Detection and distribution of insertion sequence 1 (IS1)-containing bacteria in the freshwater environment

Abstract

The distribution of insertion sequence 1 (IS1)-containing bacteria was investigated in Windermere (Cumbria, UK), a freshwater body impacted by treated sewage discharge and run-off from the surrounding catchment. Culturable IS1-containing bacteria were recovered from the water column at three depths in Windermere North Basin (WNB) and South Basin (WSB), and from sediment at both sites (at the sediment surface in WSB and to a depth of 12^13 cm in WNB). Polymerase chain reaction amplification of IS1 and the Escherichia coli/ Shigella sp. specific gene uidA, from community DNA from shallow sediments, extended the detection limit beyond that of culture at both sites. This detection was extended further into deep sediment extracted from WNB as IS1 and uidA were detected in sub-samples to a depth of 4.7 and 2.3 m, respectively. Analysis of a representative subset of 90 IS1-carrying isolates recovered from water and sediment at both sites demonstrated 21 heterogeneous IS1 profiles with estimated copy numbers ranging from 1 to 16. Identification of the host bacteria showed that the element was confined mainly to Enterobacter spp. However, this study showed IS1 to be present in Citrobacter freundii for the first time. Plasmids were carried by 75.3% of enterobacterial isolates and four plasmids (2.6%) carried IS1. DNA sequence analysis of five IS1 clones demonstrated that IS1 isoforms from this study were similar ( s 89% nucleotide identity) to known IS1 isoforms. Two isoforms of IS1 from a single Enterobacter cloacae isolate differed by 6.7% at the nucleotide level suggesting that they had been acquired independently. ß : S 0 1 6 8 -6 4 9 6 ( 0 0 ) 0 0 0 7 7 -5

Biodegradation of Aromatic Compounds by Escherichia coli

“…Soil, water, sediment, and perhaps food are other habitats of E. coli, and the bacterium might spend comparable times in each of its two main habitats (88,281). While pollution from human sources may be the most important source of E. coli in the environment (29,260), the fact that this bacterium was found in pristine tropical waters, where it remained physiologically active and grew at rates dependent on nutrient levels, suggests that it can be a natural inhabitant in these environments and that it may be part of a previously established community (22). E. coli can also replicate and survive in soil protozoa.…”

Detecting low concentrations ofShigella sonneiin environmental water samples by PCR

“…IS 1 (SB) and IS 1 (SS), and the nucleotide sequences of IS 1 (SD) and IS 1 (SF) in Shigella dysenteriae and Shigella flexneri , respectively, have been reported (Ohtsubo et al , 1981, 1984; Hsu & Chen, 2003; Yang et al , 2005). These IS 1 sequences and nucleotide sequences of IS 1 elements in other bacterial species, including Citrobacter freundii , Enterobacter aerogenes , Enterobacter cloacae , Escherichia coli , Escherichia fergusonii , Eschreichia hermannii , Escherichia vulneris , as well as an unknown bacterial species in sediment, were compiled (Ohtsubo et al , 1981, 1984; Umeda & Ohtsubo, 1991; Lawrence et al , 1992; Rhodes et al , 2000; Perna et al , 2001; Hsu & Chen, 2003), and PCR primer pairs specific for Shigella sonnei were designed. Figure 1 shows the sequences of one such IS 1 primer pair, IS1SS and IS1SR3, which are identical to 250–265 and 618–603 bp of IS 1 (SS) in Shigella sonnei (Ohtsubo et al , 1984).…”

“…The 33 Shigella sonnei isolates included 28 Shigella sonnei isolates recovered from patients in southern, northern, central and eastern Taiwan, and five Shigella sonnei ATCC strains, while the 72 non‐ Shigella sonnei isolates included eight bacteria that had been previously recovered from ground‐water samples and identified in the laboratory of this study and the bacteria reported to contain IS 1 sequences, i.e. Citrobacter freundii , Enterobacter aerogenes , Enterobacter cloacae , Escherichia coli , Escherichia fergusonii , Escherichia hermannii , Escherichia vulneris , Klebsiella pneumoniae , Salmonella typhimurium, Serratia marcescens , Shigella dysenteriae , Shigella boydii and Shigella flexneri (Nyman et al , 1981; Ohtsubo et al , 1984; Bustos‐Martinez & Gomez‐Eichelmann, 1987; Umeda & Ohtsubo, 1991; Lawrence et al , 1992; Matsutani & Ohtsubo, 1993; Rhodes et al , 2000; Hsu & Chen, 2003). Characteristics of these isolates are described in Table 1.…”

“…The nucleotide sequences of primers IS1SS and IS1SR3 and their locations in the major IS1 element of Shigella sonnei, IS1(SS) (Ohtsubo et al, 1984;Yang et al, 2005). Also shown are the nucleotide sequences at the same locations in other IS1 elements from non-Shigella sonnei bacteria and an unknown bacteria in sediment (sed) (Ohtsubo et al, 1984;Umeda & Ohtsubo, 1991;Lawrence et al, 1992;Chen et al, 1998;Rhodes et al, 2000;Perna et al, 2001;Jin et al, 2002;, and the nucleotide sequence from 169 to 180 bp of 11 IS1 elements. The IS1 elements and/or their accession numbers are shown in parentheses.…”

“…Insertion sequence 1 (IS1) is a 768-bp DNA fragment found in the chromosomes and plasmids of Enterobacteriaceae bacteria with sequence variations from several basepairs up to about 10% (Ohtsubo et al, , 1984Umeda & Ohtsubo, 1991;Lawrence et al, 1992;Chen et al, 1998;Rhodes et al, 2000;Perna et al, 2001;. Among them, Shigella spp.…”