The cost of antibiotic resistance from a bacterial perspective

Interaction with a phage gene underlie costs of a β-lactamase

The fitness cost of an antibiotic resistance gene (ARG) can differ across host strains, creating refuges that allow the maintenance of an ARG in the absence of direct selection for its resistance phenotype. Despite the importance of such ARG-host interactions for predicting ARG dynamics, the basis of ARG fitness costs and their variability between hosts are not well understood. We determined the genetic basis of a host-dependent cost of a β-lactamase, blaTEM-116*, that conferred a significant cost in one Escherichia coli strain but was close to neutral in 11 other Escherichia spp. strains. Selection of a blaTEM-116*-encoding plasmid in the strain in which it initially had a high cost resulted in rapid and parallel compensation for that cost through mutations in a P1-like phage gene, relAP1. When the wild-type relAP1 gene was added to a strain in which it was not present and in which blaTEM-116* was neutral, it caused the ARG to become costly. Thus, relAP1 is both necessary and sufficient to explain blaTEM-116* costs in at least some host backgrounds. To our knowledge, these findings represent the first demonstrated case of the cost of an ARG being influenced by a genetic interaction with a phage gene. The interaction between a phage gene and a plasmid-borne ARG highlights the complexity of selective forces determining the maintenance and spread of ARGs and, by extension, encoding phage and plasmids in natural bacterial communities.IMPORTANCEAntibiotic resistance genes (ARGs) play a major role in the increasing problem of antibiotic resistance in clinically relevant bacteria. Selection of these genes occurs in the presence of antibiotics, but their eventual success also depends on the sometimes substantial costs they impose on host bacteria in antibiotic-free environments. We evolved an ARG that confers resistance to penicillin-type antibiotics in one host in which it did confer a cost and in one host in which it did not. We found that costs were rapidly and consistently reduced through parallel genetic changes in a gene encoded by a phage that was infecting the costly host. The unmutated version of this gene was sufficient to cause the ARG to confer a cost in a host in which it was originally neutral, demonstrating an antagonism between the two genetic elements and underlining the range and complexity of pressures determining ARG dynamics in natural populations.

Using evolutionary principles to make clinical decisions: a case series of urinary tract infections

The principles of evolutionary medicine have significant potential to be useful in a wide variety of clinical situations. Despite this, few demonstrations of clinical applications exist. To address this paucity, a case series applying evolutionary medicine principles to urinary tract infections, a common medical condition is presented. This series demonstrates how applying evolutionary medicine principles can be used to augment clinical decision-making.

Characterization of IncI1/ST71 and IncF18:A-:B1 multidrug-resistance plasmids from an avian Escherichia coli isolate

To characterize IncI1 and IncF18:A-:B1 multidrug-resistance plasmids from an avian Escherichia coli isolate, antibiotic susceptibility testing, conjugation assays, transformation assays, S1-PFGE, and WGS analysis were performed. The 119,457-bp plasmid pEC014-1 with a multidrug-resistance region (MRR) containing four different segments interspersed with six IS26 elements, belonged to incompatibility group I1 and sequence type 71. The 154,516-bp plasmid pEC014-2 with two replicons, typed as FII-18 and FIB-1, carried 14 resistance determinants including bla_TEM-1b, bla_OXA-1, oqxAB, dfrA17, aac(6')-Ib-cr, sul1, sul2, tet(A), floR, catB3, hph(aph(4)-Ia), aacC4(aac(3)-IV), aadA5, arr-3, and a merEDACPTR loci in MRR, and additionally encoded three virulence loci: iroNEDCB, sitABCD, and iucABCD-iutA. Plasmid stability assays showed that pEC014-1 and pEC014-2 were stable in recipient E. coli C600 for at least 15 days of passage. Competition assays were carried out to evaluate the fitness impact of pEC014-2 carriage in vitro, revealing a decrease in host fitness. Growth kinetics showed that the growth rate for pEC014-1 or/and pEC014-2 bearing cells was significantly slower than that of the E. coli C600 host strain in the exponential stage (p < 0.01), with only cells carrying pEC014-1 sustaining rapid growth after 6 h of exponential growth. Our findings highlight the mosaic structures of epidemic plasmid IncI1/ST71 and F18:A-:B1 lineages and contribute to a better understanding of the evolution and dissemination of these multidrug resistance and virulence plasmids.

Inter-Relationship Between a Transcriptional Regulator of Flagella Genes cj0440c and Thiamine Metabolic Pathway in Campylobacter jejuni

Campylobacter jejuni is a major cause of gastroenteritis in humans. It has been reported that the pathogenesis of C. jejuni is closely related to the formation, adhesion, and invasion of flagella toxin in host epithelial cells. A putative transcriptional regulator, known as cj0440c, is thought to be involved in the regulation of flagellar synthesis. However, confirmation of this hypothesis requires deep insight into the regulation mechanism of cj0440c and its possible relationship with different antibiotics. Therefore, the study explained here was designed to determine the relationship and function (phenotypically and genotypically) of cj0440c in the flagellar synthesis of C. jejuni NCTC11168. The study determined the mode of expression of cj0440c and flagella-related genes under exposure to various drugs. To verify the involvement of cj0440c protein in the metabolic pathway of thiamine, an enzymatic hydrolysis experiment was performed and analyzed through the application of mass spectrometry. The overexpression vector of C. jejuni NCTC11168 was also constructed to find out whether or not target genes were regulated by cj0440c. The findings of the study showed that cj0440c and other flagella-related genes were expressed differentially under the influence of various antibiotics including erythromycin, tylosin, azithromycin, gentamicin, etimicin, enrofloxacin, gatifloxacin, tetracycline, and tigecycline. The analysis showed that the cj0440c protein did not catalyze the degradation of thiamine. In conclusion, the study aids in the understanding of the inter-relationship between the regulatory mechanism of flagella genes and the thiamine metabolic pathway.

The role of self-maintaining resilient reaction networks in the origin and evolution of life

We characterize living systems as resilient "chemical organizations", i.e. self-maintaining networks of reactions that are able to resist a wide range of perturbations. Dissipative structures, such as flames or convection cells, are also self-maintaining, but much less resilient. We try to understand how life could have originated from such self-organized structures, and evolved further, by acquiring various mechanisms to increase resilience. General mechanisms include negative feedback, buffering of resources, and degeneracy (producing the same resources via different pathways). Specific mechanisms use catalysts, such as enzymes, to enable reactions that deal with specific perturbations. This activity can be regulated by "memory" molecules, such as DNA, which selectively produce catalysts when needed. We suggest that major evolutionary transitions take place when living cells of different types or species form a higher-order organization by specializing in different functions and thus minimizing interference between their reactions.

Microbial Community Structure and Bacterial Lineages Associated with Sulfonamides Resistance in Anthropogenic Impacted Larut River

Anthropogenic activities often contribute to antibiotic resistance in aquatic environments. Larut River Malaysia is polluted with both organic and inorganic pollutants from domestic and industrial wastewater that are probably treated inadequately. The river is characterized by high biochemical oxygen demand, chemical oxygen demand, total suspended solids, ammonia, and heavy metals. In our previous study, sulfonamides (SAs) and sulfonamide resistance genes (sul) were detected in the Larut River. Hence, in this study, we further examined the microbial community structure, diversity of sulfonamide-resistant bacteria (SARB), and their resistance genes. The study also aimed at identifying cultivable bacteria potential carriers of sul genes in the aquatic environment. Proteobacteria (22.4–66.0%), Firmicutes (0.8–41.6%), Bacteroidetes (2.0–29.4%), and Actinobacteria (5.5–27.9%) were the most dominant phyla in both the effluents and river waters. SARB isolated consisted only 4.7% of the total genera identified, with SAR Klebsiella as the most dominant (38.0–61.3%) followed by SAR Escherichia (0–22.2%) and Acinetobacter (3.2–16.0%). The majority of the SAR Klebsiella isolated from the effluents and middle downstream were positive for sul genes. Sul genes-negative SAR Escherichia and Acinetobacter were low (<20%). Canonical-correlation analysis (CCA) showed that SAs residues and inorganic nutrients exerted significant impacts on microbial community and total sul genes. Network analysis identified 11 SARB as potential sul genes bacterial carriers. These findings indicated that anthropogenic activities exerted impacts on the microbial community structure and SAs resistance in the Larut River.

Rapid decline of ceftazidime resistance in antibiotic-free and sub-lethal environments is contingent on genetic background

Trade-offs of antibiotic resistance evolution, such as fitness cost and collateral sensitivity (CS), could be exploited to drive evolution toward antibiotic susceptibility. Decline of resistance may occur when resistance to other drug leads to CS to the first one and when compensatory mutations, or genetic reversion of the original ones, reduce fitness cost. Here we describe the impact of antibiotic-free and sublethal environments on declining ceftazidime resistance in different Pseudomonas aeruginosa resistant mutants. We determined that decline of ceftazidime resistance occurs within 450 generations, which is caused by newly acquired mutations and not by reversion of the original ones, and that the original CS of these mutants is preserved. In addition, we observed that the frequency and degree of this decline is contingent on genetic background. Our results are relevant to implement evolution-based therapeutic approaches, as well as to redefine global policies of antibiotic use, such as drug cycling.

Chromosomally Located fosA7 in Salmonella Isolates From China

This study aimed to investigate the prevalence of fosfomycin fosA7 in Salmonella enterica isolates from food animals and retail meat products in China and the impact of fosA7 on bacterial fitness. A total of 360 Salmonella isolates collected from 11 provinces and cities in China were detected for fosA7. All fosA7-positive Salmonella isolates were determined minimum inhibitory concentrations (MICs) and sequenced by Illumina Hiseq. The fosA7 gene of S. Derby isolate HA2-WA5 was knocked out. The full length of fosA7 was cloned into vector pBR322 and then transformed into various hosts. MICs of fosfomycin, growth curves, stability, and fitness of fosA7 were evaluated. The fosA7 gene was identified in S. Derby (ST40, n = 30) and S. Reading (ST1628, n = 5). MICs to fosfomycin of 35 fosA7-positive isolates were 1 to 32 mg/L. All fosA7 were located on chromosomes of Salmonella. The deletion of fosA7 in HA2-WA5 decreased fosfomycin MIC by 16-fold and slightly affected its fitness. The acquisition of plasmid-borne fosA7 enhanced MICs of fosfomycin in Salmonella (1,024-fold) and Escherichia coli (16-fold). The recombinant plasmid pBR322-fosA7 was stable in Salmonella Typhimurium, S. Pullorum, S. Derby, and E. coli, except for Salmonella Enteritidis, and barely affected on the growth of them but significantly increased biological fitness in Salmonella. The spread of specific Salmonella serovars such as S. Derby ST40 will facilitate the dissemination of fosA7. fosA7 can confer high-level fosfomycin resistance and enhance bacterial fitness in Salmonella if transferred on plasmids; thus, it has the potential to be a reservoir of the mobilized fosfomycin resistance gene.

Evolutionary biology and development model of medicines: A necessary 'pas de deux' for future successful bacteriophage therapy

The increase in frequency of multidrug-resistant bacteria worldwide is largely the result of the massive use of antibiotics in the second half of the 20th century. These relatively recent changes in human societies revealed the great evolutionary capacities of bacteria towards drug resistance. In this article, we hypothesize that the success of future antibacterial strategies lies in taking into account both these evolutionary processes and the way human activities influence them. Faced with the increasing prevalence of multidrug-resistant bacteria and the scarcity of new antibacterial chemical molecules, the use of bacteriophages is considered as a complementary and/or alternative therapy. After presenting the evolutionary capacities of bacteriophages and bacteria, we show how the development model currently envisaged (based on the classification of bacteriophages as medicinal products similar to antibacterial chemical molecules) ignores the evolutionary processes inherent in bacteriophage therapy. This categorization imposes to bacteriophage therapy a specific conception of what a treatment and a therapeutic scheme should be as well as its mode of production and prescription. We argue that a new development model is needed that would allow the use of therapeutic bacteriophages fully adapted (after in vitro 'bacteriophage training') to the aetiologic bacteria and/or aimed at rendering bacteria either avirulent or antibiotic-susceptible ('bacteriophage steering'). To not repeat the mistakes made with antibiotics, we must now think about and learn from the ways in which the materialities of microbes (e.g. evolutionary capacities of both bacteriophages and bacteria) are intertwined with those of societies.

Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design

Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.

Fecal indicators, pathogens, antibiotic resistance genes, and ecotoxicity in Galveston Bay after Hurricane Harvey

Unprecedented rainfall after Hurricane Harvey caused a catastrophic flood in the southern coast of Texas, and flushed significant floodwater and sediments into Galveston Bay, the largest estuary along the Texas Gulf Coast. This study investigated the immediate and long-term (6 months post-Harvey) fecal indicators, pathogenic bacteria, antibiotic resistance genes (ARGs), and ecotoxicity in the Galveston Bay. Dramatic decrease of salinity profile to zero, increased levels of fecal indicator bacteria and pathogenic bacteria, and detection of various ARGs were observed in the water and sediment samples collected 2 weeks post-Harvey. High levels of Bla_TEM and cytotoxicity measured by yeast bioluminescent assay (BLYR) were also observed especially near the river mouths. While Vibrio spp. was dominant in water, much higher abundance of fecal indicator bacteria and pathogen were detected in the sediments. A decreasing trend of Bla_TEM and cytotoxicity was observed in March 2018 samples, suggesting the Bay has returned to its pre-hurricane conditions 6 months post-Harvey. Interestingly, the abundance of fecal indicator bacteria and pathogens were shifted dramatically according to high-streamflow and low-streamflow seasons in the Bay. The data are useful to construct the model of risk assessment in coastal estuaries system and predict the effects of extreme flooding events in the future.

Carriage of antibiotic resistant bacteria flora and its role in the guidance of clinical decision making

There is considerable literature on the threat of antibiotic resistance and its impact on morbidity. However, an under-studied consideration is how carriage of these antibiotic resistant bacteria persist in an individual. The duration that a person harbors a resistant organism is critical in guiding future antimicrobial therapy. Key unexplored questions are the rate of clearance of these organisms and what drives their persistence. This paper attempts to examine these questions and offers some initial answers as well as avenues for further study.

Antimicrobial resistance and COVID-19: Intersections and implications

Before the coronavirus 2019 (COVID-19) pandemic began, antimicrobial resistance (AMR) was among the top priorities for global public health. Already a complex challenge, AMR now needs to be addressed in a changing healthcare landscape. Here, we analyse how changes due to COVID-19 in terms of antimicrobial usage, infection prevention, and health systems affect the emergence, transmission, and burden of AMR. Increased hand hygiene, decreased international travel, and decreased elective hospital procedures may reduce AMR pathogen selection and spread in the short term. However, the opposite effects may be seen if antibiotics are more widely used as standard healthcare pathways break down. Over 6 months into the COVID-19 pandemic, the dynamics of AMR remain uncertain. We call for the AMR community to keep a global perspective while designing finely tuned surveillance and research to continue to improve our preparedness and response to these intersecting public health challenges.

Growth Inhibition and Alternation of Virulence Genes of Salmonella on Produce Products Treated with Polyphenolic Extracts from Berry Pomace

ABSTRACT

Organic farming, including integrated crop-livestock farms and backyard farming, is gaining popularity in the United States, and products from these farms are commonly sold at farmers' markets, local stores, and roadside stalls. Because organic farms avoid using antibiotics and chemicals and because they use composted animal waste and nonprofessional harvesting and packaging methods, their products have an increased risk of cross-contamination with zoonotic pathogens. This study sets out to evaluate the efficiency of new postharvest disinfection processes using natural berry pomace extracts (BPEs) as a means to reduce the bacterial load found in two common leafy greens, spinach and celery. Spinach and celery were inoculated with a fixed bacterial load of Salmonella Typhimurium and later were soaked in BPE-supplemented water (wBPE) for increasing periods of time, at two different temperatures (24 and 4°C). The remaining live bacteria were quantified (log CFU per leaf), and numbers were compared with those on vegetables soaked in water alone. The relative expression of virulence genes (hilA1/C1/D1, invA1/C1/E1/F1) of wBPE-treated Salmonella Typhimurium was determined. For spinach, there was a significant (P < 0.05) reduction of Salmonella Typhimurium: 0.2 to 1.2 log CFU/mL and 0.5 to 5 log CFU/mL at 24 and 4°C, respectively. For celery, there was also a significant (P < 0.05) reduction of Salmonella Typhimurium at either 24 or 4°C. The changes in relative expression of virulence genes of Salmonella Typhimurium isolated from spinach and celery varied depending on the treatment conditions but showed a significant down-regulation of inv genes when treated at 24°C for 1,440 min (P < 0.05). After seven uses, the total polyphenolic compounds in wBPE remained at an effective concentration. This research suggests that soaking these vegetables with BPE-containing water at lower temperatures can still reduce the Salmonella Typhimurium load enough to minimize the risk of infection and alter virulence properties.

HIGHLIGHTS

Neisseria gonorrhoeae 23S rRNA A2059G mutation is the only determinant necessary for high-level azithromycin resistance and improves in vivo biological fitness

Objectives

The global emergence of Neisseria gonorrhoeae isolates displaying high-level azithromycin resistance is a major concern for the currently recommended azithromycin/ceftriaxone dual therapy. N. gonorrhoeae high-level azithromycin resistance has been associated with an A2059G mutation in 23S rRNA. Here we investigated the specific contribution of this 23S rRNA A2059G mutation to high-level azithromycin resistance and its impact on biological fitness.

Methods

A2059G/G2059A alleles were specifically cloned into all four genomic copies of 23S rDNA of an azithromycin-susceptible isolate and a high-level azithromycin-resistant isolate. WT and mutant strains were subsequently investigated for azithromycin susceptibility using the agar dilution method. In addition, their biological fitness was studied by comparative liquid growth in the presence of hydrophobic and amphipathic compounds, by competition assays in a mouse vaginal tract infection model and by competition assays for invasion and intracellular survival.

Results

Azithromycin susceptibility analyses showed that the 23S rRNA A2059G mutation is the only genetic determinant required for N. gonorrhoeae to display the high-level azithromycin resistance phenotype. Further analysis of biological fitness showed that strains containing 2059G outcompeted isogenic strains containing 2059A for colonization in the mouse vaginal tract infection model and for invasion of HeLa cervical epithelial cells. Furthermore, the A2059G mutation enhanced growth in the presence of lithocholic acid or Triton X-100.

Conclusions

Our findings that the 23S rRNA A2059G mutation is sufficient for high-level azithromycin resistance and that this mutation generally enhanced the biological fitness of N. gonorrhoeae have important implications for the currently recommended treatment policies and antimicrobial stewardship programmes.

Catabolism of aromatic β-glucosides by bacteria can lead to antibiotics resistance

Antimicrobial resistance is a serious public health threat worldwide today. Escherichia coli is known to resist low doses of antibiotics in the presence of sodium salicylate and related compounds by mounting non-heritable transient phenotypic antibiotic resistance (PAR). In the present study, we demonstrate that Bgl⁺ bacterial strains harboring a functional copy of the β-glucoside (bgl) operon and are actively hydrolyzing plant-derived aromatic β-glucosides such as salicin show PAR to low doses of antibiotics. The aglycone released during metabolism of aromatic β-glucosides is responsible for conferring this phenotype by de-repressing the multiple antibiotics resistance (mar) operon. We also show that prolonged exposure of Bgl⁺ bacteria to aromatic β-glucosides in the presence of sub-lethal doses of antibiotics can lead to a significant increase in the frequency of mutants that show heritable resistance to higher doses of antibiotics. Although heritable drug resistance in many cases is known to reduce the fitness of the carrier strain, we did not see a cost associated with resistance in the mutants, most of which carry clinically relevant mutations. These findings indicate that the presence of the activated form of the bgl operon in the genome facilitates the survival of bacteria in environments in which both aromatic β-glucosides and antibiotics are present.

Bacterial Transformation Buffers Environmental Fluctuations through the Reversible Integration of Mobile Genetic Elements

Horizontal gene transfer (HGT) promotes the spread of genes within bacterial communities. Among the HGT mechanisms, natural transformation stands out as being encoded by the bacterial core genome. Natural transformation is often viewed as a way to acquire new genes and to generate genetic mixing within bacterial populations. Another recently proposed function is the curing of bacterial genomes of their infectious parasitic mobile genetic elements (MGEs). Here, we propose that these seemingly opposing theoretical points of view can be unified. Although costly for bacterial cells, MGEs can carry functions that are at points in time beneficial to bacteria under stressful conditions (e.g., antibiotic resistance genes). Using computational modeling, we show that, in stochastic environments, an intermediate transformation rate maximizes bacterial fitness by allowing the reversible integration of MGEs carrying resistance genes, although these MGEs are costly for host cell replication. Based on this dual function (MGE acquisition and removal), transformation would be a key mechanism for stabilizing the bacterial genome in the long term, and this would explain its striking conservation.IMPORTANCE Natural transformation is the acquisition, controlled by bacteria, of extracellular DNA and is one of the most common mechanisms of horizontal gene transfer, promoting the spread of resistance genes. However, its evolutionary function remains elusive, and two main roles have been proposed: (i) the new gene acquisition and genetic mixing within bacterial populations and (ii) the removal of infectious parasitic mobile genetic elements (MGEs). While the first one promotes genetic diversification, the other one promotes the removal of foreign DNA and thus genome stability, making these two functions apparently antagonistic. Using a computational model, we show that intermediate transformation rates, commonly observed in bacteria, allow the acquisition then removal of MGEs. The transient acquisition of costly MGEs with resistance genes maximizes bacterial fitness in environments with stochastic stress exposure. Thus, transformation would ensure both a strong dynamic of the bacterial genome in the short term and its long-term stabilization.

Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution

Evolutionary dynamics in large asexual populations is strongly influenced by multiple competing beneficial lineages, most of which segregate at very low frequencies. However, technical barriers to tracking a large number of these rare lineages in bacterial populations have so far prevented a detailed elucidation of evolutionary dynamics. Here, we overcome this hurdle by developing a chromosomal-barcoding technique that allows simultaneous tracking of approximately 450,000 distinct lineages in Escherichia coli, which we use to test the effect of sub-inhibitory concentrations of common antibiotics on the evolutionary dynamics of low-frequency lineages. We find that populations lose lineage diversity at distinct rates that correspond to their antibiotic regimen. We also determine that some lineages have similar fates across independent experiments. By analysing the trajectory dynamics, we attribute the reproducible fates of these lineages to the presence of pre-existing beneficial mutations, and we demonstrate how the relative contribution of pre-existing and de novo mutations varies across drug regimens. Finally, we reproduce the observed lineage dynamics by simulations. Altogether, our results provide a valuable methodology for studying bacterial evolution as well as insights into evolution under sub-inhibitory antibiotic levels.

Efficient reduction of antibiotic residues and associated resistance genes in tylosin antibiotic fermentation waste using hyperthermophilic composting

Insufficient removal of antibiotics and antibiotic resistance genes (ARGs) from waste products can increase the risk of selection for antibiotic resistance in non-clinical environments. While composting is an efficient way to reduce ARGs, most conventional methods are ineffective at processing highly contaminated antibiotic fermentation waste. Here we explored the efficacy and underlying mechanisms of hyperthermophilic composting at removing tylosin antibiotic fermentation residues (TFR) and associated ARGs and mobile genetic elements (MGEs; plasmids, integrons and transposon). Hyperthermophilic composting removed 95.0% of TFR, 75.8% of ARGs and 98.5% of MGEs and this reduction mainly occurred after extended exposure to temperatures above 60 °C for at least 6 days. Based on sequencing and culture-dependent experiments, reduction in ARGs and MGEs was strongly associated with a decrease in the number of bacterial taxa that were initially associated with ARGs and MGEs. Moreover, we found 94.1% reduction in plasmid genes abundances (ISCR1 and IncQ-oriV) that significantly correlated with reduced ARGs during the composting, which suggests that plasmids were the main carriers for ARGs. We verified this using direct culturing to show that ARGs were more often found in plasmids during the early phase of composting. Together these results suggest that hyperthermophilic composting is efficient at removing ARGs and associated resistance genes from antibiotic fermentation waste by decreasing the abundance of antibiotic resistance plasmids and associated host bacteria.

The ecology of killer yeasts: Interference competition in natural habitats

Killer yeasts are ubiquitous in the environment: They have been found in diverse habitats ranging from ocean sediment to decaying cacti to insect bodies and on all continents including Antarctica. However, environmental killer yeasts are poorly studied compared with laboratory and domesticated killer yeasts. Killer yeasts secrete so-called killer toxins that inhibit nearby sensitive yeasts, and the toxins are frequently assumed to be tools for interference competition in diverse yeast communities. The diversity and ubiquity of killer yeasts imply that interference competition is crucial for shaping yeast communities. Additionally, these toxins may have ecological functions beyond use in interference competition. This review introduces readers to killer yeasts in environmental systems, with a focus on what is and is not known about their ecology and evolution. It also explores how results from experimental killer systems in laboratories can be extended to understand how competitive strategies shape yeast communities in nature. Overall, killer yeasts are likely to occur everywhere yeasts are found, and the killer phenotype has the potential to radically shape yeast diversity in nature.

Multiple antibiotic resistance as a risk factor for mortality and prolonged hospital stay: A cohort study among neonatal intensive care patients with hospital-acquired infections caused by gram-negative bacteria in Vietnam

BACKGROUND

Antibiotic resistance (ABR) is an increasing burden for global health. The prevalence of ABR in Southeast Asia is among the highest worldwide, especially in relation to hospital-acquired infections (HAI) in intensive care units (ICU). However, little is known about morbidity and mortality attributable to ABR in neonates.

AIM

This study aimed to assess mortality and the length of hospitalization attributable to ABR in gram-negative bacteria (GNB) causing HAI in a Vietnamese neonatal ICU (NICU).

METHODS

We conducted a prospective cohort study (n = 296) in a NICU in Hanoi, Vietnam, from March 2016 to October 2017. Patients isolated with HAI caused by GNB were included. The exposure was resistance to multiple antibiotic classes, the two outcomes were mortality and length of hospital stay (LOS). Data were analysed using two regression models, controlling for confounders and effect modifiers such as co-morbidities, time at risk, severity of illness, sex, age, and birthweight.

RESULTS

The overall case fatality rate was 44.3% and the 30 days mortality rate after infection was 31.8%. For every additional resistance to an antibiotic class, the odds of a fatal outcome increased by 27% and LOS increased by 2.1 days. These results were statistically significant (p < 0.05).

CONCLUSION

ABR was identified as a significant risk factor for adverse outcomes in neonates with HAI. These findings are generally in line with previous research in children and adults. However, heterogeneous study designs, the neglect of important confounders and varying definitions of ABR impair the validity, reliability, and comparability of results.

Development of attenuated erythromycin-resistant Streptococcus agalactiae vaccine for tilapia (Oreochromis niloticus) culture

Streptococcus agalactiae is an important pathogen in fish, causing great losses of intensive tilapia farming. To develop a potential live attenuated vaccine, a re-attenuated S. agalactiae (named TFJ-ery) was developed from a natural low-virulence S. agalactiae strain TFJ0901 through selection of resistance to erythromycin. The biological characteristics, virulence, stability and the immunization protective efficacy to tilapia of TFJ-ery were determined. The results indicated that TFJ-ery grew at a slower rate than TFJ0901. The capsule thickness of TFJ-ery was significantly less (p < 0.05) than TFJ0901. When Nile tilapia were intraperitoneally (IP) injected with TFJ-ery, the mortality of fish was decreased than that injected with TFJ0901. The RPS of fish immunized with TFJ-ery at a dose of 5.0 × 10⁷ CFU was 95.00%, 93.02% and 100.00% at 4, 8 and 16 weeks post-vaccination, respectively. ELISA results showed that the vaccinated fish produced significantly higher (p < 0.05) antibody titres compared to those of control at 2 or 4 weeks post-vaccination. Taken together, our results suggest that erythromycin could be used to attenuate S. agalactiae, and TFJ-ery is a potent attenuated vaccine candidate to protect tilapia against S. agalactiae infections.

Involvement of the RND efflux pump transporter SmeH in the acquisition of resistance to ceftazidime in Stenotrophomonas maltophilia

The emergence of antibiotic resistant Gram-negative bacteria has become a serious global health issue. In this study, we have employed the intrinsically resistant opportunistic pathogen Stenotrophomonas maltophilia as a model to study the mechanisms involved in the acquisition of mutation-driven resistance to antibiotics. To this aim, laboratory experimental evolution studies, followed by whole-genome sequencing, were performed in the presence of the third-generation cephalosporin ceftazidime. Using this approach, we determined that exposure to increasing concentrations of ceftazidime selects high-level resistance in S. maltophilia through a novel mechanism: amino acid substitutions in SmeH, the transporter protein of the SmeGH RND efflux pump. The recreation of these mutants in a wild-type background demonstrated that, in addition to ceftazidime, the existence of these substitutions provides bacteria with cross-resistance to other beta-lactam drugs. This acquired resistance does not impose relevant fitness costs when bacteria grow in the absence of antibiotics. Structural prediction of both amino acid residues points that the observed resistance phenotype could be driven by changes in substrate access and recognition.

Adaptation Through Lifestyle Switching Sculpts the Fitness Landscape of Evolving Populations: Implications for the Selection of Drug-Resistant Bacteria at Low Drug Pressures

Novel genotypes evolve under selection through mutations in pre-existing genes. However, mutations have pleiotropic phenotypic effects that influence the fitness of emerging genotypes in complex ways. The evolution of antimicrobial resistance is mediated by selection of mutations in genes coding for antibiotic-target proteins. Drug-resistance is commonly associated with a fitness cost due to the impact of resistance-conferring mutations on protein function and/or stability. These costs are expected to prohibit the selection of drug-resistant mutations at low drug pressures. Using laboratory evolution of rifampicin resistance in Escherichia coli, we show that when exposed intermittently to low concentration (0.1 × minimal inhibitory concentration) of rifampicin, the evolution of canonical drug resistance was indeed unfavorable. Instead, these bacterial populations adapted by evolving into small-colony variants that displayed enhanced pellicle-forming ability. This shift in lifestyle from planktonic to pellicle-like was necessary for enhanced fitness at low drug pressures, and was mediated by the genetic activation of the fim operon promoter, which allowed expression of type I fimbriae. Upon continued low drug exposure, these bacteria evolved exclusively into high-level drug-resistant strains through mutations at a limited set of loci within the rifampicin-resistance determining region of the rpoB gene. We show that our results are explained by mutation-specific epistasis, resulting in differential impact of lifestyle switching on the competitive fitness of different rpoB mutations. Thus, lifestyle-alterations that are selected at low selection pressures have the potential to modify the fitness effects of mutations, change the genetic structure, and affect the ultimate fate of evolving populations.

Rifampicin resistance in Staphylococcus epidermidis: molecular characterisation and fitness cost of rpoB mutations

The molecular mechanisms and characteristics of rifampicin (RIF) resistance in Staphylococcus epidermidis are poorly characterised, even though S. epidermidis is one of the most common nosocomial pathogens associated with indwelling medical device-related infections. The aim of this study was to investigate the evolution of RIF resistance and to characterise the associated molecular mechanisms in S. epidermidis. RIF-resistant mutants from two RIF-susceptible S. epidermidis strains (RP62A and IDRL-8883) were selected through in vitro and in vivo exposure to RIF. A total of 16 colonies with an RP62A background and 63 colonies with an IDRL-8883 background were analysed for rpoB mutations. The fitness of RIF-susceptible and isogenic RIF-resistant strains was assessed using a paired competition assay and by comparing generation times. All mutations detected were in cluster I of rpoB. The following five amino acid substitutions were selected in vitro: Asp471→Asn; Asp471→Gly; Asp471→Val; Ser486→Tyr; and His481→Tyr. The following three amino acid substitutions were selected in vivo: His481→Tyr; Gln468→Lys; and Ser486→Phe. Asp471→Asn and Asp471→Gly changes were associated with susceptible minimal inhibitory concentrations (MICs). In vitro competition assays revealed that all RIF-resistant mutants other than Ser486→Tyr and Ser486→Phe had a relative fitness of <1.0. His481→Tyr mutations had their own specific fitness costs and effects on growth rate, irrespective of strain background. In conclusion, the current study presents molecular characterisations and fitness costs of several rpoB mutations in S. epidermidis.

Modulation of Global Transcriptional Regulatory Networks as a Strategy for Increasing Kanamycin Resistance of the Translational Elongation Factor-G Mutants in Escherichia coli

Evolve and resequence experiments have provided us a tool to understand bacterial adaptation to antibiotics. In our previous work, we used short-term evolution to isolate mutants resistant to the ribosome targeting antibiotic kanamycin, and reported that Escherichia coli develops low cost resistance to kanamycin via different point mutations in the translation Elongation Factor-G (EF-G). Furthermore, we had shown that the resistance of EF-G mutants could be increased by second site mutations in the genes rpoD/cpxA/topA/cyaA Mutations in three of these genes had been discovered in earlier screens for aminoglycoside resistance. In this work, we expand our understanding of these second site mutations, the goal being to understand how these mutations affect the activities of the mutated gene products to confer resistance. We show that the mutation in cpxA most likely results in an active Cpx stress response. Further evolution of an EF-G mutant in a higher concentration of kanamycin than what was used in our previous experiments identified the cpxA locus as a primary target for a significant increase in resistance. The mutation in cyaA results in a loss of catalytic activity and probably results in resistance via altered CRP function. Despite a reduction in cAMP levels, the CyaA^N600Y mutant has a transcriptome indicative of increased CRP activity, pointing to an unknown role for CyaA and / or cAMP in gene expression. From the transcriptomes of double and single mutants, we describe the epistasis between the mutation in EF-G and these second site mutations. We show that the large scale transcriptomic changes in the topoisomerase I (FusA^A608E-TopA^S180L) mutant likely result from increased negative supercoiling in the cell. Finally, genes with known roles in aminoglycoside resistance were present among the misregulated genes in the mutants.

Universal attenuators and their interactions with feedback loops in gene regulatory networks

Using a combination of mathematical modelling, statistical simulation and large-scale data analysis we study the properties of linear regulatory chains (LRCs) within gene regulatory networks (GRNs). Our modelling indicates that downstream genes embedded within LRCs are highly insulated from the variation in expression of upstream genes, and thus LRCs act as attenuators. This observation implies a progressively weaker functionality of LRCs as their length increases. When analyzing the preponderance of LRCs in the GRNs of Escherichia coli K12 and several other organisms, we find that very long LRCs are essentially absent. In both E. coli and M. tuberculosis we find that four-gene LRCs are intimately linked to identical feedback loops that are involved in potentially chaotic stress response, indicating that the dynamics of these potentially destabilising motifs are strongly restrained under homeostatic conditions. The same relationship is observed in a human cancer cell line (K562), and we postulate that four-gene LRCs act as ‘universal attenuators’. These findings suggest a role for long LRCs in dampening variation in gene expression, thereby protecting cell identity, and in controlling dramatic shifts in cell-wide gene expression through inhibiting chaos-generating motifs.

Cj0440c Affects Flagella Formation and In Vivo Colonization of Erythromycin-Susceptible and -Resistant Campylobacter jejuni

Campylobacter jejuni is one of the most common foodborne pathogen worldwide. A putative transcriptional regulator, Cj0440c, was up-regulated in the erythromycin-resistant C. jejuni, however, the precise role of Cj0440c is yet to be determined. The aim of this study was to determine the biological functions of Cj0440c. The Cj0440c isogenic mutants were constructed from erythromycin-susceptible C. jejuni NCTC 11168 (S) and -resistant C. jejuni 68-ER (R), designating as SM and RM, respectively. The isogenic Cj0440c mutants (SM and RM) and parental strains (S and R) were subjected to microarray and qRT-PCR analysis to examine the transcriptional profile changes contributed by Cj0440c. The antimicrobial susceptibility, flagellar morphology, in vitro growth and in vivo colonization in chickens were carried out to analyze the biological function of Cj0440c. The results showed that 17 genes were down-regulated in SM compared to S, while 9 genes were down-regulated in RM compared to R. The genes with transcriptional change were mainly involved in flagella biosynthesis and assembly. Using transmission electron microscopy, we found that the filaments were impaired in SM and lost in RM. The chicken colonization experiments showed that Cj0440c mutants (SM and RM) had reduced colonization ability in chickens when compared with corresponding parental strains (S and R). In conclusion, Cj0440c regulates flagella biosynthesis and assembly, and consequently affect the in vivo colonization of erythromycin-susceptible and -resistant C. jejuni.

Fitness costs associated with the acquisition of antibiotic resistance

Acquisition of antibiotic resistance is a relevant problem for human health. The selection and spread of antibiotic-resistant organisms not only compromise the treatment of infectious diseases, but also the implementation of different therapeutic procedures as organ transplantation, advanced surgery or chemotherapy, all of which require proficient methods for avoiding infections. It has been generally accepted that the acquisition of antibiotic resistance will produce a general metabolic burden: in the absence of selection, the resistant organisms would be outcompeted by the susceptible ones. If that was always true, discontinuation of antibiotic use would render the disappearance of resistant microorganisms. However, several studies have shown that, once resistance emerges, the recovery of a fully susceptible population even in the absence of antibiotics is not easy. In the present study, we review updated information on the effect of the acquisition of antibiotic resistance in bacterial physiology as well as on the mechanisms that allow the compensation of the fitness costs associated with the acquisition of resistance.

Prevalence of Multidrug-Resistant Bacteria from U.S.-Grown and Imported Fresh Produce Retailed in Chain Supermarkets and Ethnic Stores of Davidson County, Tennessee

The aim of this study was to determine whether U.S.-grown and imported fresh produce retailed in ethnic stores and chain supermarkets was a reservoir of antibiotic-resistant bacteria. A total of 360 (129 imported and 231 U.S.-grown) samples of fresh produce were purchased from retail stores and analyzed for Enterobacteriaceae , including three pathogenic bacteria ( Escherichia coli O157:H7, Shigella , and Salmonella ), using standard methods. Presumptive pathogenic isolates were confirmed using PCR. The mean Enterobacteriaceae counts for imported produce were 6.87 ± 0.15 log CFU/g and 7.16 ± 0.11 log CFU/g in ethnic stores and chain supermarkets, respectively. For U.S.-grown produce, the contamination levels were at 8.35 ± 0.17 log CFU/g and 7.52 ± 0.13 log CFU/g in ethnic stores and chain supermarkets, respectively. Salmonella (0 and 0.3%), Shigella (1.7 and 0.6%), E. coli (3.1 and 1.4%), Enterobacter (9.4 and 8.6%), Klebsiella (6.7 and 0.6%), and Serratia (5.8 and 1.4%) were detected in produce from ethnic stores and chain supermarkets, respectively. None of the samples were positive for E. coli O157:H7. Regarding distribution by produce type, leafy vegetables had a significantly (P < 0.05) higher prevalence of Enterobacteriaceae (19.2%) than the other types, followed by root vegetables (6.4%), tomatoes (5.6%), and fruits (3.9%). Antibiotic-resistant Salmonella , Shigella , E. coli , Enterobacter , Klebsiella , and Erwinia bacteria were also isolated from fresh produce. The frequencies of vancomycin resistance (98.1 and 100%) were significantly higher (P < 0.05) than the frequencies of ampicillin resistance (42.3 and 72.9%) for imported and U.S.-grown produce, respectively. Despite the increased attention to the role of imported produce as a source of antimicrobial resistance, this study indicates that U.S.-grown produce is also contaminated with antibiotic-resistant bacteria. Good agricultural practices on the farms and washing of fresh produce before consumption are greatly recommended to avoid possible public health hazards.

A Naturally Occurring Single Nucleotide Polymorphism in a Multicopy Plasmid Produces a Reversible Increase in Antibiotic Resistance

ColE1 plasmids are small mobilizable replicons that play an important role in the spread of antibiotic resistance in Pasteurellaceae In this study, we describe how a natural single nucleotide polymorphism (SNP) near the origin of replication of the ColE1-type plasmid pB1000 found in a Pasteurella multocida clinical isolate generates two independent plasmid variants able to coexist in the same cell simultaneously. Using the Haemophilus influenzae Rd KW20 strain as a model system, we combined antibiotic susceptibility tests, quantitative PCRs, competition assays, and experimental evolution to characterize the consequences of the coexistence of the pB1000 plasmid variants. This coexistence produced an increase of the total plasmid copy number (PCN) in the host bacteria, leading to a rise in both the antibiotic resistance level and the metabolic burden produced by pB1000. Using experimental evolution, we showed that in the presence of ampicillin, the bacteria maintained both plasmid variants for 300 generations. In the absence of antibiotics, on the other hand, the bacteria are capable of reverting to the single-plasmid genotype via the loss of one of the plasmid variants. Our results revealed how a single mutation in plasmid pB1000 provides the bacterial host with a mechanism to increase the PCN and, consequently, the ampicillin resistance level. Crucially, this mechanism can be rapidly reversed to avoid the extra cost entailed by the increased PCN in the absence of antibiotics.

Generation of a Stable Plasmid for In Vitro and In Vivo Studies of Staphylococcus Species

A major shortcoming to plasmid-based genetic tools is the necessity of using antibiotics to ensure plasmid maintenance. While selectable markers are very powerful, their use is not always practical, such as during in vivo models of bacterial infection. During previous studies, it was noted that the uncharacterized LAC-p01 plasmid in Staphylococcus aureus USA300 isolates was stable in the absence of a known selection and therefore could serve as a platform for new genetic tools for Staphylococcus species. LAC-p01 was genetically manipulated into an Escherichia coli-S. aureus shuttle vector that remained stable for at least 100 generations without antibiotic selection. The double- and single-stranded (dso and sso) origins were identified and found to be essential for plasmid replication and maintenance, respectively. In contrast, deletion analyses revealed that none of the four LAC-p01 predicted open reading frames were necessary for stability. Subsequent to this, the shuttle vector was used as a platform to generate two plasmids. The first plasmid, pKK22, contains all genes native to the plasmid for use in S. aureus USA300 strains, while the second, pKK30, lacks the four predicted open reading frames for use in non-USA300 isolates. pKK30 was also determined to be stable in Staphylococcus epidermidis Moreover, pKK22 was maintained for 7 days postinoculation during a murine model of S. aureus systemic infection and successfully complemented an hla mutant in a dermonecrosis model. These plasmids that eliminate the need for antibiotics during both in vitro and in vivo experiments are powerful new tools for studies of StaphylococcusIMPORTANCE Plasmid stability has been problematic in bacterial studies, and historically antibiotics have been used to ensure plasmid maintenance. This has been a major limitation during in vivo studies, where providing antibiotics for plasmid maintenance is difficult and has confounding effects. Here, we have utilized the naturally occurring plasmid LAC-p01 from an S. aureus USA300 strain to construct stable plasmids that obviate antibiotic usage. These newly modified plasmids retain stability over a multitude of generations in vitro and in vivo without antibiotic selection. With these plasmids, studies requiring genetic complementation, protein expression, or genetic reporter systems would not only overcome the burden of antibiotic usage but also eliminate the side effects of these antibiotics. Thus, our plasmids can be used as a powerful genetic tool for studies of Staphylococcus species.

Prevalence and Antimicrobial Resistance of Enterobacteriaceae in Shell Eggs from Small-Scale Poultry Farms and Farmers' Markets

Public health concerns over the emergence of antimicrobial resistant bacteria have increased recently. The purpose of this study was to investigate the prevalence of antimicrobial resistant Enterobacteriaceae in shell eggs purchased from small poultry farms and farmers' markets. A total of 504 eggs were pooled to make 252 composite samples, consisting of 2 eggs per composite. The microbial quality of shell eggs was determined by standard quantitative, biochemical, and PCR techniques. Susceptibility to 13 antimicrobial agents was determined by the Kirby-Bauer disk diffusion technique, and results were interpreted based on Clinical and Laboratory Standards Institute values. Shell eggs and egg contents were positive for Escherichia coli (11.9 and 5.2%, respectively), Enterobacter (9.1 and 7.9%), and Serratia (11.5 and 4.8%). Salmonella was isolated from 3.6% of egg shells but not from egg contents. Mean (±SD) Enterobacteriaceae levels (4.4 ± 2.0 log CFU per eggshell) on shell eggs from poultry farms was significantly higher (P ≤ 0.05) than that on shell eggs from farmers' markets (2.1 ± 1.3 log CFU per eggshell). Of the 134 isolates recovered, resistance among isolates from farm and market shell eggs to erythromycin was most common (48.5 and 32.8%, respectively) followed by ampicillin (44.8 and 17.2%), and tetracycline (29.9 and 17.2%). The multiple antibiotic resistance index value for E. coli and Pantoea was 0.62, and that for Salmonella and Klebsiella terrigena was 0.08, indicating that Enterobacteriaceae in shell eggs can be resistant to multiple antimicrobial agents. These data reveal that shell eggs from small poultry farms and farmers' markets can harbor antimicrobial resistant pathogenic and commensal bacteria. Thus, failure to properly handle shell eggs poses a potential health hazard to consumers.

Harnessing Intra-Host Strain Competition to Limit Antibiotic Resistance: Mathematical Model Results

Antibiotic overuse has promoted the spread of antibiotic resistance. To compound the issue, treating individuals dually infected with antibiotic-resistant and antibiotic-vulnerable strains can make their infections completely resistant through competitive release. We formulate mathematical models of transmission dynamics accounting for dual infections and extensions accounting for lag times between infection and treatment or between cure and ending treatment. Analysis using the Next-Generation Matrix reveals how competition within hosts and the costs of resistance determine whether vulnerable and resistant strains persist, coexist, or drive each other to extinction. Invasion analysis predicts that treatment of dually infected cases will promote resistance. By varying antibiotic strength, the models suggest that physicians have two ways to achieve a particular resistance target: prescribe relatively weak antibiotics to everyone infected with an antibiotic-vulnerable strain or give more potent prescriptions to only those patients singly infected with the vulnerable strain after ruling out the possibility of them being dually infected with resistance. Through selectivity and moderation in antibiotic prescription, resistance might be limited.

Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective

Streptococcus pneumoniae inflicts a huge disease burden as the leading cause of community-acquired pneumonia and meningitis. Soon after mainstream antibiotic usage, multiresistant pneumococcal clones emerged and disseminated worldwide. Resistant clones are generated through adaptation to antibiotic pressures imposed while naturally residing within the human upper respiratory tract. Here, a huge array of related commensal streptococcal strains transfers core genomic and accessory resistance determinants to the highly transformable pneumococcus. β-Lactam resistance is the hallmark of pneumococcal adaptability, requiring multiple independent recombination events that are traceable to nonpneumococcal origins and stably perpetuated in multiresistant clonal complexes. Pneumococcal strains with elevated MICs of β-lactams are most often resistant to additional antibiotics. Basic underlying mechanisms of most pneumococcal resistances have been identified, although new insights that increase our understanding are continually provided. Although all pneumococcal infections can be successfully treated with antibiotics, the available choices are limited for some strains. Invasive pneumococcal disease data compiled during 1998 to 2013 through the population-based Active Bacterial Core surveillance program (U.S. population base of 30,600,000) demonstrate that targeting prevalent capsular serotypes with conjugate vaccines (7-valent and 13-valent vaccines implemented in 2000 and 2010, respectively) is extremely effective in reducing resistant infections. Nonetheless, resistant non-vaccine-serotype clones continue to emerge and expand.

Use of phenotype microarrays to study the effect of acquisition of resistance to antimicrobials in bacterial physiology

It is widely accepted that the acquisition of resistance to antimicrobials confers a fitness cost. Different works have shown that the effect of acquiring resistance in bacterial physiology may be more specific than previously thought. Study of these specific changes may help to predict the outcome of resistant organisms in different ecosystems. In addition to changing bacterial physiology, acquisition of resistance either increases or reduces susceptibility to other antimicrobials. In the current article, we review recent information on the effect of acquiring resistance upon bacterial physiology, with a specific focus on studies using phenotype microarray technology.

The complex evolution of antibiotic resistance in Mycobacterium tuberculosis

Multidrug-resistant and extensively drug-resistant tuberculosis (TB) represent a major threat to the control of the disease worldwide. The mechanisms and pathways that result in the emergence and subsequent fixation of resistant strains of Mycobacterium tuberculosis are not fully understood and recent studies suggest that they are much more complex than initially thought. In this review, we highlight the exciting new areas of research within TB resistance that are beginning to fill these gaps in our understanding, whilst also raising new questions and providing future directions.

Evolution of Resistance to Continuously Increasing Streptomycin Concentrations in Populations of Escherichia coli

The evolution of antibiotic resistance in bacteria has become one of the defining problems in modern biology. Bacterial resistance to antimicrobial therapy threatens to eliminate one of the pillars of the practice of modern medicine. Yet, in spite of the importance of this problem, only recently have the dynamics of the shift from antibiotic sensitivity to resistance in a bacterial population been studied. In this study, a novel chemostat method was used to observe the evolution of resistance to streptomycin in a sensitive population of Escherichia coli, which grew while the concentration of antibiotic was constantly increasing. The results indicate that resistant mutants remain at a low frequency for longer than expected and do not begin to rise to a high frequency until the antibiotic concentrations are above the measured MIC, creating a "lull period" in which there were few bacterial cells growing in the chemostats. Overall, mutants resistant to streptomycin were found in >60% of the experimental trial replicates. All of the mutants detected were found to have MICs far above the maximum levels of streptomycin to which they were exposed and reached a high frequency within 96 h.

Interplay between pathogenicity island carriage, resistance profile and plasmid acquisition in uropathogenic Escherichia coli

This study aimed to characterize the relationship between pathogenicity islands (PAIs), single virulence genes and resistance among uropathogenic Escherichia coli, evaluating the resistance plasmid carriage fitness cost related to PAIs. For 65 urinary E. coli, antimicrobial susceptibility and extended-spectrum β-lactamase production were determined with the Vitek 2 Advanced Expert system. Phylogroup determination, detection of PAIs and virulence genes papAH, papC, sfa/foc, afa/dra, iutA, kpsMII, cnf1, eaeA, hlyA, stx1 and stx2, plasmid replicon typing and screening for plasmidic resistance determinants qnr, aac(6')-Ib-cr, qepA and bla(CTX-M) were carried out by PCR. Conjugation was performed between a donor carrying IncF, IncK and bla(CTX-M-15), and receptors carrying one to six PAIs. The relative fitness of transconjugants was estimated by pairwise competition experiments. PAI IV(536) (68 %), gene iutA (57 %) and resistance to ampicillin were the most prevalent traits. PAI I(536), PAI II(536), PAI III(536) and PAI II(J96) were exclusively associated with susceptibility to amoxicillin/clavulanic acid, cefotaxime, ceftazidime, ciprofloxacin, gentamicin and trimethoprim/sulfamethoxazole, and were more prevalent in strains susceptible to ampicillin and cefalotin. PAI IV(536), PAI II(CFT073) and PAI I(CFT073) were more prevalent among isolates showing resistance to amoxicillin/clavulanic acid, cefalotin, cefotaxime, ceftazidime and gentamicin. An inverse relationship was observed between the number of plasmids and the number of PAIs carried. Transconjugants were obtained for receptors carrying three or fewer PAIs. The mean relative fitness rates of these transconjugants were 0.87 (two PAIs), 1.00 (one PAI) and 1.09 (three PAI). The interplay between resistance, PAI carriage and fitness cost of plasmid acquisition could be considered PAI specific, and not necessarily associated with the number of PAIs.

Ultraviolet germicidal irradiation susceptibility of methicillin-resistant Staphylococcus aureus compared with methicillin-susceptible S. aureus

Antibiotic misuse and overuse in both the healthcare and agricultural fields have dramatically increased the prevalence of antibiotic resistance in human pathogens. Two strains of methicillin-resistant Staphylococcus aureus (MRSA) (ATCC 43330 and a wild-type) and 1 strain of methicillin-susceptible S. aureus (ATCC 25923) were challenged (9 runs in triplicate) in a preliminary study with ultraviolet germicidal irradiation (UVGI) doses ranging from 0.25 to 3.00 mJ/cm(2). The mean percent kill was calculated for each strain when compared with the control plates (no exposure to UVGI). Then, each strain was challenged (22 runs in triplicate) with UVGI doses of 2.00, 2.50, and 3.00 mJ/cm(2). The results suggest a difference between the doses required to disinfect surfaces with each strain. Assuming a standard error rate of α = 0.05, there was a significant difference in variance between the MRSA (ATCC 43330 and wild type) strains and the S. aureus (ATCC 25923) methicillin-susceptible strain.

Malthusian Parameters as Estimators of the Fitness of Microbes: A Cautionary Tale about the Low Side of High Throughput

The maximum exponential growth rate, the Malthusian parameter (MP), is commonly used as a measure of fitness in experimental studies of adaptive evolution and of the effects of antibiotic resistance and other genes on the fitness of planktonic microbes. Thanks to automated, multi-well optical density plate readers and computers, with little hands-on effort investigators can readily obtain hundreds of estimates of MPs in less than a day. Here we compare estimates of the relative fitness of antibiotic susceptible and resistant strains of E. coli, Pseudomonas aeruginosa and Staphylococcus aureus based on MP data obtained with automated multi-well plate readers with the results from pairwise competition experiments. This leads us to question the reliability of estimates of MP obtained with these high throughput devices and the utility of these estimates of the maximum growth rates to detect fitness differences.

Influence of carbapenem resistance on mortality of patients with Pseudomonas aeruginosa infection: a meta-analysis

Treatment of infectious diseases caused by the carbapenem-resistant Pseudomonas aeruginosa (CRPA) is becoming more challenging with each passing year. We conducted a meta-analysis to assess the impact of carbapenem resistance on mortality of patients with P. aeruginosa infection. We searched PUBMED, Web of science, EMBASE, Google Scholar and the Cochrane Library up to December 25, 2014, to identify published cohort or case-control studies. 17 studies, including 6660 patients carrying P. aeruginosa, were identified. The pooling analysis indicated that patients infected with CRPA had significantly higher mortality than those infected with carbapenem-susceptible P. aeruginosa (CSPA) (crude OR = 1.64; 95%CI = 1.40, 1.93; adjusted OR = 2.38; 95%CI = 1.53, 3.69). The elevated risk of mortality in patients with CRPA infection was not lessened when stratified by study design, sites of infection, or type of carbapenem, except that the estimate effect vanished in CRPA high-incidence region, South America (crude OR = 1.12; 95%CI = 0.64, 1.99). Begg's (z = 0.95, p = 0.34) and Egger's test (t = 1.23, p = 0.24) showed no evidence of publication bias. Our results suggest that carbapenem resistance may increase the mortality of patients with P. aeruginosa infection, whether under univariate or multivariate analysis.

Myo-inositol improves the host's ability to eliminate balofloxacin-resistant Escherichia coli

Antibiotic-resistant mechanisms are associated with fitness costs. However, why antibiotic-resistant bacteria usually show increasing adaptation to hosts is largely unknown, especially from the host's perspective. The present study reveals the host's varied response to balofloxacin-resistant Escherichia coli (BLFX-R) using an integrated proteome and metabolome approach and identifies myo-inositol and phagocytosis-related proteins as crucial biomarkers. Originally, macrophages have an optimal attractive preference to BLFX-S due to more polarization of BLFX-S than BLFX-R, which renders faster elimination to BLFX-S than BLFX-R. The slower elimination to BLFX-R may be reversed by exogenous myo-inositol. Primarily, myo-inositol depolarizes macrophages, elevating adherence to both BLFX-S and BLFX-R. Since the altered adherence is equal to both strains, the myo-inositol-treated macrophages are free of the barrier to BLFX-R and thereby promote phagocytosis of BLFX-R. This work provides a novel strategy based on metabolic modulation for eliminating antibiotic-resistant bacteria with a high degree of host adaptation.

Studies of Antibiotic Resistance of Beta-Lactamase Bacteria under Different Nutrition Limitations at the Single-Cell Level

Drug resistance involves many biological processes, including cell growth, cell communication, and cell cooperation. In the last few decades, bacterial drug resistance studies have made substantial progress. However, a major limitation of the traditional resistance study still exists: most of the studies have concentrated on the average behavior of enormous amounts of cells rather than surveying single cells with different phenotypes or genotypes. Here, we report our study of beta-lactamase bacterial drug resistance in a well-designed microfluidic device, which allows us to conduct more controllable experiments, such as controlling the nutrient concentration, switching the culture media, performing parallel experiments, observing single cells, and acquiring time-lapse images. By using GFP as a beta-lactamase indicator and acquiring time-lapse images at the single-cell level, we observed correlations between the bacterial heterogeneous phenotypes and their behavior in different culture media. The feedback loop between the growth rate and the beta-lactamase production suggests that the beta-lactamase bacteria are more resistant in a rich medium than in a relatively poor medium. In the poorest medium, the proportion of dormant cells may increase, which causes a lower death rate in the same generation. Our work may contribute to assaying the antibiotic resistance of pathogenic bacteria in heterogeneous complex media.

A tortoise-hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria

In the context of Wright's adaptive landscape, genetic epistasis can yield a multipeaked or "rugged" topography. In an unstructured population, a lineage with selective access to multiple peaks is expected to fix rapidly on one, which may not be the highest peak. In a spatially structured population, on the other hand, beneficial mutations take longer to spread. This slowdown allows distant parts of the population to explore the landscape semiindependently. Such a population can simultaneously discover multiple peaks, and the genotype at the highest discovered peak is expected to dominate eventually. Thus, structured populations sacrifice initial speed of adaptation for breadth of search. As in the fable of the tortoise and the hare, the structured population (tortoise) starts relatively slow but eventually surpasses the unstructured population (hare) in average fitness. In contrast, on single-peak landscapes that lack epistasis, all uphill paths converge. Given such "smooth" topography, breadth of search is devalued and a structured population only lags behind an unstructured population in average fitness (ultimately converging). Thus, the tortoise-hare pattern is an indicator of ruggedness. After verifying these predictions in simulated populations where ruggedness is manipulable, we explore average fitness in metapopulations of Escherichia coli. Consistent with a rugged landscape topography, we find a tortoise-hare pattern. Further, we find that structured populations accumulate more mutations, suggesting that distant peaks are higher. This approach can be used to unveil landscape topography in other systems, and we discuss its application for antibiotic resistance, engineering problems, and elements of Wright's shifting balance process.

Small-plasmid-mediated antibiotic resistance is enhanced by increases in plasmid copy number and bacterial fitness

Plasmids play a key role in the horizontal spread of antibiotic resistance determinants among bacterial pathogens. When an antibiotic resistance plasmid arrives in a new bacterial host, it produces a fitness cost, causing a competitive disadvantage for the plasmid-bearing bacterium in the absence of antibiotics. On the other hand, in the presence of antibiotics, the plasmid promotes the survival of the clone. The adaptations experienced by plasmid and bacterium in the presence of antibiotics during the first generations of coexistence will be crucial for the progress of the infection and the maintenance of plasmid-mediated resistance once the treatment is over. Here we developed a model system using the human pathogen Haemophilus influenzae carrying the small plasmid pB1000 conferring resistance to β-lactam antibiotics to investigate host and plasmid adaptations in the course of a simulated ampicillin therapy. Our results proved that plasmid-bearing clones compensated for the fitness disadvantage during the first 100 generations of plasmid-host adaptation. In addition, ampicillin treatment was associated with an increase in pB1000 copy number. The augmentation in both bacterial fitness and plasmid copy number gave rise to H. influenzae populations with higher ampicillin resistance levels. In conclusion, we show here that the modulations in bacterial fitness and plasmid copy number help a plasmid-bearing bacterium to adapt during antibiotic therapy, promoting both the survival of the host and the spread of the plasmid.

Lytic phages obscure the cost of antibiotic resistance in Escherichia coli

The long-term persistence of antibiotic-resistant bacteria depends on their fitness relative to other genotypes in the absence of drugs. Outside the laboratory, viruses that parasitize bacteria (phages) are ubiquitous, but costs of antibiotic resistance are typically studied in phage-free experimental conditions. We used a mathematical model and experiments with Escherichia coli to show that lytic phages strongly affect the incidence of antibiotic resistance in drug-free conditions. Under phage parasitism, the likelihood that antibiotic-resistant genetic backgrounds spread depends on their initial frequency, mutation rate and intrinsic growth rate relative to drug-susceptible genotypes, because these parameters determine relative rates of phage-resistance evolution on different genetic backgrounds. Moreover, the average cost of antibiotic resistance in terms of intrinsic growth in the antibiotic-free experimental environment was small relative to the benefits of an increased mutation rate in the presence of phages. This is consistent with our theoretical work indicating that, under phage selection, typical costs of antibiotic resistance can be outweighed by realistic increases in mutability if drug resistance and hypermutability are genetically linked, as is frequently observed in clinical isolates. This suggests the long-term distribution of antibiotic resistance depends on the relative rates at which different lineages adapt to other types of selection, which in the case of phage parasitism is probably extremely common, as well as costs of resistance inferred by classical in vitro methods.

Molecular characterization of the cytochrome b gene and in vitro atovaquone susceptibility of Plasmodium falciparum isolates from Kenya

The prevalence of a genetic polymorphism(s) at codon 268 in the cytochrome b gene, which is associated with failure of atovaquone-proguanil treatment, was analyzed in 227 Plasmodium falciparum parasites from western Kenya. The prevalence of the wild-type allele was 63%, and that of the Y268S (denoting a Y-to-S change at position 268) mutant allele was 2%. There were no pure Y268C or Y268N mutant alleles, only mixtures of a mutant allele(s) with the wild type. There was a correlation between parasite 50% inhibitory concentration (IC50) and parasite genetic polymorphism; mutant alleles had higher IC50s than the wild type.