AUTHOR=Sivaraman Gopalan Krishnan , Rajan Vineeth , Vijayan Ardhra , Elangovan Ravikrishnan , Prendiville Alison , Bachmann Till T. 

TITLE=Antibiotic Resistance Profiles and Molecular Characteristics of Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli and Klebsiella pneumoniae Isolated From Shrimp Aquaculture Farms in Kerala, India

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.622891

DOI=10.3389/fmicb.2021.622891

ISSN=1664-302X

ABSTRACT=<p>This study was undertaken to evaluate the prevalence of extended-spectrum beta-lactamase (ESBL)-producing <italic>Escherichia coli</italic> and <italic>Klebsiella pneumoniae</italic> in selected shrimp aquaculture farms (<italic>n</italic> = 37) in Kerala, South India and to characterize the isolates using molecular tools. Overall, a low prevalence of ESBL-producers was found in the farms, most likely due to the reduced antibiotic usage in the shrimp farming sector. Out of the 261 samples (77 shrimp and 92 each of water and sediment), 14 (5.4%) tested positive for ESBL-<italic>E. coli</italic> or ESBL-<italic>K. pneumoniae</italic>. A total of 32 ESBL-<italic>E. coli</italic> and 15 ESBL- <italic>K. pneumoniae</italic> were recovered from these samples. All ESBL isolates were cefotaxime-resistant with minimal inhibitory concentration (MIC) ≥32 μg/ml. Of all isolates, 9 (28.1%) <italic>E. coli</italic> and 13 (86.7%) <italic>K. pneumoniae</italic> showed simultaneous resistance to tetracycline, ciprofloxacin, and trimethoprim-sulfamethoxazole. PCR analysis identified CTX-M group 1 (<italic>bla</italic><sub><italic>CTX–M–15</italic></sub>) as the predominant ESBL genotype in both <italic>E. coli</italic> (23, 71.9%) and <italic>K. pneumoniae</italic> (15, 100%). Other beta-lactamase genes detected were as follows: <italic>bla</italic><sub><italic>TEM</italic></sub> and <italic>bla</italic><sub><italic>SHV</italic></sub> (11 <italic>K. pneumoniae</italic>), <italic>bla</italic><sub><italic>CTX–M group 9</italic></sub> (9 <italic>E. coli</italic>), and <italic>bla</italic><sub><italic>CMY–2</italic></sub> (2 <italic>E. coli</italic>). Further screening for AMR genes identified <italic>tetA</italic> and <italic>tetB</italic> (13, 40.6%), <italic>sul1</italic> (11, 34.4%), <italic>sul2</italic> (9, 28.1%), <italic>catA</italic> and <italic>cmlA</italic> (11, 34.4%), <italic>qepA</italic> and <italic>aac(6</italic>′<italic>)-Ib-cr</italic> (9, 28.1%) and <italic>strAB</italic> and <italic>aadA1</italic> (2, 6.3%) in <italic>E. coli</italic>, and <italic>qnrB</italic> (13, 86.7%), <italic>qnrS</italic> (3, 20%), <italic>oqxB</italic> (13, 86.7%), <italic>tetA</italic> (13, 86.7%), and <italic>sul2</italic> (13, 86.7%) in <italic>K. pneumoniae</italic> isolates. Phylogenetic groups identified among <italic>E. coli</italic> isolates included B1 (4, 12.5%), B2 (6, 18.8%), C (10, 31.3%), D (3, 9.4%), and E (9, 28.1%). PCR-based replicon typing (PBRT) showed the predominance of IncFIA and IncFIB plasmids in <italic>E. coli</italic>; however, in <italic>K. pneumoniae</italic>, the major replicon type detected was IncHI1. Invariably, all isolates of <italic>K. pneumoniae</italic> harbored virulence-associated genes viz., <italic>iutA</italic>, <italic>entB</italic>, and <italic>mrkD</italic>. Epidemiological typing by pulsed-field gel electrophoresis (PFGE) revealed that <italic>E. coli</italic> isolates recovered from different farms were genetically unrelated, whereas isolates of <italic>K. pneumoniae</italic> showed considerable genetic relatedness. In conclusion, our findings provide evidence that shrimp aquaculture environments can act as reservoirs of multi-drug resistant <italic>E. coli</italic> and <italic>K. pneumoniae.</italic></p>