Observations on macrolide resistance and susceptibility testing performance in field isolates collected from clinical bovine respiratory disease cases

Abstract

The objectives of this study were; first, to describe gamithromycin susceptibility of Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni isolated from cattle diagnosed with bovine respiratory disease (BRD) and previously treated with either gamithromycin for control of BRD (mass medication=MM) or sham-saline injected (control=CON); second, to describe the macrolide resistance genes present in genetically typed M. haemolytica isolates; third, use whole-genome sequencing (WGS) to correlate the phenotypic resistance and genetic determinants for resistance among M. haemolytica isolates. M. haemolytica (n=276), P. multocida (n=253), and H. somni (n=78) were isolated from feedlot cattle diagnosed with BRD. Gamithromycin susceptibility was determined by broth microdilution. Whole-genome sequencing was utilized to determine the presence/absence of macrolide resistance genes and to genetically type M. haemolytica. Generalized linear mixed models were built for analysis. There was not a significant difference between MM and CON groups in regards to the likelihood of culturing a resistant isolate of M. haemolytica or P. multocida. The likelihood of culturing a resistant isolate of M. haemolytica differed significantly by state of origin in this study. A single M. haemolytica genetic subtype was associated with an over whelming majority of the observed resistance. H. somni isolation counts were low and statistical models would not converge. Phenotypic resistance was predicted with high sensitivity and specificity by WGS. Additional studies to elucidate the relationships between phenotypic expression of resistance/genetic determinants for resistance and clinical response to antimicrobials are necessary to inform judicious use of antimicrobials in the context of relieving animal disease and suffering.

Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes

“…Another 276 isolates from North American cattle that were previously sequenced at the same level of coverage were also included in this study [29, 30]. The isolates were arranged into two collections, Zoetis and KSU-USMARC, that each consisted of two groups (Table 1, Additional file 1).…”

“…Previously sequenced isolates are included in this group ( n  = 276), [29, 30]. All other isolates of both collections were sequenced in this study ( n  = 857)…”

“…The genomes of 505 isolates from this group were sequenced for this study. The genomes of the remaining 276 isolates were sequenced as previously described [29, 30], (Additional file 1). …”

“…This included all 317 isolates in the Zoetis collection, all 35 isolates in the group of nasopharyngeal non-clinical isolates, and 505 of the 781 isolates in the group of clinical and non-clinical isolates. Genomic sequencing of the remaining 276 isolates in the group of clinical and non-clinical isolates has been described elsewhere [29, 30]. The sequence data of those 276 isolates were included in this study for nucleotide polymorphism identification and downstream analyses.…”

“…For example, ICE Mh1 has five antibiotic resistance genes, while yet another putative homolog found in M. haemolytica strain USDA_ARS_USMARC 183 has none [23]. Homologs to ICE Pmu1 and ICE Mh1 that contain antibiotic resistance genes do not appear restricted to one geographical region of North America [21, 27, 29], and may have a wide distribution and role in M. haemolytica antibiotic resistance. Given that capsular serotypes and PFGE profiles both indicate that M. haemolytica strains do not all equally associate with BRD, it is plausible that homologs containing antibiotic resistance genes could be more prevalent in M. haemolytica strains that associate with disease, as they would be more frequently exposed to BRD prevention and control measures that include antimicrobials.…”