Bacteria that attach to surfaces aggregate in a hydrated polymeric matrix of their own synthesis to form biofilms. Formation of these sessile communities and their inherent resistance to antimicrobial agents are at the root of many persistent and chronic bacterial infections. Studies of biofilms have revealed differentiated, structured groups of cells with community properties. Recent advances in our understanding of the genetic and molecular basis of bacterial community behavior point to therapeutic targets that may provide a means for the control of biofilm infections.

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Bacterial biofilms : A common cause of persistent infections

https://www.thelancet.com/pdfs/journals/lancet/PIIS0140-6736(01)05321-1.pdf

Antibiotic resistance of bacteria in biofilms

https://www.cell.com/trends/microbiology/pdf/S0966-842X(00)01913-2.pdf

Mechanisms of biofilm resistance to antimicrobial agents

The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. Concurrent sequencing of negative control samples is strongly advised.

/pdf/reagent-and-laboratory-contamination-can-critically-impact-3f8o71vvck.pdf

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

According to a public announcement by the US National Institutes of Health
 , “Biofilms are medically important, accounting for over 80% of microbial infections in the body”. Yet bacterial biofilms remain poorly understood and strategies for their control remain underdeveloped. Standard antimicrobial treatments typically fail to eradicate biofilms, which can result in chronic infection and the need for surgical removal of afflicted areas. The need to create effective therapies to counter biofilm infections presents one of the most pressing challenges in anti-bacterial drug development. In this article, the mechanisms that underlie biofilm resistance to antimicrobial chemotherapy will be examined, with particular attention being given to potential avenues for the effective treatment of biofilms.

/pdf/understanding-biofilm-resistance-to-antibacterial-agents-pnlgfboaq5.pdf

Understanding biofilm resistance to antibacterial agents.

Stress resulting from a variety of chemical and physical environments has been recognized in indicator bacteria. A review by Busta (1976) summarizes the extensive work that has been carried out to describe indicator microorganisms sublethally impaired due to a variety of causes associated with foods. Workers in the area of water microbiology are also gaining an appreciation of the importance of these stressed cells in the assessment of water quality using bacterial indicators. Chemical agents, including chlorine, that are employed in water disinfection processes are important causes of bacterial stress injury. As a result, a significant portion of the total population of indicator bacteria in water might not be enumerated (using the selective procedures that are currently employed) and inaccurate water quality determinations could result. Alternative water disinfection agents that are being suggested, such as ozone, chlorine dioxide, and ultraviolet irradiation, will also probably lead to the same result. In addition, heat from thermal pollution and interactions with other microorganisms or chemicals (including disinfectants and metals) also exert stress that could further debilitate indicator bacteria in various waters and effluents. A need for improved enumeration procedures has accompanied the recognition of injured indicator bacteria in chlorinated waters and wastewaters. This movement has also stimulated interest in the underlying mechanism of cellular damage that is responsible for the submaximal recovery of coliforms from disinfected waters. Various groups have reported that a number of biochemical, genetic, and physiological processes are impaired by chlorine exposure under differing conditions. Evidence from our laboratory and elsewhere implicates functions associated with the cell envelope, i.e., the uptake of extracellular organic substrates, as the primary cellular target of chlorine under conditions that are similar to those in the field. Additional data from our group indicate that sublethal damage from chlorine can be reversed under suitable nonselective conditions. Recent efforts have led to the development of new methods to enumerate injured fecal streptococcus, total and fecal coliform bacteria from chlorinated waters and wastewater. These procedures each yield data that are comparable with that obtained using the more cumbersome MPN method. As a result, the best characteristics of both methods may now be found in three relatively simple MF procedures. Some of these advances have been described in a new section (#921) of the fifteenth edition of "Standard Methods for the Examination of Water and Wastewater" entitled "Stressed Organisms" (APHA, 1981). However, it is anticipated that new and better water quality assessment methodologies will emerge from the growing literature concerning the physiological and biochemical behavior of indicator microorganisms in water and wastewater.(ABSTRACT TRUNCATED AT 400 WORDS)

Enumeration of Indicator Bacteria Exposed to Chlorine

Distribution of the McMurdo Station sewage plume

Health significance and occurrence of injured bacteria in drinking water

The origin of hydrogen sulfide in southeastern Montana groundwaters was investigated. Sulfate‐reducing bacteria were detected in 25 of 26 groundwater samples in numbers ranging from 2.0 × 101 to greater than 2.4 × 104 bacteria per 100 ml. Stable sulfur isotope fractionation studies indicated a biological role in sulfate reduction. However, sulfate‐reducing activity as determined by use of a radioactive sulfur isotope was observed in only 1 of 16 samples. It is postulated that bacterial dissimilatory sulfate reduction is responsible for a major portion of the sulfide produced in these groundwaters and that these bacteria are most likely active in the adsorbed state, possibly in subsurface microzones where environmental conditions are conducive to sulfate reduction.

Dissimilatory bacterial sulfate reduction in montana groundwaters

Physiological and morphological changes in Escherichia coli exposed to oligotrophic natural waters and reagent grade water were studied Several lines of evidence indicated that short-term exposure in water causes cellular envelope damage Increasing susceptibility to lysozyme, lag time before cell division, and injury as defined by differential counts on selective and nonselective media occurred with exposure time Electron micrographs of injured cells showed morphological changes in cell envelope

Gordon A. McFeters

Papers

Enumeration of Indicator Bacteria Exposed to Chlorine

Distribution of the McMurdo Station sewage plume

Health significance and occurrence of injured bacteria in drinking water

Dissimilatory bacterial sulfate reduction in montana groundwaters

Cell envelope damage in Escherichia coli caused by short-term stress in water.