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Silver gulls carry phylogenetically diverse Escherichia coli, including globally dominant extraintestinal pathogenic E. coli (ExPEC) sequence types and pandemic ExPEC-ST131 clades; however, our large-scale study (504 samples) on silver gulls nesting off the coast of New South Wales identified E. coli ST457 as the most prevalent. A phylogenetic analysis of whole-genome sequences (WGS) of 138 ST457 samples comprising 42 from gulls, 2 from humans (Australia), and 14 from poultry farmed in Paraguay were compared with 80 WGS deposited in public databases from diverse sources and countries. E. coli ST457 strains are phylogenetic group F, carry fimH145, and partition into five main clades in accordance to predominant flagella H-antigen carriage. Although we identified considerable phylogenetic diversity among the 138 ST457 strains, closely related subclades (

A multiple-antibiotic-resistant Salmonella enterica serovar Kentucky strain was found to contain SGI1-K, a variant form of the Salmonella genomic island 1 (SGI1) with an In4-type class 1 integron that contains only one cassette array, aacCA5-aadA7 , and an adjacent mercury resistance module. Part of the 3′-conserved segment (3′-CS) of the integron, together with the inverted short segment from the right-hand end of the integron transposition module normally found between the 3′-CS and IS 6100 in In4 family integrons, has been removed by an IS 6100 -mediated deletion. IRt, the right-hand inverted repeat found at the outer end of the integron, abuts a mercury resistance region instead of the usual SGI1 backbone segment. The mer module is a hybrid of those found in Tn 501 and Tn 21 . This mer region and a further uncharacterized segment of at least 10 kb appear to have been incorporated between IRt and the SGI1 backbone. These findings demonstrate that the multidrug resistance region in SGI1 can incorporate new DNA segments in the same way as multiple antibiotic resistance regions in plasmids.

The first Australian isolate of Salmonella enterica serovar Paratyphi B d -tartrate-utilizing (dT + ) that is resistant to ampicillin, chloramphenicol, florfenicol, streptomycin, spectinomycin, sulfonamides, and tetracycline (ApCmFlSmSpSuTc) and contains SGI1 was isolated from a patient with gastroenteritis in early 1995. This is the earliest reported isolation globally. The incidence of infections caused by these SGI1-containing multiply antibiotic-resistant S. enterica serovar Paratyphi B dT + strains increased during the next few years and occurred sporadically in all states of Australia. Several molecular criteria were used to show that the early isolates are very closely related to one another and to strains isolated during the following few years and in 2000 and 2003 from home aquariums and their owners. Early isolates from travelers returning from Indonesia shared the same features. Thus, they appear to represent a true clone arising from a single cell that acquired SGI1. Some minor differences in the resistance profiles and molecular profiles also were observed, indicating the ongoing evolution of the clone, and phage type differences were common, indicating that this is not a useful epidemiological marker over time. Three isolates from 1995, 1998, and 1999 contained a complete sul1 gene but were susceptible to sulfamethoxazole due to a point mutation that creates a premature termination codon. This SGI1 type was designated SGI1-R. The loss of resistance genes also was examined. When strains were grown for many generations in the absence of antibiotic selection, the loss of SGI1 was not detected. However, variants SGI1-C (resistance profile SmSpSu) and SGI1-B (resistant to ApSu), which had lost part of the integron, arose spontaneously, presumably via homologous recombination between duplications in the In104 complex integron.

IncA/C plasmids carrying an unusual cassette configuration in a class 1 integron and five further shared resistance genes, aacC4 , aphA1 , hph , sul2 , and tetA (D) were found in Salmonella enterica serovars Senftenberg and Ohio. A deletion formed using a short region of homology in the 5′ conserved segment and the orfF cassette created an array with only part of orfF followed by the aadA2 cassette. The IncA/C plasmids were not recoverable by conjugation, but additional conjugative resistance plasmids were present in some strains.

Multiply antibiotic-resistant Salmonella enterica serovar Emek strains isolated in Australia and the United Kingdom had similar features, suggesting that they all belong to a single clone. These strains all contain SGI2 (formerly SGI1-J), an independently formed relative of Salmonella genomic island SGI1. In SGI2, the complex class 1 integron which includes all of the resistance genes is not located between tnpR (S027) and S044 as in SGI1 and SGI1 variants. Instead, tnpR was found to be adjacent to S044, and the integron is located 6.9 kb away, within S023. In both SGI1 and SGI2, the 25-bp inverted repeats that mark the outer ends of class 1 integrons are flanked by a 5-bp duplication of the target, indicating that incorporation of the integron was by transposition. A small number of differences between the sequences of the backbones of SGI1 and SGI2 were also found. Hence, a class 1 integron has entered two different variants of the SGI backbone to generate two distinct lineages. Despite this, the integron in SGI2 has a complex structure that is very similar to that of In104 in SGI1. Differences are in the cassette arrays and in the gene which encodes the chloramphenicol and florfenicol efflux protein. The CmlA9 protein, encoded by InEmek, is only 92.8% identical to FloRc (also a CmlA family protein) from SGI1. A variant form of SGI2, SGI2-A, which has lost the tet (G) and cmlA9 resistance determinants, was found in one strain.

A fifth gene cassette containing an aacC gene, aacCA5 , was found in an aacCA5-aadA7 cassette array in a class 1 integron isolated from a multiply drug resistant Salmonella enterica serovar Kentucky strain. The AacC-A5 or AAC(3)-Ie acetyltransferase encoded by aacCA5 is related to other AAC(3)-I enzymes and confers resistance to gentamicin.

Lincosamide antibiotics include lincomycin, a compound produced by several actinomycetes, and its semisynthetic chlorinated derivative clindamycin. These antibiotics block the peptidyltransferase activity of the 50S subunit of the bacterial ribosome, inhibiting protein synthesis, and are active against most gram-positive cocci and anaerobes. However, they are not generally effective against gram-negative bacilli due to intrinsic resistance (3, 5). Resistance to lincosamides is most commonly due to N6 dimethylation of an adenine residue in the 23S rRNA, which usually confers broad-spectrum cross-resistance to macrolides, lincosamides, and streptogramin B antibiotics or to efflux (5). However, antibiotic inactivation by nucleotidylation (1, 2) has also been described as a mechanism of resistance. Despite the fact that lincosamides are not used to treat enterobacterial infections, a gene, linF, that confers low levels of resistance to both lincomycin (fourfold) and clindamycin (twofold) was recently found in a gene cassette in a class 1 integron recovered from an Escherichia coli blood isolate (4). The linF gene encodes a 273-amino-acid lincosamide nucleotidyltransferase. The LinF protein shares approximately 35% identity with the nucleotidyltransferases encoded by the linB gene from Enterococcus faecium (1) (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AF110130","term_id":"4633124"}}AF110130) and linB′ from Enterococcus faecalis (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AF408195","term_id":"15667874"}}AF408195). We have identified a second lin gene in a gene cassette. This cassette was recovered from a multiply antibiotic-resistant Salmonella enterica serovar Stanley strain (SRC54) isolated in 2001 from a traveler who had recently returned from Thailand. This strain was resistant to chloramphenicol, gentamicin, kanamycin, spectinomycin, streptomycin, sulfathiazole, and tetracycline but susceptible to ampicillin and nalidixic acid at levels described previously (6). It displayed intermediate resistance to ciprofloxacin. The gene cassette array was amplified by using standard primers (L2 and R1) in the 5′ conserved sequence and 3′ conserved sequence of class 1 integrons, and the 2.25-kb amplicon was cloned into pPCRscript and sequenced as previously described (see reference 6 for primer details). E. coli strain DH5α containing pPCR-Script with the cassette array was at least 10-fold more resistant to lincomycin (MIC, ≥2,000 μg/ml) than DH5α containing only pPCR-Script (MIC, 180 μg/ml). The first cassette in the array was identical to the aadA2 cassette in GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"L06822","term_id":"56786619"}}L06822. The second cassette was 937 bp long and 93.4% identical to the linF gene cassette. It encoded a 273-amino-acid protein that is 93.1% identical to LinF (17 amino acid differences). An alignment of these proteins with LinB is shown in Fig. ​Fig.1A.1A. The sequence of the aadA2-linG cassette array was identical to a region found in GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AY522431","term_id":"116294654"}}AY522431. The 59-base elements (59-be; attC sites) of the linG and linF cassettes are 58 bp long (Fig. ​(Fig.1B)1B) and not closely related to any other known 59-be. They retain the critical features of 59-be, namely, complementary sites 1L-1R and 2L-2R (7). FIG. 1. Analysis of LinG sequences. (A) Alignment of Lin proteins. Amino acids that are completely conserved across all sequences are shown as white letters on a black background. The protein sequences of LinB and LinF were from GenBank accession numbers {"type":"entrez-nucleotide","attrs":{"text":"AF110130","term_id":"4633124"}} ...