Diverse gene cassettes in class 1 integrons of facultative oligotrophic bacteria of River Mahananda,West Bengal, India.
BACKGROUND
In this study a large random collection (n=2188) of facultative oligotrophic bacteria, from 90 water samples gathered in three consecutive years (2007-2009) from three different sampling sites of River Mahananda in Siliguri, West Bengal, India, were investigated for the presence of class 1 integrons and sequences of the amplification products.


RESULTS
Replica plating method was employed for determining the antibiotic resistance profile of the randomly assorted facultative oligotrophic isolates. Genomic DNA from each isolate was analyzed by PCR for the presence of class 1 integron. Amplicons were cloned and sequenced. Numerical taxonomy and 16S rRNA gene sequence analyses were done to ascertain putative genera of the class 1 integron bearing isolates. Out of 2188 isolates, 1667 (76.19%) were antibiotic-resistant comprising of both single-antibiotic resistance (SAR) and multiple-antibiotic resistant (MAR), and 521 (23.81%) were sensitive to all twelve different antibiotics used in this study. Ninety out of 2188 isolates produced amplicon(s) of varying sizes from 0.15 to 3.45 KB. Chi-square (χ(2)) test revealed that the possession of class 1 integron in sensitive, SAR and MAR is not equally probable at the 1% level of significance. Diverse antibiotic-resistance gene cassettes, aadA1, aadA2, aadA4, aadA5, dfrA1, dfrA5, dfrA7, dfrA12, dfrA16, dfrA17, dfrA28, dfrA30, dfr-IIe, blaIMP-9, aacA4, Ac-6'-Ib, oxa1, oxa10 and arr2 were detected in 64 isolates. The novel cassettes encoding proteins unrelated to any known antibiotic resistance gene function were identified in 26 isolates. Antibiotic-sensitive isolates have a greater propensity to carry gene cassettes unrelated to known antibiotic-resistance genes. The integron-positive isolates under the class Betaproteobacteria comprised of only two genera, Comamonas and Acidovorax of family Comamonadaceae, while isolates under class Gammaproteobacteria fell under the families, Moraxellaceae, Pseudomonadaceae, Aeromonadaceae and Enterobacteriaceae.


CONCLUSIONS
Oligotrophic bacteria are good sources of novel genes as well as potential reservoirs of antibiotic resistance gene casettes.
Department of Biotechnology, Omics Laboratory, University of North Bengal, Siliguri, West Bengal, India. rcnbu2003@yahoo.com
Ranadhir
R
Chakraborty
Arvind
A
Kumar
Suparna Saha
SS
Bhowal
Amit Kumar
AK
Mandal
Bipransh Kumar
BK
Tiwary
Shriparna
S
Mukherjee
D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001483:Base Sequence; D020562:Betaproteobacteria / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D004269:DNA, Bacterial / Q000145:classification / Q000235:genetics*; D018076:DNA, Complementary / Q000145:classification / Q000235:genetics; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D020563:Gammaproteobacteria / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D007194:India; D032023:Integrons / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000145:classification / Q000235:genetics; D045483:Rivers / Q000382:microbiology; D017422:Sequence Analysis, DNA; D014871:Water Microbiology
D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D018076:DNA, Complementary; D012336:RNA, Ribosomal, 16S