Authors: Shamsul Qumar, Mohammad Majid, Narender Kumar, Sumeet K. Tiwari, Torsten Semmler, Savita Devi, Ramani Baddam, Arif Hussain, Sabiha Shaik, Niyaz Ahmed
Summary:
Some of the life-threatening, foodborne, and zoonotic infections are transmitted through poultry birds. Inappropriate and indiscriminate use of antimicrobials in livestock industry has led to increased prevalence of multidrug resistant bacteria of epidemic potentials. Herein, we present the functional molecular epidemiological analysis entailing phenotypic as well as whole genome sequence based characterization of eleven H. pullorum isolates from broiler and free range chickens sampled from retail wet markets of Hyderabad city in India. Antimicrobial susceptibility tests revealed all isolates to be resistant to multiple antibiotic classes such as fluoroquinolones, cephalosporins, sulfonamides and macrolides. The isolates were also found to be extended-spectrum β-lactamase (ESBL) producers and were even resistant to clavulanic acid. Whole genome sequencing and comparative genomic analysis of these isolates revealed the presence of five to six well characterized antimicrobial resistance genes including those encoding Resistance- Nodulation- Division (RND) efflux pump(s). Phylogenetic analysis when combined with pan-genome analysis revealed a remarkable degree of genetic diversity among the isolates of free range chickens; in contrast, a high degree of genetic similarity was observed among broiler chicken isolates. Comparative genomic analysis of all publicly available H. pullorum genomes, including our isolates (n=16), together with the genomes of 17 other Helicobacter species revealed a high number (8560) of H. pullorum specific protein encoding genes with an average of 535 such genes per isolate. In silico virulence screening identified 182 important virulence genes and also revealed high strain specific gene content in isolates of free range chickens (average 34) as compared to broiler chicken isolates. A significant prevalence of prophages (ranging from 1-9) and abundance of genomic islands (0-4) was observed in free range and broiler chicken isolates. Taken together, these observations provide a significant baseline data for functional molecular infection epidemiology of non-pyloric Helicobacters such as H. pullorum by unraveling their evolution in chickens and the possible zoonotic transmission to humans.
Source:
Applied and Environmental Microbiology; 2016, AEM.02305-16