Genetic context and structural diversity of class 1 integrons from human commensal bacteria in a hospital intensive care unit - PubMed (original) (raw)

Genetic context and structural diversity of class 1 integrons from human commensal bacteria in a hospital intensive care unit

Thu Betteridge et al. Antimicrob Agents Chemother. 2011 Aug.

Abstract

Most surveys for class 1 integrons are at least partly predicated on PCR screening that targets integron conserved regions. However, class 1 integrons are structurally diverse, so dependence on conserved regions may lead to missing clinically relevant examples of class 1 integrons. Here, we surveyed a commensal population of bacteria from patients in an intensive care unit to identify class 1 integrons irrespective of their structure or genetic context. We identified several examples of class 1 integrons linked to complete Tn402-like or Tn402 hybrid transposition modules and diverse insertion points with respect to the inverted repeat IRi boundary. The diversity and abundance of class 1 integrons identified are such that many novel elements seen here would not have been identified by commonly used methods, and they revealed an additional level of complexity.

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Figures

Fig. 1.

Fig. 1.

Schematic representation of a Tn_402_-like integron inserted into a Tn_21_ subgroup transposon backbone. The IRi junction PCR assay using primer pair HS1065/HS818 amplifies the region existing in this kind of recombined structure. The shaded box shows the class 1 integron bounded within two inverted repeats, IRi and IRt, and its basic structural features (5′-CS, 3′-CS, potential gene cassette[s], and tni module), together with positions of specific primer pairs used to detect each feature. To detect the presence of the IS_26_ element, which could be inserted in either orientation as shown, two separate PCRs were carried out per isolate, with primer pairs HS1081/HS916 and HS1118/HS916. Similarly, two specific primer pairs were used to detect the presence of IS_6100_.

Fig. 2.

Fig. 2.

Comparison of class 1 integrons with complete tni modules. Each of the three known tni module types is indicated. The flag symbol indicates the promoter, designated Pc, that transcribes inserted resistance genes. Different cassette arrays that have been identified inserted at attI1 are shown under each type of tni module. The types of sources of the isolates carrying each array are indicated on the right. For all elements recovered in this study, the indicated regions were completely sequenced. A, JKB7 (Enterobacter cloacae) (13) and WM88a32 (Escherichia coli) (this study); B, Tn_402_ (Enterobacter aerogenes) (23, 27); C, LD209 (Pseudomonas putida) (17); D, WM2b02 (Klebsiella pneumonia) (this study); E, LMCB014 (Comomonas testosteroni) (25); F, DCB015 (Pseudomonas alcaligenes) (25); G, 11BF10 (Pseudomonas aeruginosa) (26); H, pOZ172 (Citrobacter youngae) (10); I, PPV2-2 (Pseudomonas putida) (11).

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