Presence of the cfxA gene in Bacteroides distasonis

Effect of Cephalosporin Treatment on the Microbiota and Antibiotic Resistance Genes in Feces of Dairy Cows with Clinical Mastitis

Antibiotics are frequently used to treat dairy cows with mastitis. However, the potential effects of β-lactam antibiotics, such as cephalosporins, on the fecal microbiome is unknown. The objective was to investigate the effects of ceftiofur and cefquinome on the fecal microbiota and antibiotic resistance genes of dairy cows with mastitis. The fecal samples were collected from 8 dairy cows at the following periods: the start day (Day 0), medication (Days 1, 2, and 3), withdrawal (Days 4, 6, 7, and 8), and recovery (Days 9, 11, 13, and 15). 16S rRNA gene sequencing was applied to explore the changes in microbiota, and qPCR was used to investigate the antibiotic resistance genes. The cephalosporin treatment significantly decreased the microbial diversity and richness, indicated by the decreased Shannon and Chao 1 indexes, respectively (p < 0.05). The relative abundance of Bacteroides, Bacteroidaceae, Bacteroidales, and Bacteroidia increased, and the relative abundance of Clostridia, Clostridiales, Ethanoligenens, and Clostridium IV decreased at the withdrawal period. The cephalosporin treatment increased the relative abundance of β-lactam resistance genes (bla_TEM and cfxA) at the withdrawal period (p < 0.05). In conclusion, the cephalosporin treatment decreased the microbial diversity and richness at the medication period, and increased the relative abundance of two β-lactam resistance genes at the withdrawal period.

Detection of beta-lactamase production in clinical Prevotella species by MALDI-TOF MS method

Penicillins, can be used in treatment of infections due to Prevotella species if they are susceptible to penicillin. Early and accurate preliminary detection of β-lactamase-producing isolates is crucial for treatment of infection. The aim of this study was to determine β-lactamase-producing Prevotella species by MALDI-TOF MS and screen them for the presence of cfxA gene, responsible for β-lactamase production. A total of 500 clinically relevant Prevotella isolates, collected from 13 countries for the previous European antibiotic resistance surveillance study, were tested. Susceptibility testing was performed against ampicillin and ampicillin/sulbactam by Etest methodology. EUCAST guidelines were used for susceptibility interpretations; the isolates with MIC value ≤ 0.5 for ampicillin were considered susceptible and >2 resistant. All Prevotella isolates, were tested for detection of β-lactamase activity by MALDI-TOF MS (Vitek® MS Research Use Only) system and the presence of the cfxA gene by PCR method. The susceptibility levels of the isolates to ampicillin/sulbactam and ampicillin were 99.6% and 43.4%, respectively. A total 59% of isolates presented β-lactamase activity and 60.8% were cfxA gene positive. Both these tests were positive for isolates in the resistant category. Additionally, >95% of the isolates (n = 65) which ampicillin MIC values ranged from >0.5 μg/mL to 2 μg/ml displayed β-lactamase activity. We also found that the MALDI-TOF MS-based β-lactamase assay delivers results in 2 h. We found a high concordance between the MALDI-TOF MS β-lactamase results in terms of cfxA β-lactamase gene presence. MALDI-TOF MS may serve as a simple and efficient alternative method of the existing phenotypic and PCR-based methods.

Antimicrobial susceptibility patterns of anaerobic bacteria identified from clinical specimens of diseased dogs and cats

We aimed to clarify antimicrobial susceptibility patterns of anaerobes from diseased companion animals. Bacterial identification was based on the Japanese 2012 guidelines for the testing of anaerobic bacteria. AST was performed using the broth microdilution method. The anaerobe-containing samples collected from 2014 to 2018 included blood (anaerobe recovery rate, 5.0%), bile (9.4%), joint fluids (0.6%), pleural effusions (42.6%), ascites (64.1%), cerebrospinal fluids (3.0%), and punctures (75.0%). The anaerobes identified included Bacteroides spp. (33.2%), Peptostreptococcus spp. (19.6%), Prevotella spp. (13.6%), Propionibacterium spp. (10.3%), Clostridium spp. (9.3%), and Fusobacterium spp. (7.5%). Bacteroides fragilis group isolates were resistant to penicillin G (100%), ampicillin (100%), cefmetazole (63.6%), ceftizoxime (90.0%), and clindamycin (40.0%). Our observations demonstrated antimicrobial susceptibility in anaerobes isolated from Japanese companion animals.

Occurrence, Antimicrobial Resistance Patterns, and Genetic Characterization of Staphylococcus aureus Isolated from Raw Milk in the Dairy Farms over Two Seasons in China

This study investigated the occurrence and resistance rates of Staphylococcus aureus strains isolated from raw milk in the dairy farms over two seasons (spring and autumn) and across four regions that included 11 provinces in China. In total, 750 raw milk samples from the 405 dairy farms were collected. Fifteen antimicrobial agents were tested for antimicrobial resistance via disk diffusion tests, and PCR tests were performed to identify drug resistance genes of S. aureus isolates. Out of 750 samples, 276 (36.8%) were positive for S. aureus, with 150 (41.1%) being positive in spring and 126 (32.7%) being positive in autumn. The occurrence rate of S. aureus in northeastern China (45%) was higher than that in western China (33%) and southern China (31.9%), respectively, and the rate significantly (p < 0.05) differed from those of western China and southern China. Of 276 isolates, 261 (94.6%) strains were resistant to more than 1 antimicrobial drug, and 193 (69.9%) strains were multidrug resistant. The blaZ (46.3%), dfrG (35.5%), and tetM (27.2%) genes were detected at a high frequency in the S. aureus strains. Our data revealed a variation (p < 0.05) in the resistance patterns in the different regions and across the two seasons. The occurrence and drug resistance rates of S. aureus isolated from raw milk obtained from dairy farms may still cause severe problems in China.

Comparative Metagenomics and Network Analyses Provide Novel Insights Into the Scope and Distribution of β-Lactamase Homologs in the Environment

The β-lactams are the largest group of clinically applied antibiotics, and resistance to these is primarily associated with β-lactamases. There is increasing understanding that these enzymes are ubiquitous in natural environments and henceforth, elucidating the global diversity, distribution, and mobility of β-lactamase-encoding genes is crucial for holistically understanding resistance to these antibiotics. In this study, we screened 232 shotgun metagenomes from ten different environments against a custom-designed β-lactamase database, and subsequently analyzed β-lactamase homologs with a suite of bioinformatic platforms including cluster and network analyses. Three interrelated β-lactamase clusters encompassed all of the human and bovine feces metagenomes, while β-lactamases from soil, freshwater, glacier, marine, and wastewater grouped within a separate "environmental" cluster that displayed high levels of inter-network connectivity. Interestingly, almost no connectivity occurred between the "feces" and "environmental" clusters. We attributed this in part to the divergence in microbial community composition (dominance of Bacteroidetes and Firmicutes vs. Proteobacteria, respectively). The β-lactamase diversity in the "environmental" cluster was significantly higher than in human and bovine feces microbiomes. Several class A, B, C, and D β-lactamase homologs (bla _CTX-M, bla _KPC, bla _GES) were ubiquitous in the "environmental" cluster, whereas bovine and human feces metagenomes were dominated by class A (primarily cfxA) β-lactamases. Collectively, this study highlights the ubiquitous presence and broad diversity of β-lactamase gene precursors in non-clinical environments. Furthermore, it suggests that horizontal transfer of β-lactamases to human-associated bacteria may be more plausible from animals than from terrestrial and aquatic microbes, seemingly due to phylogenetic similarities.

Molecular analysis of the effector mechanisms of cefoxitin resistance among Bacteroides strains

OBJECTIVES

The characterization of Bacteroides strains with regard to the cfxA gene, the MTn4555 mobilizable transposon, the role of penicillin-binding proteins (PBPs) and heterogeneous cefoxitin resistance.

METHODS

Eighty-four randomly selected and 11 heterogeneously or highly cefoxitin-resistant Bacteroides isolates were included. Agar dilution and Etest methods were used for the determination of cefoxitin MICs. PCR experiments and nucleotide sequencing were used to detect the cfxA gene and the molecular features of MTn4555. Cefoxitin-binding experiments to determine its affinity (IC(50)) for PBPs and cefoxitinase assays were also applied. Southern blotting was used to determine the copy number of the cfxA genes.

RESULTS

Sixteen strains from the random collection proved to be positive for cfxA, and the MIC distribution for the cfxA-negative and -positive strains did not display a clear separation. The majority of the cfxA-positive strains in this collection harboured a 1.2 kb common region at the 3' end of MTn4555. This region encoded an open reading frame that exhibited homology to abortive phage infection proteins (AbiD). The cfxA genes were transferable only at low frequencies in conjugation experiments. In PBP affinity studies, the PBP-A and PBP3 species were largely insensitive to cefoxitin, whereas the other PBP species were affected at very low concentrations. Seven of the heterogeneously resistant strains were positive for cfxA and most of them had mutations in the regulatory regions of cfxA.

CONCLUSIONS

Major and minor roles for Bacteroides fragilis PBPs and the CfxA cefoxitinase, respectively, were inferred. The role of the newly recognized abiD may be to control the copy number of cfxA.

Association between the cfxA gene and transposon Tn4555 in Bacteroides distasonis strains and other Bacteroides species

The Bacteroides genus, the most prevalent anaerobic bacteria of the intestinal tract, carries a plethora of the mobile elements, such as plasmids and conjugative and mobilizable transposons, which are probably responsible for the spreading of resistance genes. Production of beta-lactamases is the most important resistance mechanism including cephalosporin resistance to beta-lactam agents in species of the Bacteroides fragilis group. In our previous study, the cfxA gene was detected in B. distasonis species, which encodes a clinically significant broad-spectrum beta-lactamase responsible for widespread resistance to cefoxitin and other beta-lactams. Such gene has been associated with the mobilizable transposon Tn4555. Therefore, the aim of this study was to detect the association between the cfxA gene and the presence of transposon Tn4555 in 53 Bacteroides strains isolated in Rio de Janeiro, Brazil, by PCR assay. The cfxA gene was detected in 11 strains and the Tn4555 in 15. The transposon sequence revealed similarities of approximately 96% with the B. vulgatus sequence which has been deposited in GenBank. Hybridization assay was performed in attempt to detect the cfxA gene in the transposon. It was possible to associate the cfxA gene in 11 of 15 strains that harbored Tn4555. Among such strains, 9 presented the cfxA gene as well as Tn4555, but in 2 strains the cfxA gene was not detected by PCR assay. Our results confirm the involvement of Tn4555 in spreading the cfxA gene in Bacteroides species.

Decreased Susceptibility to Nitroimidazoles Among Bacteroides Species in Brazil

In this study, 197 strains of Bacteroides genus from different species and origins were evaluated with regard to their susceptibility to 5-nitroimidazoles (5-Ni)-such as tinidazole, ornidazole, and metronidazole-using the agar dilution method. The presence of nim genes was also investigated by polymerase chain reaction. It was found that 5.6% of Bacteroides strains among all origins showed decreased susceptibility (minimum inhibitory concentrations varying from 4 to 16 microg/ml) to at least one of the imidazoles studied without any known nim gene associate. Also, we detected one strain isolated from a polluted aquatic environment in which one nim gene was found and characterized as nim B using restriction fragment length polymorphism and sequencing. Hence, resistance to 5-Ni should be monitored closely because they constitute, among few drugs, the ones quite effective in treating Bacteroides infections.

Determinants of resistance in Bacteroides fragilis strains according to recent Brazilian profiles of antimicrobial susceptibility

Susceptibility profiles of 99 Bacteroides fragilis strains for 9 antimicrobial agents were defined by using an agar dilution method. The isolates were uniformly susceptible to imipenen and metronidazole. All isolates were resistant to ampicillin. The resistance rates to amoxicillin/clavulanate, cefoxitin, cefotaxime, chloramphenicol, clindamycin and tetracycline were 3.0, 12.1, 15.1, 1.0, 18.2 and 75.7%, respectively. Sixteen strains showed reduced susceptibility to metronidazole (MIC 2-4 mg/L) but none had nim genes using PCR. All strains were also investigated for the presence of cepA, cfiA, cfxA, ermF and tetQ genes by PCR methodology and 92.9, 4.9, 24.2, 2 and 64.6% of the strains were respectively found positive. These results reflect the importance of surveys of susceptibility profiles and the relevance of detecting major genetic determinants to monitor the dissemination of these genes.