Determination of total antibiotic resistance in waterborne bacteria in rivers and streams in Northern Ireland: Can antibiotic-resistant bacteria be an indicator of ecological change?

Antibiotic resistance (ABR) has now become a major public health issue. Relatively little studies have been published on the incidence of ABR in environmental isolates circulating within the community. A study was performed to determine the diversity of total ABR (intrinsic + acquired resistance) in waterborne bacteria. Surface water from 12 waterways, including 11 rivers/steams and 1 lake, were examined for the presence of ABR phenotypes, using a direct antibiotic susceptibility assay and demonstrated the presence of ABR (in increasing order of resistance), to the following 19 agents: amikacin (17%), gentamicin (17%), ciprofloxacin (33%), colistin (42%), linezolid (42%), tobramycin (42%), vancomycin (42%), ertapenem (67%), erythromycin (75%), meropenem (75%), rifampin (75%), teichoplanin (75%), tetracycline (75%), trimethoprim (75%), fusidic acid (83%), aztreonam (92%), clindamycin (92%), penicillin (92%) and cefoxitin (100%). Multiple resistance to the major classes of antibiotics was noted, which varied from one to six classes, with a mean resistance to 3.7 major antibiotics classes, with diminishing antibacterial effectiveness in the following order: aminoglycosides > fluoroquinolones > glycopeptides > macrolides > tetracyclines > β-lactams. Overall, these data indicate that waterborne bacteria are an important source of ABR determinants and contribute to the mass balance of ABR in the environment, and may be used as an indicator of ecological change in water ecosystems. The waterborne ABR organisms may potentially act as donors in pathogens, which may acquire these through horizontal gene transfer or other genetic exchange events, thus leading to clinically significant cases in both animal and human health. Therefore, environmental bacteria should not be regarded as being devoid of ABR determinants, simply because they are physically removed from clinical settings. Such bacteria have natural intrinsic resistance, as well as having the ability to acquire determinants from agricultural run-off and human wastewater discharge, which may contain ABR organisms, as well as sublethal concentrations of metabolically active antibiotic. The tracking of such organisms to their source may help determine the source of fecal pollution in aquatic ecosystems.     

I think autophagy controls the death of my cells: What do I do to get my paper published?

Many people are studying how autophagy intersects with cell death. While most of those studies relate to autophagy acting as a protective mechanism (e.g., to block apoptosis), many papers conclude that autophagy is a death mechanism, and there is a widespread belief that autophagy (in most, but not all cases, we are talking about macroautophagy) can both kill and protect cells depending on the circumstances. Not surprisingly therefore, many of the papers submitted to Autophagy study the relationship between autophagy and cell death.     

What bacteria are living in my food? An open-ended practical series involving identification of unknown foodborne bacteria using molecular techniques

This open-ended practical series titled "Molecular Identification of Unknown Food Bacteria" which extended over a 6-week period was designed with the aims of giving students an opportunity to gain an understanding of naturally occurring food bacteria and skills in contemporary molecular methods using real food samples. The students first isolated two unknown bacterial strains from two food sources from which they extracted DNA and performed PCR targeting the 16S rRNA gene. Gel electrophoresis was used to analyze both genomic DNA preparations and PCR products. Following purification of PCR products, DNA sequencing was carried out and sequence trace quality was analyzed. The students successfully identified the two unknown bacteria using the BLAST search engine and a wide variety of different organisms were found. Assessment of their understanding of the procedure and ability to explain their findings using supporting primary research literature was via an individually prepared written report. Feedback from students over 2 years (n = 52) in a questionnaire revealed that the practical series was an engaging learning experience and lead to perceived improvements in knowledge of molecular techniques and bioinformatics and also about commonly occurring bacteria in foods.     

Dendrometer and intra-annual tree growth: What kind of information can be inferred?

Dendrometer measurements provide time series composed of the rhythm of water storage fluctuations over the year and seasonal tree growth. For slow-growing trees, however, difficulties have been found in the identification of crucial events such as growth onset, stem growth period and cessation, rendering it necessary to define what can be measured and at which time scale. Time scale means the time interval (from one day to one month) at which stem radius variation is extracted. In this study, two conifer species were monitored by an automatic band dendrometer to assess several time scales and analysis approaches. Data were collected from 8 trees of Picea abies (L.) Karst and Larix decidua L., growing at 1020 and 2080 m a.s.l. in the eastern Italian Alps, from 2000 to 2003. Time series of stem radius variation were extracted with different approaches, such as the stem cycle, daily mean and daily maximum. Several approaches can be used, as very similar time series of stem radius variations were produced with high coefficients of correlation among the series. At lower altitude, the approximate onset was identified at the beginning of May with a 10-day time scale, when the distribution of stem radius variation differed from zero. The main growth period, from May to June–July, corresponded mainly with earlywood cell formation. At higher altitude, a time scale of at least 15 days facilitated identification of the main period of stem growth only, corresponding with earlywood cell formation. Even if latewood cells were produced in August at both altitudes, the variability in stem radius changes was higher than the amount of growth in terms of cell-wood production. For a slow-growing species in a cold environment, an understanding of the growth period, assessed with several time scales, is necessary when using time series of stem radius variation to assess growth and climate relationships. The period used for growth and climate analysis should correspond only with the main period of stem growth.     

Metal resistance systems in cultivated bacteria: are they found in complex communities?

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The fallacies of hope: will we discover new antibiotics to combat pathogenic bacteria in time?

While newly developed technologies have revolutionized the classical approaches to combating infectious diseases, the difficulties associated with developing novel antimicrobials mean that these technologies have not yet been used to introduce new compounds into the market. The new technologies, including genomics and structural biology, open up exciting possibilities for the discovery of antibiotics. However, a substantial effort to pursue research, and moreover to incorporate the results into the production chain, is required in order to bring new antimicrobials to the final user. In the current scenario of emerging diseases and the rapid spread of antibiotic resistance, an active policy to support these requirements is vital. Otherwise, many valuable programmes may never be fully developed for lack of "interest" and funds (private and public). Will we react in time to avoid potential disaster?     

Mechanosensitive channels in bacteria: signs of closure?

Bacterial mechanosensitive channels are activated by increases in tension in the lipid bilayer of the cytoplasmic membrane, where they transiently create large pores in a controlled manner. Mechanosensitive channel research has benefited from advances in electrophysiology, genomics and molecular genetics as well as from the application of biophysical techniques. Most recently, new analytical methods have been used to complement existing knowledge and generate insights into the molecular interactions that take place between mechanosensitive channel proteins and the surrounding membrane lipids. This article reviews the latest developments.     

Trypanosomes and mammalian sperm: one of a kind?

Flagellar-mediated motility is an indispensable function for cell types as evolutionarily distant as mammalian sperm and kinetoplastid parasites, a large group of flagellated protozoa that includes several important human pathogens. Despite the obvious importance of flagellar motility, little is known about the signalling processes that direct the frequency and wave shape of the flagellar beat, or those that provide the motile cell with the necessary environmental cues that enable it to aim its movement. Similarly, the energetics of the flagellar beat and the problem of a sufficient ATP supply along the entire length of the beating flagellum remain to be explored. Recent proteome projects studying the flagella of mammalian sperm and kinetoplastid parasites have provided important information and have indicated a surprising degree of similarities between the flagella of these two cell types.     

How could preventive therapy affect the prevalence of drug resistance? Causes and consequences

Various forms of preventive and prophylactic antimicrobial therapies have been proposed to combat HIV (e.g. pre-exposure prophylaxis), tuberculosis (e.g. isoniazid preventive therapy) and malaria (e.g. intermittent preventive treatment). However, the potential population-level effects of preventative therapy (PT) on the prevalence of drug resistance are not well understood. PT can directly affect the rate at which resistance is acquired among those receiving PT. It can also indirectly affect resistance by altering the rate at which resistance is acquired through treatment for active disease and by modifying the level of competition between transmission of drug-resistant and drug-sensitive pathogens. We propose a general mathematical model to explore the ways in which PT can affect the long-term prevalence of drug resistance. Depending on the relative contributions of these three mechanisms, we find that increasing the level of coverage of PT may result in increases, decreases or non-monotonic changes in the overall prevalence of drug resistance. These results demonstrate the complexity of the relationship between PT and drug resistance in the population. Care should be taken when predicting population-level changes in drug resistance from small pilot studies of PT or estimates based solely on its direct effects.