Long-term shifts in patterns of antibiotic resistance in enteric bacteria

Several mechanisms are responsible for the ability of microorganisms to tolerate antibiotics, and the incidence of resistance to these compounds within bacterial species has increased since the commercial use of antibiotics became widespread. To establish the extent of and changes in the diversity of antibiotic resistance patterns in natural populations, we determined the MICs of five antibiotics for collections of enteric bacteria isolated from diverse hosts and geographic locations and during periods before and after commercial application of antibiotics began. All of the pre-antibiotic era strains were susceptible to high levels of these antibiotics, whereas 20% of strains from contemporary populations of Escherichia coli and Salmonella enterica displayed high-level resistance to at least one of the antibiotics. In addition to the increase in the frequency of high-level resistance, background levels, conferred by genes providing nonspecific low-level resistance to multiple antibiotics, were significantly higher among contemporary strains. Changes in the incidence and levels of antibiotic resistance are not confined to particular segments of the bacterial population and reflect responses to the increased exposure of bacteria to antimicrobial compounds over the past several decades.     

Combating antibiotic resistance in bacteria

Combinations of certain antibiotics select against resistant strains of bacteria. This finding may provide a strategy of combating antibiotic resistant bacteria.     

Determining sources of fecal pollution in a rural Virginia watershed with antibiotic resistance patterns in fecal streptococci

Nonpoint sources of pollution that contribute fecal bacteria to surface waters have proven difficult to identify. Knowledge of pollution sources could aid in restoration of the water quality, reduce the amounts of nutrients leaving watersheds, and reduce the danger of infectious disease resulting from exposure to contaminated waters. Patterns of antibiotic resistance in fecal streptococci were analyzed by discriminant and cluster analysis and used to identify sources of fecal pollution in a rural Virginia watershed. A database consisting of patterns from 7,058 fecal streptococcus isolates was first established from known human, livestock, and wildlife sources in Montgomery County, Va. Correct fecal streptococcus source identification averaged 87% for the entire database and ranged from 84% for deer isolates to 93% for human isolates. To field test the method and the database, a watershed improvement project (Page Brook) in Clarke County, Va., was initiated in 1996. Comparison of 892 known-source isolates from that watershed against the database resulted in an average correct classification rate of 88%. Combining all animal isolates increased correct classification rates to > or = 95% for separations between animal and human sources. Stream samples from three collection sites were highly contaminated, and fecal streptococci from these sites were classified as being predominantly from cattle (>78% of isolates), with small proportions from waterfowl, deer, and unidentified sources ( approximately 7% each). Based on these results, cattle access to the stream was restricted by installation of fencing and in-pasture watering stations. Fecal coliforms were reduced at the three sites by an average of 94%, from prefencing average populations of 15,900 per 100 ml to postfencing average populations of 960 per 100 ml. After fencing, <45% of fecal streptococcus isolates were classified as being from cattle. These results demonstrate that antibiotic resistance profiles in fecal streptococci can be used to reliably determine sources of fecal pollution, and water quality improvements can occur when efforts to address the identified sources are made.     

Long-term starvation-induced loss of antibiotic resistance in bacteria

Escherichia coli, Pseudomonas fluorescens, and aPseudomonas sp. strain 133B containing the pSa plasmid were starved in well water for up to 523 days. There were two patterns of apparent antibiotic resistance loss observed. InPseudomonas sp. strain 133B, there was no apparent loss of antibiotic resistance even after starvation for 340 days. InE. coli, by day 49 there was a ten-fold difference between the number of cells that would grow on antibiotic- and nonantibiotic-containing plates. However, over 76% of the cells that apparently lost their antibiotic resistance were able to express antibiotic resistance after first being resuscitated on non-selective media. By day 523, only 12% of these cells were able to express their antibiotic resistance after being resuscitated. After starvation for 49 days, cells that could not grow on antibiotic medium even after resuscitation, showed a permanent loss of chloramphenicol (Cm) resistance but retained resistance to kanamycin (Km) and streptomycin (Sm). Restriction enzyme digests show that a 2.5 to 3.0 Kb region from map location 12.5 to 15.5 Kb was deleted. This coincides with the 2.5 Kb reduction in plasmid size observed in 3 isolates that had lost antibiotic resistance after starvation for 49 days.Published as Technical Paper #9224, Oregon Agricultural Experiment Station.     

Analysis of antibiotic resistance regions in Gram-negative bacteria

Antibiotic resistance in Gram-negative bacteria is often due to the acquisition of resistance genes from a shared pool. In multiresistant isolates these genes, together with associated mobile elements, may be found in complex conglomerations on plasmids or on the chromosome. Analysis of available sequences reveals that these multiresistance regions (MRR) are modular, mosaic structures composed of different combinations of components from a limited set arranged in a limited number of ways. Components common to different MRR provide targets for homologous recombination, allowing these regions to evolve by combinatorial evolution, but our understanding of this process is far from complete. Advances in technology are leading to increasing amounts of sequence data, but currently available automated annotation methods usually focus on identifying ORFs and predicting protein function by homology. In MRR, where the genes are often well characterized, the challenge is to identify precisely which genes are present and to define the boundaries of complete and fragmented mobile elements. This review aims to summarize the types of mobile elements involved in multiresistance in Gram-negative bacteria and their associations with particular resistance genes, to describe common components of MRR and to illustrate methods for detailed analysis of these regions.     

Spatial autocorrelation patterns of stream invertebrates: exogenous and endogenous factors

Aim To investigate spatial autocorrelation of taxonomic stream invertebrate groups (richness and composition) at a large geographical scale and to analyse the importance of exogenous and endogenous factors. Location The Mediterranean Basin. Methods For exogenous factors, we used large‐scale factors related to climate, geology and river zonation; for endogenous factors, we used the dispersal mode of each taxonomic group. After describing and analysing spatial patterns of genus richness and genus composition of stream invertebrate groups in the Mediterranean Basin, we computed Moran’s I before and after accounting for the exogenous factors and related it to the endogenous factors. Results In relation to genus richness, most of the taxonomic groups did not show significant spatial autocorrelation, suggesting that no main large‐scale exogenous or endogenous factors were important and that local‐scale factors were probably controlling taxonomic richness. In contrast, for genus composition, all taxonomic groups except Odonata had significant spatial autocorrelation before accounting for the environment. After accounting for the environment, most taxonomic groups still had a significant spatial autocorrelation, but it decreased with their increasing dispersal ability (from Crustacea to Coleoptera). Thus, spatial taxonomic composition of groups with the strongest dispersal potential is mainly related to exogenous factors, whereas that of groups with weaker dispersal potential is related to a combination of exogenous and endogenous factors. Main conclusions Our results illustrate the importance of dispersal as an endogenous factor causing spatial autocorrelation and suggest that ignoring endogenous factors can lead to misunderstandings when explaining large‐scale community patterns.     

Molecular strategies for overcoming antibiotic resistance in bacteria

Overuse of antibiotics in humans and livestock has led to the rapid evolution of bacteria that are resistant to multiple drugs such that even vancomycin, the drug of last resort, is no longer effective against some strains. Apart from the discovery and exploitation of the natural peptide antimicrobial agents that form part of the innate immune systems of plants and animals, there have been few new antibiotics developed in recent years. Here we review strategies designed to exploit recent advances in molecular biology, including recombinant DNA technology, molecular modelling and genomics to develop new antibacterial agents that overcome antibiotic resistance.     

养猪场空气中抗性基因和条件致病菌污染特征

养殖场空气中含有较高浓度的抗生素抗性基因和条件致病菌,对人畜健康具有潜在威胁.采用中流量TSP采样器在某养猪场的生活区、猪舍内和猪舍外3个地点分别采样24 h和48 h,并采集猪舍内的饲料、粪便和饮水添加剂样品.采用普通PCR检测样品中的3类抗生素抗性基因(大环内酯类、β-内酰胺类、四环素类各3个基因)和7种致病菌/条件致病菌基因(弯曲杆菌属、产气荚膜梭菌、肠球菌属、大肠杆菌、小肠结肠炎耶尔森菌、葡萄球菌属和猪链球菌);选取检出率较高的6种基因,采用荧光定量PCR对其浓度进行测定.结果表明: 空气中大环内酯类抗性基因检出了3个,四环素类检出了2个,肠球菌、大肠杆菌、小肠结肠炎耶尔森菌、葡萄球菌等4种条件致病菌在空气样品中和饮水添加剂中都被检测到.绝大部分目的基因的浓度均在10⁴ copies·m^-3以上,并且猪舍附近浓度远高于生活区;猪场内主要的抗生素抗性基因和条件致病菌的可能来源是猪粪便和饮水添加剂.在养猪场内采样24 h即可满足PCR检测要求;在生活区采样48 h的采样效率高于采样24 h,而在猪舍外和猪舍内采样24 h的效率高于采样48 h.     

Epigenetic inheritance based evolution of antibiotic resistance in bacteria

Background  

The evolution of antibiotic resistance in bacteria is a topic of major medical importance. Evolution is the result of natural selection acting on variant phenotypes. Both the rigid base sequence of DNA and the more plastic expression patterns of the genes present define phenotype.     

Genetic determinants of antibiotic resistance in gram negative bacteria

Modern data on spreading, structural and functional organization and evolution of the genetic determinants of antibiotic resistance in the gram-negative bacteria are reviewed. Some mechanisms for resistance to trimethoprime, sulphonamides, tetracyclines, chloramphenicol aminoglycosides, beta-lactam antibiotics controlled by the plasmid and chromosomal genes are presented. The problem of using the molecular DNA-probes containing the genetical determinants for antibiotic resistance in the practical work of clinical laboratories is discussed.     

The patterns and transmissibility of antibiotic resistance among clinical strains of Pseudomonas aeruginosa.

Four hundred and ninety-eight predominantly pyocin-type 10 clinical strains of Pseudomonas aeruginosa were analyzed for resistance to carbenicillin, cefoperazone, cefotaxime, ceftazidime, gentamicin, amikacin and netilmicin. Based on NCCLS-recommended MIC breakpoints, 245 strains were found to be resistant, of which 41.6% were resistant to carbenicillin, 38% to gentamicin, 37.8% to netilmicin, 26.3% to cefoperazone, 17.9% to cefotaxime, 0.6% to amikacin and none to ceftazidime. Quadruple resistance to carbenicillin, cefoperazone, gentamicin and netilmicin was the most frequent pattern observed. Resistance to older antibiotics (kanamycin, streptomycin and tetracycline) and to mercuric chloride were also common. Conjugation experiments suggested that self-transmissible and non-transmissible plasmids occurred in at least 66 strains.     

革兰阴性细菌耐药特性的双聚类分析

目的通过双聚类分析了解临床分离的革兰阴性菌的耐药特征。方法采用K-B法对临床分离的113株细菌进行药物敏感试验,用软件WHONET 5.6和MATLAB对药敏试验结果进行统计分析。结果传统耐药分析方法表明113株细菌总体耐药率较低,其中大肠埃希菌、铜绿假单胞菌和鲍曼不动杆菌的耐药率则较高,而肺炎克雷伯菌耐药率较低。通过双聚类分析,所有菌株被聚为三大类,I类菌株占23.0%,耐药率最高,几乎对18种药物都耐药,细菌种类以肺炎克雷伯菌、铜绿假单胞菌、鲍曼不动杆菌为主;Ⅱ类菌株占56.6%,耐药率普遍较低,以肺炎克雷伯菌为主;Ⅲ类菌株占20.4%,菌株的耐药率介于I和Ⅱ类之间,包括肺炎克雷伯菌、铜绿假单胞菌和大肠埃希菌。其中Ⅱ大类,根据所耐抗生素的不同又分为Ⅱ-A、Ⅱ-B、Ⅱ-C三个亚类,每一亚类都具有相似的耐药特点。结论本实验收集的革兰阴性菌株根据耐药特征被聚为Ⅰ、Ⅱ、Ⅲ类,耐药程度为IⅢⅡ,双聚类分析法有利于快速找到具有相同耐药特征的菌株以及不同菌株之间的耐药差别。     

Airborne bacteria and antibiotic resistance genes in hospital rooms

The microbial biodiversity of bioaerosols in recently occupied hospital rooms was assessed in a pulmonology unit. Environmental samples and isolates were also screened for antibiotics resistance genes. Biofilms from sink drains were also studied to evaluate whether sink drains constitute a potential source of bioaerosols in this environment and a reservoir for opportunistic bacteria and antibiotic resistance genes. Stenotrophomonas maltophilia was by far the most frequently isolated microorganisms from the biofilm, followed by Enterobacter cloacae. Airborne bacterial concentration ranged from 14 to 74 CFU m⁻³ and fungi ranged from 50 to 600 CFU m⁻³. Biofilm bacteria were outnumbered in aerosols by microorganisms affiliated with human skin flora. Nonetheless, they were recovered from air samples in low concentrations. Erythromycin resistance genes were detected in all air samples collected from hospital rooms, and tetracycline resistance genes were detected sporadically. Antibiotic resistance genes were found in a single drain suggesting that genes present in DNA extracts from air samples were not aerosolized from sink drains, but rather from an unknown source. Results obtained in this study suggest that bacteria from sink drains were not aerosolized in significant concentration. They still remain a concern because of the risk of aerial transmission associated with their presence.     

Acquired antibiotic resistance in lactic acid bacteria from food

Acquired antibiotic resistance, i.e. resistance genes located on conjugative or mobilizable plasmids and transposons can be found in species living in habitats (e.g. human and animal intestines) which are regularly challenged with antibiotics. Most data are available for enterococci and enteric lactobacilli. Raw material from animals (milk and meat) which are inadvertantly contaminated with fecal matters during production will carry antibiotic resistant lactic acid bacteria into the final fermented products such as raw milk cheeses and raw sausages. The discovered conjugative genetic elements of LAB isolated from animals and food are very similar to elements studied previously in pathogenic streptococci and enterococci, e.g. -type replicating plasmids of the pAM1, pIP501-family, and transposons of the Tn916-type. Observed resistance genes include known genes like tetM, ermAM, cat, sat and vanA. A composite 29'871 bp resistance plasmid detected in Lactococcus lacti s subsp. lactis isolated from a raw milk soft cheese contains tetS previously described in Listeria monocytogenes, cat and str from Staphylococcus aureus. Three out of five IS elements on the plasmid are almost or completely identical to IS1216 present in the vanA resistance transposon Tn1546. These data support the view that in antibiotic challenged habitats lactic acid bacteria like other bacteria participate in the communication systems which transfer resistance traits over species and genus borders. The prevalence of such bacteria with acquired resistances like enterococci is high in animals (and humans) which are regularly treated with antibiotics. The transfer of antibiotic resistant bacteria from animals into fermented and other food can be avoided if the raw substrate milk or meat is pasteurized or heat treated. Antibiotic resistance traits as selectable markers in genetic modification of lactic acid bacteria for different purposes are presently being replaced, e.g. by metabo lic traits to generate food-grade vectors.