AUTHOR=Bhowmick Sneha , Pal Surajit , Sunder Jai , Sujatha T. , De Arun Kumar , Mondal Tousif , Singh Abhishek D. , Joardar Siddhartha Narayan , Batabyal Kunal , Dutta Tapan Kumar , Bandyopadhyay Samiran , Tiwari Ananda , Samanta Indranil 

TITLE=Exploring broilers and native fowls of Andaman and Nicobar Islands as a source of β-lactamase-producing Enterobacteriaceae even with limited anthropogenic activities and docking-based identification of catalytic domains in novel β-lactamase variants

JOURNAL=Frontiers in Veterinary Science

VOLUME=9

YEAR=2023

URL=https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2022.1075133

DOI=10.3389/fvets.2022.1075133

ISSN=2297-1769

ABSTRACT=<sec><title>Objectives</title><p>The present study was conducted to detect the occurrence of β-lactamase and biofilm-producing <italic>Escherichia coli, Salmonella</italic>, and <italic>Klebsiella</italic> in broilers and native fowl reared in the Andaman and Nicobar Islands, India. The study also included molecular docking experiments to confirm the nature of the catalytic domains found in the β-lactamase variants obtained and to reveal the clonal relationship of the isolates with human clinical strains from the database.</p></sec><sec><title>Materials and methods</title><p>A total of 199 cloacal swabs were collected from five poultry breeds/varieties (broiler, <italic>Vanraja, Desi, Nicobari</italic>, and layer) in three districts of the Andaman and Nicobar Islands. <italic>E. coli, Salmonella enterica</italic>, and <italic>Klebsiella pneumoniae</italic> were isolated by standard techniques and confirmed by PCR. Phenotypical β-lactamase producers were identified by a double-disc test. The genes (<italic>bla</italic><sub>CTX</sub>, <italic>bla</italic><sub>SHV</sub>, <italic>bla</italic><sub><italic>TEM</italic></sub>, and <italic>bla</italic><sub>AmpC</sub>) were screened, and selected sequences of β-lactamase variants were submitted to DDBJ. Homology modeling, model validation, and active site identification of different β-lactamase variants were done by the SWISS-MODEL. Molecular docking was performed to identify the catalytic domains of the β-lactamase variants. The selected β-lactamase sequences were compared with the Indian ESBL sequences from human clinical strains in NCBI-GenBank.</p></sec><sec><title>Results</title><p>In total, 425 <italic>Enterobacteriaceae</italic> strains were isolated from the collected samples. <italic>Klebsiella pneumoniae</italic> (42.58%) was found to be the most prevalent, followed by <italic>Salmonella enterica</italic> (30.82%) and <italic>E. coli</italic> (26.58%). The phenotypical antibiogram of all 425 isolates showed the highest resistance against oxytetracycline (61–76%) and the lowest against gentamicin (15–20%). Phenotypical production of β-lactamase enzymes was observed in 141 (33.38%) isolates. The isolation rate of β-lactamase producing <italic>E. coli, Salmonella enterica</italic>, and <italic>Klebsiella pneumoniae</italic> was significantly higher (<italic>p</italic> &lt; 0.05) in the birds reared in the South Andaman district (25.6, 17.5, and 18.7%, respectively) than in Nicobar (11.5, 7.6, 7.1%, respectively). Genotyping of the β-lactamase-producing isolates revealed the maximum possession of <italic>bla</italic><sub>TEM</sub>, followed by <italic>bla</italic><sub>SHV</sub> and <italic>bla</italic><sub>CTX − M</sub>. The nucleotide sequences were found to be similar with <italic>bla</italic><sub>CTX − M−15</sub>, <italic>bla</italic><sub>SHV − 11</sub>, <italic>bla</italic><sub>SHV − 27</sub>, <italic>bla</italic><sub>SHV − 228</sub>, <italic>bla</italic><sub>TEM − 1</sub>, and <italic>bla</italic><sub>AmpC</sub> in BLAST search. Distribution of studied biofilm-associated genes in <italic>Enterobacteriaceae</italic> strains from different varieties of the birds revealed that the layer birds had the maximum possession, followed by <italic>Vanraja, Desi</italic>, broilers, and <italic>Nicobari</italic> fowls. The phylogenetic analysis of selected sequences revealed a partial clonal relationship with human clinical strains of the Indian subcontinent. Molecular docking depicted the Gibbs free energy release for 10 different macromolecules (proteins) and ligand (antibiotic) complexes, ranging from −8.1 (SHV-27 + cefotaxime) to −7 (TEM-1 + cefotaxime) kcal/mol.</p></sec><sec><title>Conclusion and relevance</title><p>The study revealed β-lactamase variants circulating in the fowl population of the Andaman and Nicobar Islands (India), even in remote places with low anthropogenic activity. Most of the strains possessed <italic>bla</italic><sub>TEM − 1</sub>, followed by <italic>bla</italic><sub>CTX − M−15</sub>. Possession of <italic>bla</italic><sub>SHV − 11</sub>, <italic>bla</italic><sub>SHV − 27</sub>, and <italic>bla</italic><sub>SHV − 228</sub> in poultry <italic>Enterobacteriaceae</italic> strains was not reported earlier from any part of the world. The phylogenetic analysis revealed a partial clonal relationship of β-lactamase sequences with the human clinical strains isolated from the Indian subcontinent.</p></sec>