaccines commercially available in South Africa, but were distinct from that of F strain vaccine, which is not registered for use in South Africa. The IGSR, mgc2 or MGA_0319 sequences of three South African genotypes were identical to those of the ts-11 vaccine strain, necessitating a combination of mgc2 and IGSR targeted sequencing to differentiate South African wild-type genotypes from ts-11 vaccine. To identify and differentiate all 12 wild-types, mgc2, IGSR and MGA_0319 sequencing was required. Sequencing of gapA was least effective at strain differentiation. This research serves as a model for the development of an M. gallisepticum sequence database, and illustrates its application to characterize M. gallisepticum genotypes, select diagnostic tests and better understand the epidemiology of M. gallisepticum.

Identification of strain-specific sequences that distinguish a Mycoplasma gallisepticum vaccine strain from field isolates

SUMMARY. We evaluated the pathogenicity of three live Mycoplasma gallisepticum (MG) vaccine candidates by infection via aerosol of 3-wk-old chickens with log phase broth cultures (trial 1). Two of the candidates (K3020 and K4649A) colonized only 10% and 20% of the chickens, respectively, unlike K2101 (K-strain), which was reisolated from all of the vaccinated chickens tested. K-strain inoculation did not result in significant air sac or tracheal lesions in chickens at 10 and 39 days postinfection (P ≤ 0.05). The efficacy of K-strain as a live vaccine was evaluated in trial 2, by challenge of vaccinated chickens with virulent R-strain via aerosol at 6 wk postvaccination. K-strain vaccination resulted in significant protection from air sac and tracheal lesions (P ≤ 0.05). The K-strain was further investigated to evaluate transmissibility (trial 3), colonization and persistence of infection following aerosol administration (trial 4), genetic and phenotypic stability following back passage through chickens (trial 5), and vertical transmission (trial 6). The K-strain had a low rate of horizontal transmission; it remained primarily in the respiratory system of inoculated birds and persisted in the upper respiratory tract for the duration of the trial 4 (5 mo). There was no increase in virulence of K-strain when it was back passaged five times through chickens, and no vertical transmission of K-strain was detected. K-strain showed great potential as a safe and effective live MG vaccine.