Salmonella gallinarum strains from outbreaks of fowl typhoid fever in Southern Africa closely related to SG9R vaccines.

Introduction: Salmonella enterica subspecies enterica serovar Gallinarum biovar Gallinarum (SG) is associated with fowl typhoid fever, and the attenuated rough strain SG9R is widely used as a vaccine in many regions. Reversion to virulence of vaccine strains was suspected as the cause during recent fowl typhoid fever outbreaks in poultry in South Africa and Eswatini. Methods: To compare nine field isolates with global wild-type SG9 strains and the two commercial SG9R vaccines in use, Nobilis® SG9R and Cevac®-SG, we used whole-genome comparison with single-nucleotide polymorphism (SNP) detection. Results: SNP phylogenic analysis showed that all the southern African field isolates were more closely related to the vaccine strains than wild-type SG9 strains. Furthermore, SNPs in the pyruvate dehydrogenase (aceE) and/or lipopolysaccharide 1,2-glucosyltransferase (rfaJ) genes, which are known markers of attenuation, were found in four of the field isolates along with intact spv, SPI-1, and SPI-2 gene clusters, providing conclusive evidence that these four isolates were originally vaccine strains that reverted to virulence. Five other field isolates lacked the SG9R attenuation markers, but variant analysis identified an SNP in the yihX gene, insertions in the ybjX and hydH genes, and deletions in the ftsK and sadA genes that were shared between the field isolates and vaccine strains but absent in wild-type SG9, indicating that these field isolates were also likely revertant vaccines. Discussion: Overall, this study highlights different mechanisms of reversion of two commercial vaccines, where virulence caused by field isolates closely related to the Nobilis® SG9R vaccine was associated with the restoration of intact virulence gene clusters, and those derived from the Cevac®-SG vaccine were characterized by point mutations resulting in restored aceE and rfaJ genes. A possible new marker of attenuation was identified as a point mutation in the yihX gene, as well as four new candidate genes that could potentially be used to distinguish current vaccine strains from wild-type strains using PCR assays.

Evidence for Multidrug Resistance in Nonpathogenic Mycoplasma Species Isolated from South African Poultry.

One hundred seventy-eight mycoplasma strains isolated from South African poultry flocks between 2003 and 2015 were identified by full-genome sequencing and phylogenetic analysis of the 16S rRNA gene and were classified as follows: Mycoplasma gallisepticum (25%), M. gallinarum (25%), M. gallinaceum, (23%), M. pullorum (14%), M. synoviae (10%), and M. iners (3%), as well as one Acheoplasma laidlawii strain (1%). MIC testing was performed on the axenic samples, and numerous strains of each species were resistant to either chlortetracycline or tylosin or both, with variable sensitivity to enrofloxacin. The strains of all species tested remained sensitive to tiamulin, except for one M. gallinaceum sample that demonstrated intermediate sensitivity. The mutation of A to G at position 2059 (A2059G) in the 23S rRNA gene, which is associated with macrolide resistance, was found in the South African M. gallisepticum and M. synoviae strains, as well as a clear correlation between macrolide resistance in M. gallinarum and M. gallinaceum and mutations G354A and G748A in the L4 ribosomal protein and 23S rRNA gene, respectively. No correlation between resistance and point mutations in the genes studied could be found for M. pullorum Only a few strains were resistant to enrofloxacin, apart from one M. synoviae strain with point mutation D420N, which has been associated with quinolone resistance, and no other known markers for quinolone resistance were found in this study. Proportionally more antimicrobial-resistant strains were detected in M. gallinaceum, M. gallinarum, and M. pullorum than in M. gallisepticum and M. synoviae Of concern, three M. gallinaceum strains showed multidrug resistance to chlortetracycline, tylosin, and oxytetracycline.IMPORTANCE Nonpathogenic poultry Mycoplasma species are often overlooked due to their lesser impact on poultry health and production compared to the OIE-listed pathogenic strains M. gallisepticum and M. synoviae The use of antimicrobials as in-feed growth promoters and for the control of mycoplasmosis is common in poultry production across the world. Here, we provide evidence that certain nonpathogenic Mycoplasma species are acquiring multidrug resistance traits. This would have significant implications if these species, for which no vaccines are applied, are able to transfer their antibiotic resistance genes to other mycoplasmas and bacteria that may enter the human food chain.

Complete Genome Sequence of Mycoplasma pullorum Isolated from Domestic Chickens.

The 1,007,172-bp complete genome of Mycoplasma pullorum strain B359_6, isolated from domestic chickens, has been sequenced, assembled, and annotated.

Complete Genome Sequence of Mycoplasma gallinaceum.

Mycoplasma gallinaceum strain B2096 8B was isolated from domestic chickens in South Africa. The 845,307-bp full genome was sequenced, assembled, and annotated.