A Novel, Integron-Regulated, Class C β-Lactamase

AmpC-type β-lactamases severely impair treatment of many bacterial infections, due to their broad spectrum (they hydrolyze virtually all β-lactams, except fourth-generation cephalosporins and carbapenems) and the increasing incidence of plasmid-mediated versions. The original chromosomal AmpCs are often tightly regulated, and their expression is induced in response to exposure to β-lactams. Regulation of mobile ampC expression is in many cases less controlled, giving rise to constitutively resistant strains with increased potential for development or acquisition of additional resistances. We present here the identification of two integron-encoded ampC genes, bla_IDC-1 and bla_IDC-2 (integron-derived cephalosporinase), with less than 85% amino acid sequence identity to any previously annotated AmpC. While their resistance pattern identifies them as class C β-lactamases, their low isoelectric point (pI) values make differentiation from other β-lactamases by isoelectric focusing impossible. To the best of our knowledge, this is the first evidence of an ampC gene cassette within a class 1 integron, providing a mobile context with profound potential for transfer and spread into clinics. It also allows bacteria to adapt expression levels, and thus reduce fitness costs, e.g., by cassette-reshuffling. Analyses of public metagenomes, including sewage metagenomes, show that the discovered ampCs are primarily found in Asian countries.

Lysobacter alkalisoli sp. nov., a chitin-degrading strain isolated from saline-alkaline soil

Strains of Lysobacter, thought to play vital roles in the environment for their high enzyme production capacity, are ubiquitous in various ecosystems. During an analysis of bacterial diversity in saline soil, a Gram-stain-negative, aerobic, chitin-degrading bacterial strain, designated SJ-36^T, was isolated from saline-alkaline soil sampled at Tumd Right Banner, Inner Mongolia, PR China. Strain SJ-36^T grew at 4-40 °C (optimum, 30 °C), pH 5.0-10.0 (optimum, pH 7.0-8.0) and 0-6 % NaCl (optimum, 1.0 %). Oxidase and catalase activities were positive. A phylogenetic tree based on 16S rRNA gene sequences and the phylogenomic tree both showed that strain SJ-36^T formed a tight clade with Lysobacter maris KMU-14^T (sharing 97.6 % 16S rRNA gene similarity) and Lysobacter aestuarii S2-C^T (97.8 %). The major polar lipids of strain SJ-36^T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified lipids and one unidentified phospholipid. The major fatty acids were iso-C_15 : 0 (37.5 %), summed feature 9 (14.0 %; iso-C_17 : 1ω9c and/or C_16 : 0 10-methyl) and iso-C_11 : 0 (10.6 %). Q-8 was the predominant ubiquinone. Its genomic DNA G+C content was 66.6 mol%. The average nucleotide identity values of strain SJ-36^T to L. maris KMU-14^T, L. aestuarii S2-C^T and other type strains were 81.5, 79.1 and <79.0 %, respectively. The results of physiological, phenotypic and phylogenetic characterizations allowed the discrimination of strain SJ-36^T from its phylogenetic relatives. Lysobacter alkalisoli sp. nov. is therefore proposed with strain SJ-36^T (=CGMCC 1.16756^T=KCTC 43039^T) as the type strain.

Lysobacter prati sp. nov., isolated from a plateau meadow sample

A novel proteobacterial strain designated SYSU H10001^T was isolated from a soil sample collected from plateau meadow in Hongyuan county, Sichuan province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU H10001^T was most closely related to Lysobacter soli KCTC 22011^T (98.6%, sequence similarity) and Lysobacter panacisoli JCM 19212^T (98.2%). The prediction result of secondary metabolites based on genome shown that the strain SYSU H10001^T contained 3 clusters of bacteriocins, 1 cluster of non-ribosomal peptide synthetase, 1 cluster of type 1 polyketide synthase and 1 cluster of arylpolyene. In addition, the major isoprenoid quinone was Q-8 and the major fatty acids were identified as iso-C_15:0, iso-C_17:0 and Summed feature 9. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and three unidentified phospholipids. The genomic DNA G + C content of strain SYSU H10001^T was 66.5% (genome). On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU H10001^T represents a novel species of the genus Lysobacter, for which the name Lysobacter prati sp. nov. is proposed. The type strain is SYSU H10001^T (= KCTC 72062^T = CGMCC 1.16662^T).