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Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.

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The in vitro antibacterial activity of four 18-lactam antibiotics (cefatrizine

The in vitro antibacterial activity of piperacillin and cefuroxime against 180 isolates of cephalothin-resistant Enterobacteriaceae and of piperacillin against 46 isolates of Pseudomonas aeruginosa was determined. Amikacin, gentamicin, carbenicillin, cefoxitin, and cefamandole were included for comparison. The activities of piperacillin and carbenicillin against Enterobacteriaceae were comparable. Piperacillin was appreciably more active against Pseudomonas than carbenicillin and was equivalent in activity to arnikacin on a weight basis. The following beta-lactam agents were the most active against the indicated organisms (in parentheses): cefoxitin (indole-positive Proteus spp.), cefuroxime and cefoxitin, (Klebsiella spp.), piperacillin (Enterobacter spp.), cefuroxime and cefoxitin (E. coli), piperacillin and cefoxitin (Serratia spp.), and cefoxitin (Providencia spp.). Amikacin inhibited 98% of Enterobacteriaceae at clinically achievable serum levels.

Background: Detection of carbapenem-resistant Pseudomonas aeruginosa (CRPA) with carbapenamase-producing (CP) genes is critical for preventing transmission. Our objective was to assess whether certain antimicrobial susceptibility testing (AST) profiles can efficiently identify CP-CRPA. Methods: We defined CRPA as P. aeruginosa with imipenem or meropenem MICs of ≥8μg/ml; CP-CRPA were CRPA with CP genes (blaKPC/blaIMP/blaNDM/blaVIM). We assessed the sensitivity and specificity of AST profiles to detect CP-CRPA among CRPA collected by CDC’s Antibiotic Resistance Laboratory Network (AR Lab Network) and the Emerging Infections Program (EIP) during 2017–2019. Results: Three percent (195/6192) of AR Lab Network CRPA were CP-CRPA. Among CRPA, adding not susceptible (NS) to cefepime or ceftazidime to the definition had 91% sensitivity and 50% specificity for identifying CP-CRPA; NS to ceftolozane-tazobactam had 100% sensitivity and 86% specificity. Of 965 EIP CRPA evaluated for CP genes, seven CP-CRPA were identified; 6 of 7 were NS to cefepime and ceftazidime, and all 7 were NS to ceftolozane-tazobactam. Among 4182 EIP isolates, clinical laboratory AST results were available for 96% for cefepime, 80% for ceftazidime, and 4% for ceftolozane-tazobactam. The number of CRPA needed to test (NNT) to identify one CP-CRPA decreased from 138 to 64 if the definition of NS to cefepime or ceftazidime was used and to 7 with NS to ceftolozane-tazobactam. Conclusion: Adding not susceptible to cefepime or ceftazidime to CRPA carbapenemase testing criteria would reduce the NNT by half and can be implemented in most clinical laboratories; adding not susceptible to ceftolozane-tazobactam could be even more predictive once AST for this drug is more widely available.

The activity of erythromycin against 317 strains of anaerobic bacteria, including 133 strains of the Bacteroides fragilis group, was tested by the agar dilution method in an anaerobic atmosphere with two different concentrations of carbon dioxide and without C02. The effect of the atmosphere of incubation on the agar surface pH was also determined. All strains grew well in the GasPak (GP) environment. However, 3.5 and 30.3% of strains failed to grow in the 2 and 0% C02 environments, respectively. The quality of growth was best in the GP environment and poorest in the 0% C02 environment. Minimal inhibitory concentrations in the GP and 2% C02 environments were frequently the same or one dilution lower in the 0% than in the GP environment. In the 0% C02 atmosphere, minimal inhibitory concentrations were usually two to three dilutions lower than in the GP environment. Consequently, only 24% of B. fragilis strains were susceptible to erythromycin in the GP environment, whereas 77% were susceptible in the 0% C02 environment. For Fusobacterium species, 12% were susceptible to erythromycin in the GP environment, and 73% were susceptible in the 0% C02 environment. There was a comparable decrease in pH in all three atmospheres tested. In vitro susceptibility testing of erythromycin against anaerobic bacteria should be performed in an atmosphere containing carbon dioxide.Numerous variables affect the results of susceptibility testing of anaerobic bacteria. Differences due to such factors as the pH of the medium and the presence and amount of C02 in the atmosphere of incubation remain to be fully defined. Data from several laboratories show considerable variation in the susceptibility of anaerobic bacteria to erythromycin (1,5,6,16,17 MATERIALS AND METHODSThe activity of erythromycin was tested against 317 strains of anaerobic bacteria, including 133 RESULTSSusceptibility tests. The effect of atmospheric carbon dioxide on the susceptibility of anaerobic strains tested by the agar dilution method is shown in Table 1. Whereas all anaerobes grew well in the GP jar environment, some strains (3.5%) failed to grow in the 2% C02 environment, and many strains (30.3%) failed to grow in the 0% C02 environment. The quality and quantity of growth of B. fragilis and most other anaerobic bacteria were best in the GP environment. Growth was somewhat less in the 2% C02 environment, but was distinctly less in the 0% C02 environment on both control and