Comparison of Consumption Data and Phenotypical Antimicrobial Resistance in E. coli Isolates of Human Urinary Samples and of Weaning and Fattening Pigs from Surveillance and Monitoring Systems in Germany

Antimicrobial resistance (AMR) data from humans are mostly collected from clinical isolates, whereas from livestock data also exist from colonizing pathogens. In Germany, livestock data are collected from clinical and nonclinical isolates. We compared resistance levels of clinical and nonclinical isolates of Escherichia coli from weaning and fattening pigs with clinical outpatient isolates of humans from urban and rural areas. We also studied the association of AMR with available antimicrobial use (AMU) data from humans and pigs. Differences between rural and urban isolates were minor and did not affect the comparison between human and pig isolates. We found higher resistance levels to most antimicrobials in human isolates compared to nonclinical isolates of fattening pigs. Resistance to ampicillin, however, was significantly more frequent in clinical isolates of fattening pigs and in clinical and nonclinical isolates of weaning pigs compared to isolates from humans. The opposite was observed for ciprofloxacin. Co-trimoxazole resistance proportions were higher in clinical isolates of weaning and fattening pigs as compared to isolates from humans. Resistance proportions were higher in clinical isolates than in nonclinical isolates from pigs of the same age group and were also higher in weaner than in fattening pigs. Significant associations of AMU and AMR were found for gentamicin resistance and aminoglycoside use in humans (borderline) and for ampicillin resistance in clinical isolates and penicillin use in fattening pigs. In summary, we found significant differences between isolates from all populations, requiring more detailed analyses supported by molecular data and better harmonized data on AMU and AMR.

A one health genomic investigation of gentamicin resistance in Salmonella from human and chicken sources in Canada, 2014-2017

Objectives: We investigated whether the increased prevalence of gentamicin resistance in Salmonella from human infections was related to a similar increased prevalence in isolates from broiler chickens and whether this increase may have been due to co-selection from use of lincomycin-spectinomycin in chickens on farms. Methods: Whole genome sequencing was performed on gentamicin-resistant (gen-R) Salmonella isolates from human and chicken sources collected from 2014-2017 by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). We determined the genomic relatedness of strains and characterized resistance genes and plasmids. Results: From 2014-2017, 247 isolates of gen-R Salmonella were identified by CIPARS: 188 were from humans and 59 from chicken sources (26 from live animals on farm and 33 from retail meat). The five most common gen-R serovars were Heidelberg (n=93, 31.5%), 4,[5],12:i:- (n=42, 14.2%), Kentucky (n=37, 12.5%), Infantis (n=33, 11.2%), and Typhimurium (n=23, 7.8%). Phylogenomic analysis revealed that for S. Heidelberg and S. Infantis, there were closely related isolates from human and chicken sources. In both sources, resistance to gentamicin and spectinomycin was most frequently conferred by aac(3)-VIa and ant(3’’)-Ia , respectively. Plasmid closure confirmed linkages of gentamicin and spectinomycin resistance genes and revealed instances of similar plasmids from both sources. Conclusions: Gentamicin and spectinomycin resistance genes were linked on the same plasmids, and some plasmids and isolates from humans and chickens were genetically similar, suggesting that the use of lincomycin-spectinomycin in chickens may be selecting for gentamicin-resistant Salmonella in broiler chickens and that these resistant strains may be acquired by humans.

The Mesorhizobium huakuii transcriptional regulator AbiEi plays a critical role in nodulation and is important for bacterial stress response

Background Bacterial abortive infection (Abi) systems are type IV toxin–antitoxin (TA) system, which could elicit programmed cell death and constitute a native survival strategy of pathogenic bacteria under various stress conditions. However, no rhizobial AbiE family TA system has been reported so far. Here, a M. huakuii AbiE TA system was identified and characterized. Results A mutation in M. huakuii abiEi gene, encoding an adjacent GntR-type transcriptional regulator, was generated by homologous recombination. The abiEi mutant strain grew less well in rich TY medium, and displayed increased antioxidative capacity and enhanced gentamicin resistance, indicating the abiEi operon was negatively regulated by the antitoxin AbiEi in response to the oxidative stress and a particular antibiotic. The mRNA expression of abiEi gene was significantly up-regulated during Astragalus sinicus nodule development. The abiEi mutant was severely impaired in its competitive ability in rhizosphere colonization, and was defective in nodulation with 97% reduction in nitrogen-fixing capacity. The mutant infected nodule cells contained vacuolation and a small number of abnormal bacteroids with senescence character. RNA-seq experiment revealed it had 5 up-regulated and 111 down-regulated genes relative to wild type. Of these down-regulated genes, 21 are related to symbiosis nitrogen fixation and nitrogen mechanism, 16 are involved in the electron transport chain and antioxidant responses, and 12 belong to type VI secretion system (T6SS). Conclusions M. huakuii AbiEi behaves as a key transcriptional regulator mediating root nodule symbiosis.

High-level Gentamicin Resistance among Clinical Isolates of Enterococci in Iran: a Systematic Review and Meta-analysis

Enterococci have been considered as one of the most common causes of nosocomial infections. The spread of antibiotic resistance has posed a serious challenge to treating the enterococcal infections. High-level aminoglycosides resistance leads to failure in the synergistic combination therapy.  This study aimed to estimate the prevalence of high-level gentamicin resistance (HLGR) among clinical isolates of enterococci in Iran. Systematic literature search was conducted in the Web of Science, PubMed, Scopus and Google Scholar electronic databases from ar-ticles which were published from April 2000 to September 2018. Literature search yielded 918 studies. Eligible studies were selected ac-cording to the defined inclusion and exclusion criteria. Statistical heterogeneity was estimated by Q statistic and the I2 index. The Begg’s rank correlation test and Egger’s weighted regression tests were used to evaluate possible publication bias. Nineteen studies were included in this review. According to the meta-analysis results, the prevalence of HLGR among Enterococcus spp. was 49.4% (95% CI: 42.2%-56.6%). It was estimated 44.3% (95% CI: 38.1%-50.8%) and 66.3% (95% CI: 51.4%-78.6%) for E. faecalis and E. faecium, respectively. Since notable rate of HLGR in enterococci was seen in this analysis, improving the implementation of all aspects of the infection control programmes is required. Accurate and regular monitoring of infection control procedures are necessary for reducing the dissemination of such infections.

Integron activity accelerates the evolution of antibiotic resistance

Mobile integrons are widespread genetic platforms that allow bacteria to modulate the expression of antibiotic resistance cassettes by shuffling their position from a common promoter. Antibiotic stress induces the expression of an integrase that excises and integrates cassettes, and this unique recombination and expression system is thought to allow bacteria to ‘evolve on demand’ in response to antibiotic pressure. To test this hypothesis, we inserted a custom three-cassette integron into Pseudomonas aeruginosa and used experimental evolution to measure the impact of integrase activity on adaptation to gentamicin. Crucially, integrase activity accelerated evolution by increasing the expression of a gentamicin resistance cassette through duplications and by eliminating redundant cassettes. Importantly, we found no evidence of deleterious off-target effects of integrase activity. In summary, integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity.

Change of the Frequency of Methicillin Resistance and Antibiogram Resistance Profile of Staphylococcus aureus within a Period of 15 Years

Objective: The aim of this retrospective study was to evaluate the rate and antimicrobial resistance profile of community-acquired (CA) and hospital-acquired (HA) methicillin-resistant and sensitive Staphylococcus aureus (MRSA, MSSA) strains between 2004 and 2019. Method: Within the scope of the research, the rate of MRSA and MSSA and the change in antimicrobial resistance profile over time were investigated using two research data of 210 Staphylococcus aureus strains isolated in 2004, and 401 in 2019. Results: While any significant change was not seen in the rates of CA-MRSA (32.4%) and CA-MSSA (67.6%) in 2004, and of CA-MRSA (31.6%) and CA-MSSA (68.4%) in 2019, the prevalence of HA-MRSA decreased by 56.1% in 2004 and 30.7% in 2019 and of HA-MSSA increased by 43.9% in 2004 and 69.3% in 2019. No resistance to vancomycin and teikoplanin was observed in MRSA strains. Resistance of CA-MRSA against ciprofloxacin, levofloxacin, clindamycin and gentamicin decreased. In CA-MSSA an increase of penicillin resistance as well as a decrease in gentamicin resistance was observed. In resistance of HA-MRSA against ciprofloxacin, levofloxacin, erythromycin, clindamycin, gentamicin decreased. HA-Resistance of MSSA against fusidic acid increased and against ciprofloxacin and trimethoprim/sulfamethoxazole and erythromycin resistance decreased. Conclusion: It was found that the rate of HA-MRSA decreased during the given period of 15 years. Vancomycin or teicoplanin resistance was not observed in MRSA and MSSA. While against ciprofloxacin, levofloxacin, clindamycin, gentamicin decreased in both CA-MRSA and HA-MRSA. A closer follow-up of the prevalence and antimicrobial resistance profiles of these strains is of utmost importance for the successful control of the infections caused by MRSA and MSSA.

Genotyping of methicillin resistant Staphylococcus aureus from the United Arab Emirates

Reports from Arabian Gulf countries have demonstrated emergence of novel methicillin resistant Staphylococcus aureus (MRSA) strains. To address the lack of data from the United Arab Emirates (UAE), genetic characterisation of MRSA identified between December 2017 and August 2019 was conducted using DNA microarray-based assays. The 625 MRSA isolates studied were grouped into 23 clonal complexes (CCs) and assigned to 103 strains. CC5, CC6, CC22 and CC30 represented 54.2% (n/N = 339/625) of isolates with other common CCs being CC1, CC8, CC772, CC361, CC80, CC88. Emergence of CC398 MRSA, CC5-MRSA-IV Sri Lanka Clone and ST5/ST225-MRSA-II, Rhine-Hesse EMRSA/New York-Japan Clone in our setting was detected. Variants of pandemic CC8-MRSA-[IVa + ACME I] (PVL+) USA300 were detected and majority of CC772 strains were CC772-MRSA-V (PVL+), “Bengal- Bay Clone”. Novel MRSA strains identified include CC5-MRSA-V (edinA+), CC5-MRSA-[VT + fusC], CC5-MRSA-IVa (tst1+), CC5-MRSA-[V/VT + cas + fusC + ccrA/B-1], CC8-MRSA-V/VT, CC22-MRSA-[IV + fusC + ccrAA/(C)], CC45-MRSA-[IV + fusC + tir], CC80-MRSA-IVa, CC121-MRSA-V/VT, CC152-MRSA-[V + fusC] (PVL+). Although several strains harboured SCC-borne fusidic acid resistance (fusC) (n = 181), erythromycin/clindamycin resistance (ermC) (n = 132) and gentamicin resistance (aacA-aphD) (n = 179) genes, none harboured vancomycin resistance genes while mupirocin resistance gene mupR (n = 2) and cfr gene (n = 1) were rare. An extensive MRSA repertoire including CCs previously unreported in the region and novel strains which probably arose locally suggest an evolving MRSA landscape.

Expression of the MexXY Aminoglycoside Efflux Pump and Presence of an Aminoglycoside-Modifying Enzyme in Clinical Pseudomonas aeruginosa Isolates Are Highly Correlated

ABSTRACTThe impact of MexXY efflux pump expression on aminoglycoside resistance in clinical Pseudomonas aeruginosa isolates has been debated. In this study, we found that, in general, elevated mexXY gene expression levels in clinical P. aeruginosa isolates confer to slight increases in aminoglycoside MIC levels; however, those levels rarely lead to clinically relevant resistance phenotypes. The main driver of resistance in the clinical isolates studied here was the acquisition of aminoglycoside-modifying enzymes (AMEs). Nevertheless, acquisition of an AME was strongly associated with mexY overexpression. In line with this observation, we demonstrate that the introduction of a gentamicin acetyltransferase confers to full gentamicin resistance levels in a P. aeruginosa type strain only if the MexXY efflux pump was active. We discuss that increased mexXY activity in clinical AME-harboring P. aeruginosa isolates might affect ion fluxes at the bacterial cell membrane and thus might play a role in the establishment of enhanced fitness that extends beyond aminoglycoside resistance.

Identification of a Novel Plasmid-Borne Gentamicin Resistance Gene in Nontyphoidal Salmonella Isolated from Retail Turkey

ABSTRACT The spread of antibiotic-resistant bacteria presents a global health challenge. Efficient surveillance of bacteria harboring antibiotic resistance genes (ARGs) is a critical aspect to controlling the spread. Increased access to microbial genomic data from many diverse populations informs this surveillance but only when functional ARGs are identifiable within the data set. Current, homology-based approaches are effective at identifying the majority of ARGs within given clinical and nonclinical data sets for several pathogens, yet there are still some whose identities remain elusive. By coupling phenotypic profiling with genotypic data, these unknown ARGs can be identified to strengthen homology-based searches. To prove the efficacy and feasibility of this approach, a published data set from the U.S. National Antimicrobial Resistance Monitoring System (NARMS), for which the phenotypic and genotypic data of 640 Salmonella isolates are available, was subjected to this analysis. Six isolates recovered from the NARMS retail meat program between 2011 and 2013 were identified previously as phenotypically resistant to gentamicin but contained no known gentamicin resistance gene. Using the phenotypic and genotypic data, a comparative genomics approach was employed to identify the gene responsible for the observed resistance in all six of the isolates. This gene, grdA, is harbored on a 9,016-bp plasmid that is transferrable to Escherichia coli, confers gentamicin resistance to E. coli, and has never before been reported to confer gentamicin resistance. Bioinformatic analysis of the encoded protein suggests an ATP binding motif. This work demonstrates the advantages associated with coupling genomics technologies with phenotypic data for novel ARG identification.