Ciprofloxacin-resistant gram-negative bacilli in the fecal microflora of children

Global mapping of antibiotic resistance rates among clinical isolates of Stenotrophomonas maltophilia: a systematic review and meta-analysis

INTRODUCTION

Infections caused by Stenotrophomonas maltophilia are clinically important due to its intrinsic resistance to a broad range of antibiotics. Therefore, selecting the most appropriate antibiotic to treat S. maltophilia infection is a major challenge.

AIM

The current meta-analysis aimed to investigate the global prevalence of antibiotic resistance among S. maltophilia isolates to the develop more effective therapeutic strategies.

METHOD

A systematic literature search was performed using the appropriate search syntax after searching Pubmed, Embase, Web of Science and Scopus databases (May 2023). Statistical analysis was performed using Pooled and the random effects model in R and the metafor package. A total of 11,438 articles were retrieved. After a thorough evaluation, 289 studies were finally eligible for inclusion in this systematic review and meta-analysis.

RESULT

Present analysis indicated that the highest incidences of resistance were associated with doripenem (97%), cefoxitin (96%), imipenem and cefuroxime (95%), ampicillin (94%), ceftriaxone (92%), aztreonam (91%) and meropenem (90%) which resistance to Carbapenems is intrinsic. The lowest resistance rates were documented for minocycline (3%), cefiderocol (4%). The global resistance rate to TMP-SMX remained constant in two periods before and after 2010 (14.4% vs. 14.6%). A significant increase in resistance to tigecycline and ceftolozane/tazobactam was observed before and after 2010.

CONCLUSIONS

Minocycline and cefiderocol can be considered the preferred treatment options due to low resistance rates, although regional differences in resistance rates to other antibiotics should be considered. The low global prevalence of resistance to TMP-SMX as a first-line treatment for S. maltophilia suggests that it remains an effective treatment option.

Gut microbiota promote biotransformation and bioaccumulation of arsenic in tilapia

Aquatic organisms such as fish can accumulate high levels of arsenic (As) and transform toxic inorganic As (iAs) to non-toxic arsenobetaine (AsB). Whether the gut microbiota are involved in the process of As accumulation and transformation in fish is unclear. Herein, we subjected tilapia (Oreochromis mossambicus) to antibiotic treatment for 19 d to remove the gut microbiota, followed by the dietary exposure to arsenate (As(V)) for 16 d. The antibiotic-treated fish accumulated significantly less total As and AsB levels in the intestine and muscle than the fish in the control group. The gut contents (mixture of microbiota, digestive fluid, and diet debris) in the control fish metabolized As(V) to arsenite (As(III)) and organoarsenicals in vitro, while those in the antibiotic-treated fish lost this ability. As(V) exposure significantly changed the fish gut microbiota community. Stenotrophomonas maltophilia was found to be the dominant species (>60% of total operational taxonomic unit (OTU) number) in the gut microbiota of As-treated fish. The isolated As-resistant strain S. maltophilia SCSIOOM owned a high capability to metabolize As(V) to As(III) and organoarsenicals. Overall, these results demonstrated that the gut microbiota, at least the As-resistant bacteria, were involved in As biotransformation pathways in fish.

Quinolone Consumption by Mothers Increases Their Children's Risk of Acquiring Quinolone-Resistant Bacteriuria

BACKGROUND

Quinolone resistance has been documented in the pediatric population, although their use is limited in children. This study investigated the effect of maternal quinolone use on gram-negative bacterial resistance to quinolones in their offspring.

METHODS

We conducted a population-based, unmatched case-control study during 2010-2017. Cases were all children aged 0.5-17 years with community acquired, gram-negative quinolone-resistant bacteriuria. Controls were similar children with quinolone-sensitive bacteriuria. Only the first positive urine cultures for each child were included. Data on quinolones dispensed to the mother, any antibiotics dispensed to the children, age, sex, ethnicity, and prior hospitalizations were collected. Children with previous quinolone use were excluded.

RESULTS

The study population consisted of 40 204 children. Quinolone resistance was detected in 2182 (5.3%) urine cultures. The median age was 5 years, with 93.7% females and 77.6% Jewish. A total of 26 937 (65%) of the children received any antibiotic and 1359 (3.2%) of the mothers received quinolones in the 6 months preceding bacteriuria. Independent risk factors were quinolone dispensed to the mothers (odds ratio [OR], 1.50 [95% confidence interval {CI}, 1.22-1.85]), Arab ethnicity (OR, 1.99 [95% CI, 1.81-2.19]), and antibiotic dispensed to the child (OR, 1.54 [95% CI, 1.38-1.71]). Compared with children aged 12-17 years, younger children had 1.33-1.43 increased odds for quinolone-resistant bacteriuria.

CONCLUSIONS

Quinolone prescription to mothers was linked to increased risk of community-acquired, quinolone-resistant bacteria in their offspring, by about 50%. This is another example of the deleterious ecological effects of antibiotic use and should be considered when prescribing antibiotics.

Urinary tract infection in patients with spinal cord injury after urodynamics under fosfomycin prophylaxis: a retrospective analysis

Background:

Urinary tract infection (UTI) is a common complication of spinal cord injury (SCI). Urodynamic testing is widely used for characterization of vesico-sphincteric dysfunction and for therapeutic orientation. As an invasive procedure, the risk of UTI is increased so, in some medical centers, antibiotic prophylaxis is instituted. Fosfomycin is one of the antibiotics used.

Objective:

The aim of this study was to evaluate the incidence of UTI after urodynamics in patients with SCI, under fosfomycin prophylaxis.

Methods:

Retrospective analysis was performed on patients with SCI, admitted to a rehabilitation center between January 2016 and June 2017, who underwent urodynamics studies under fosfomycin prophylaxis. Demographic data, risk factors for UTI—bacteriuria before urodynamics, high residual volume (>100 mL), bladder emptying method, vesico-sphincteric dyssynergia, and detrusor hyperactivity were analyzed. The incidence of UTI after urodynamics was evaluated.

Results:

The study included 84 patients, predominantly men 55 (65.5%). The mean age of the patients was 55.6 (18.9). Eleven (22.5%) had vesico-sphincteric dyssynergia, 32 (65.3%) detrusor hyperactivity and 22 (44.9%) had a high residual volume. Thirty-seven (44.1%) had asymptomatic bacteriuria before the urodynamics. Urinary complaints suggestive of UTI after urodynamics were observed in 2(2.4%) of patients, without significant bacteriuria and identification of bacterial agent.

Conclusions:

The incidence of UTI after invasive procedures is reported between 3% and 20% in the literature, so antibiotic prophylaxis has been instituted, although controversial. In the study, in none of the patients the diagnosis of UTI was confirmed. Fosfomycin prophylaxis may have been important in reducing the incidence of UTI.

High prevalence of fluoroquinolone resistance amongst commensal flora of antibiotic naïve neonates: a study from India

BACKGROUND

The emergence of resistance amongst commensal flora is a serious threat to the community. However, there is paucity of data regarding antibiotic resistance in commensals in the absence of antibiotic pressure.

METHODS

Altogether, 100 vaginally delivered antibiotic naïve exclusively breastfed neonates were selected. Stool samples collected on day (D)1, D21 and D60 of birth were cultured. Enterobacteriaceae isolates were screened for nalidixic acid (NA) and ciprofloxacin susceptibility as per CLSI guidelines. In 28 randomly selected neonates, isolates (n=92) resistant to NA and ciprofloxacin were characterized for the presence of plasmid-mediated quinolone resistance (PMQR) genes (qnrA, qnrB and qnrS, qepAand aac(6')-Ib-cr) and mutations in the quinolone resistance determining region (QRDR) of gyrA and parC genes by specific primers and confirmed by sequencing.

RESULTS

A total of 343 Enterobacteriaceae were isolated from 100 neonates. On D1, 58 % of neonates were colonized with at least one Enterobacteriaceae predominantly E. coli. Overall resistance to NA was 60 % but ciprofloxacin resistance increased significantly from 15 % (14/96) on D1 to 38 % (50/132) on D60 (P-value <0.001). The predominant mechanism of fluoroquinolone resistance was mutation in gyrA (n=49) with or without PMQR. PMQR carrying isolates increased more than fivefold from D1 to D60.

CONCLUSION

A high level of fluoroquinolone resistance in gut flora of antibiotic naïve and exclusively breastfed neonates suggests a rampant rise of resistance in the community. The source of resistance genes on D1 is probably maternal flora acquired at birth. High load of PMQR genes in commensal flora are a potential source of spread to pathogenic organisms.

The Use of Systemic and Topical Fluoroquinolones

Appropriate prescribing practices for fluoroquinolones, as well as all antimicrobial agents, are essential as evolving resistance patterns are considered, additional treatment indications are identified, and the toxicity profile of fluoroquinolones in children has become better defined. Earlier recommendations for systemic therapy remain; expanded uses of fluoroquinolones for the treatment of certain infections are outlined in this report. Prescribing clinicians should be aware of specific adverse reactions associated with fluoroquinolones, and their use in children should continue to be limited to the treatment of infections for which no safe and effective alternative exists or in situations in which oral fluoroquinolone treatment represents a reasonable alternative to parenteral antimicrobial therapy.

Faecal carriage of antibiotic resistant Escherichia coli in asymptomatic children and associations with primary care antibiotic prescribing: a systematic review and meta-analysis

Background

The faecal reservoir provides optimal conditions for the transmission of resistance genes within and between bacterial species. As key transmitters of infection within communities, children are likely important contributors to endemic community resistance. We sought to determine the prevalence of antibiotic-resistant faecal Escherichia coli from asymptomatic children aged between 0 and 17 years worldwide, and investigate the impact of routinely prescribed primary care antibiotics to that resistance.

Methods

A systematic search of Medline, Embase, Cochrane and Web of Knowledge databases from 1940 to 2015. Pooled resistance prevalence for common primary care antibiotics, stratified by study country OECD status. Random-effects meta-analysis to explore the association between antibiotic exposure and resistance.

Results

Thirty-four studies were included. In OECD countries, the pooled resistance prevalence to tetracycline was 37.7 % (95 % CI: 25.9–49.7 %); ampicillin 37.6 % (24.9–54.3 %); and trimethoprim 28.6 % (2.2–71.0 %). Resistance in non-OECD countries was uniformly higher: tetracycline 80.0 % (59.7–95.3 %); ampicillin 67.2 % (45.8–84.9 %); and trimethoprim 81.3 % (40.4–100 %). We found evidence of an association between primary care prescribed antibiotics and resistance lasting for up to 3 months post-prescribing (pooled OR: 1.65, 1.36–2.0).

Conclusions

Resistance to many primary care prescribed antibiotics is common among faecal E. coli carried by asymptomatic children, with higher resistance rates in non-OECD countries. Despite tetracycline being contra-indicated in children, tetracycline resistance rates were high suggesting children could be important recipients and transmitters of resistant bacteria, or that use of other antibiotics is leading to tetracycline resistance via inter-bacteria resistance transmission.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-1697-6) contains supplementary material, which is available to authorized users.

Achromobacter respiratory infections

Achromobacteria are ubiquitous environmental organisms that may also become opportunistic pathogens in certain conditions, such as cystic fibrosis, hematologic and solid organ malignancies, renal failure, and certain immune deficiencies. Some members of this genus, such as xylosoxidans, cause primarily nosocomially acquired infections affecting multiple organ systems, including the respiratory tract, urinary tract, and, less commonly, the cardiovascular and central nervous systems. Despite an increasing number of published case reports and literature reviews suggesting a global increase in achromobacterial disease, most clinicians remain uncertain of the organism's significance when clinically isolated. Moreover, effective treatment can be challenging due to the organism's inherent and acquired multidrug resistance patterns. We reviewed all published cases to date of non-cystic fibrosis achromobacterial lung infections to better understand the organism's pathogenic potential and drug susceptibilities. We found that the majority of these cases were community acquired, typically presenting as pneumonias (88%), and were most frequent in individuals with hematologic and solid organ malignancies. Our findings also suggest that achromobacterial lung infections are difficult to treat, but respond well to extended-spectrum penicillins and cephalosporins, such as ticarcillin, piperacillin, and cefoperazone.

Real-Time PCR Assay for Detection and Differentiation of Shiga Toxin-Producing Escherichia coli from Clinical Samples

Timely accurate diagnosis of Shiga toxin-producing Escherichia coli (STEC) infections is important. We evaluated a laboratory-developed real-time PCR (LD-PCR) assay targeting stx1, stx2, and rfbEO157 with 2,386 qualifying stool samples submitted to the microbiology laboratory of a tertiary care pediatric center between July 2011 and December 2013. Broth cultures of PCR-positive samples were tested for Shiga toxins by enzyme immunoassay (EIA) (ImmunoCard STAT! enterohemorrhagic E. coli [EHEC]; Meridian Bioscience) and cultured in attempts to recover both O157 and non-O157 STEC. E. coli O157 and non-O157 STEC were detected in 35 and 18 cases, respectively. Hemolytic uremic syndrome (HUS) occurred in 12 patients (10 infected with STEC O157, one infected with STEC O125ac, and one with PCR evidence of STEC but no resulting isolate). Among the 59 PCR-positive STEC specimens from 53 patients, only 29 (54.7%) of the associated specimens were toxin positive by EIA. LD-PCR differentiated STEC O157 from non-O157 using rfbEO157, and LD-PCR results prompted successful recovery of E. coli O157 (n = 25) and non-O157 STEC (n = 8) isolates, although the primary cultures and toxin assays were frequently negative. A rapid "mega"-multiplex PCR (FilmArray gastrointestinal panel; BioFire Diagnostics) was used retrospectively, and results correlated with LD-PCR findings in 25 (89%) of the 28 sorbitol-MacConkey agar culture-negative STEC cases. These findings demonstrate that PCR is more sensitive than EIA and/or culture and distinguishes between O157 and non-O157 STEC in clinical samples and that E. coli O157:H7 remains the predominant cause of HUS in our institution. PCR is highly recommended for rapid diagnosis of pediatric STEC infections.

Gut Colonization of Healthy Children and Their Mothers With Pathogenic Ciprofloxacin-Resistant Escherichia coli

BACKGROUND

The reservoir of pathogenic ciprofloxacin-resistant Escherichia coli remains unknown.

METHODS

We conducted a prospective cohort study of 80 healthy twins and their mothers to determine the frequency of excretion of ciprofloxacin-resistant, potentially pathogenic E. coli. Stool specimens were cultured selectively for ciprofloxacin-resistant gram-negative bacteria. Isolates were categorized on the basis of additional resistance and virulence profiles. We also prospectively collected clinical metadata.

RESULTS

Fifteen children (19%) and 8 mothers (20%) excreted ciprofloxacin-resistant E. coli at least once. Overall, 33% of 40 families had at least 1 member whose stool specimen yielded ciprofloxacin-resistant E. coli on culture. Fifty-seven submitted stool specimens (2.8%) contained such organisms; clones ST131-H30 and ST405 accounted for 52 and 5 of the positive specimens, respectively. Length of hospital stay after birth (P = .002) and maternal colonization (P = .0001) were associated with subsequent childhood carriage of ciprofloxacin-resistant E. coli; antibiotic use, acid suppression, sex, mode of delivery, and maternal perinatal antibiotic use were not. Ciprofloxacin-resistant E. coli were usually resistant to additional antibiotic classes, and all had virulence genotypes typical of extraintestinal pathogenic E. coli.

CONCLUSIONS

Healthy children and their mothers commonly harbor ciprofloxacin-resistant E. coli with pathogenic potential.

Antibiotics and bacterial resistance in the 21st century

Dangerous, antibiotic resistant bacteria have been observed with increasing frequency over the past several decades. In this review the factors that have been linked to this phenomenon are addressed. Profiles of bacterial species that are deemed to be particularly concerning at the present time are illustrated. Factors including economic impact, intrinsic and acquired drug resistance, morbidity and mortality rates, and means of infection are taken into account. Synchronously with the waxing of bacterial resistance there has been waning antibiotic development. The approaches that scientists are employing in the pursuit of new antibacterial agents are briefly described. The standings of established antibiotic classes as well as potentially emerging classes are assessed with an emphasis on molecules that have been clinically approved or are in advanced stages of development. Historical perspectives, mechanisms of action and resistance, spectrum of activity, and preeminent members of each class are discussed.

Intestinal inflammatory biomarkers and outcome in pediatric Clostridium difficile infections

OBJECTIVES

To identify specific fecal biomarkers for symptomatic Clostridium difficile infection and predictors of poor outcomes.

STUDY DESIGN

We enrolled 65 children with positive C difficile testing (cases) and 37 symptomatic controls. We also analyzed stool samples from colonized and non-colonized asymptomatic children. We performed enzyme immunoassays to determine fecal interleukin (IL)-8, lactoferrin, and phosphorylated-p38 protein concentrations, and quantitative polymerase chain reaction to determine IL-8 and chemokine ligand (CXCL)-5 RNA relative transcript abundances, and C difficile bacterial burden.

RESULTS

Of 68 asymptomatic controls, 16 were colonized with C difficile. Phosphorylated-p38 was specific for C difficile infection but lacked sensitivity. Fecal cytokines were elevated in samples from symptomatic children, whether cases or controls. In children with C difficile infection, fecal CXCL-5 and IL-8 messenger RNA abundances at diagnosis correlated with persistent diarrhea after 5 days of C difficile infection therapy and with treatment with vancomycin. When children with concomitant viral gastroenteritis were excluded, these correlations persisted. Time-to-diarrhea resolution was significantly longer in patients with elevated fecal cytokines at diagnosis. A logistic regression model identified high CXCL-5 messenger RNA abundance as the only predictor of persistent diarrhea. Conversely, fecal C difficile bacterial burden was not different in symptomatic and asymptomatic children and did not correlate with any clinical outcome measure.

CONCLUSIONS

Fecal inflammatory cytokines may be useful in distinguishing C difficile colonization from disease and identifying children with C difficile infection likely to have prolonged diarrhea.

Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes

Emerging antibiotic resistance threatens human health. Gut microbes are an epidemiologically important reservoir of resistance genes (resistome), yet prior studies indicate that the true diversity of gut-associated resistomes has been underestimated. To deeply characterize the pediatric gut-associated resistome, we created metagenomic recombinant libraries in an Escherichia coli host using fecal DNA from 22 healthy infants and children (most without recent antibiotic exposure), and performed functional selections for resistance to 18 antibiotics from eight drug classes. Resistance-conferring DNA fragments were sequenced (Illumina HiSeq 2000), and reads assembled and annotated with the PARFuMS computational pipeline. Resistance to 14 of the 18 antibiotics was found in stools of infants and children. Recovered genes included chloramphenicol acetyltransferases, drug-resistant dihydrofolate reductases, rRNA methyltransferases, transcriptional regulators, multidrug efflux pumps, and every major class of beta-lactamase, aminoglycoside-modifying enzyme, and tetracycline resistance protein. Many resistance-conferring sequences were mobilizable; some had low identity to any known organism, emphasizing cryptic organisms as potentially important resistance reservoirs. We functionally confirmed three novel resistance genes, including a 16S rRNA methylase conferring aminoglycoside resistance, and two tetracycline-resistance proteins nearly identical to a bifidobacterial MFS transporter (B. longum s. longum JDM301). We provide the first report to our knowledge of resistance to folate-synthesis inhibitors conferred by a predicted Nudix hydrolase (part of the folate synthesis pathway). This functional metagenomic survey of gut-associated resistomes, the largest of its kind to date, demonstrates that fecal resistomes of healthy children are far more diverse than previously suspected, that clinically relevant resistance genes are present even without recent selective antibiotic pressure in the human host, and that cryptic gut microbes are an important resistance reservoir. The observed transferability of gut-associated resistance genes to a gram-negative (E. coli) host also suggests that the potential for gut-associated resistomes to threaten human health by mediating antibiotic resistance in pathogens warrants further investigation.

Are prophylactic antibiotics necessary for urodynamic study?

The aim of this study was to assess the efficacy of prophylactic fosfomycin tromethamine (FT) and ciprofloxacin in preventing bacteriuria caused by urodynamic studies (UDS). A total of 426 adult patients presenting for UDS were enrolled the study. A midstream urine sample was taken 72 hours before and 5 days after the procedure. All patients underwent a standard UDS. The 411 patients who had sterile urine before intervention were included in the study. Patients were randomized into three groups. Group1 received no prophylaxis (n = 133), Group 2 (n = 141) received oral ciprofloxacin (500 mg) 1 hour before the procedure, and Group 3 (n = 137) received a single dose of FT approximately 12 hours before the procedure. Bacteriuria was evaluated for each group. Bacteriuria was detected in 3 (2.3%), 6 (4.3%) and 3 patients (1.6%) in Group 1, Group 2, and Group 3, respectively. The most common identified microorganism was Escherichia coli (E coli) in 6 patients (50%). Among the E coli group, extended spectrum beta-lactamase producing E coli was seen in 2 patients (33.3%). Univariate analysis demonstrated that a history of urogenital operation (p < 0.01) and female gender (p < 0.01) were significant risk factors for bacteriuria. On multiple logistic regression analysis, the past urogenital operation history was the only significant independent risk factor for significant bacteriuria after UDS (OR = 14, 95% CI = 1.82-23.8, p = 0.01). The prevalence of bacteriuria after UDS was relatively low in the current study population. Therefore, for most patients, it may be unnecessary to use preventive prophylactic antibiotics. However, our results suggest that in patients with a previous history of urologic surgery, the risk for significant bacteriuria is increased and the use of prophylaxis should be considered.

Global fluoroquinolone resistance epidemiology and implictions for clinical use

This paper on the fluoroquinolone resistance epidemiology stratifies the data according to the different prescription patterns by either primary or tertiary caregivers and by indication. Global surveillance studies demonstrate that fluoroquinolone resistance rates increased in the past years in almost all bacterial species except S. pneumoniae and H. influenzae, causing community-acquired respiratory tract infections. However, 10 to 30% of these isolates harbored first-step mutations conferring low level fluoroquinolone resistance. Fluoroquinolone resistance increased in Enterobacteriaceae causing community acquired or healthcare associated urinary tract infections and intraabdominal infections, exceeding 50% in some parts of the world, particularly in Asia. One to two-thirds of Enterobacteriaceae producing extended spectrum β-lactamases were fluoroquinolone resistant too. Furthermore, fluoroquinolones select for methicillin resistance in Staphylococci. Neisseria gonorrhoeae acquired fluoroquinolone resistance rapidly; actual resistance rates are highly variable and can be as high as almost 100%, particularly in Asia, whereas resistance rates in Europe and North America range from <10% in rural areas to >30% in established sexual networks. In general, the continued increase in fluoroquinolone resistance affects patient management and necessitates changes in some guidelines, for example, treatment of urinary tract, intra-abdominal, skin and skin structure infections, and traveller's diarrhea, or even precludes the use in indications like sexually transmitted diseases and enteric fever.

Diversity of individual dynamic patterns of emergence of resistance to quinolones in Escherichia coli from the fecal flora of healthy volunteers exposed to ciprofloxacin

BACKGROUND

Emergence of quinolone-resistant Escherichia coli (QREC) is an increasing clinical challenge mostly originating in fecal microbiota. The dynamics of the emergence of QREC in feces from individuals exposed to ciprofloxacin is unknown.

METHODS

A total of 48 healthy volunteers received oral ciprofloxacin for 14 days. Fecal specimens were collected on days 0, 8, 14, and 42. Subpopulations of QREC were detected on selective agar, genetically characterized, and compared with quinolone-susceptible E. coli (QSEC) strains collected on different days.

RESULTS

On day 42, 34 subjects carried QSEC, and 14 carried QREC. Of the 14 who carried QREC, 9 carried quinolone-susceptible E. coli on day 0, 1 carried E. coli with a lower level of quinolone resistance on day 0, and 4 carried E. coli with similar levels of resistance and RAPD-genotypes on days 0 and 42. No plasmid acquisition and no selection of resistant mutants from the initial microbiota was evidenced in any case.

CONCLUSIONS

In QREC emerging under ciprofloxacin pressure in the fecal microbiota, no proof of selection of quinolone-resistant mutants from the initial microbiota was evidenced, suggesting that QREC strains on day 42 were either present at undetectable levels in the initial microbiota or that exogenous acquisition of QREC strains occurred. Clinical Trials Registration. NCT00190151.

Resistance surveillance studies: a multifaceted problem--the fluoroquinolone example

INTRODUCTION

This review summarizes data on the fluoroquinolone resistance epidemiology published in the previous 5 years.

MATERIALS AND METHODS

The data reviewed are stratified according to the different prescription patterns by either primary- or tertiary-care givers and by indication. Global surveillance studies demonstrate that fluoroquinolone- resistance rates increased in the past several years in almost all bacterial species except Staphylococcus pneumoniae and Haemophilus influenzae causing community-acquired respiratory tract infections (CARTIs), as well as Enterobacteriaceae causing community-acquired urinary tract infections. Geographically and quantitatively varying fluoroquinolone resistance rates were recorded among Gram-positive and Gram-negative pathogens causing healthcare-associated respiratory tract infections. One- to two-thirds of Enterobacteriaceae producing extended-spectrum β-lactamases (ESBLs) were fluoroquinolone resistant too, thus, limiting the fluoroquinolone use in the treatment of community- as well as healthcare-acquired urinary tract and intra-abdominal infections. The remaining ESBL-producing or plasmid-mediated quinolone resistance mechanisms harboring Enterobacteriaceae were low-level quinolone resistant. Furthermore, 10-30 % of H. influenzae and S. pneumoniae causing CARTIs harbored first-step quinolone resistance determining region (QRDR) mutations. These mutants pass susceptibility testing unnoticed and are primed to acquire high-level fluoroquinolone resistance rapidly, thus, putting the patient at risk. The continued increase in fluoroquinolone resistance affects patient management and necessitates changes in some current guidelines for the treatment of intra-abdominal infections or even precludes the use of fluoroquinolones in certain indications like gonorrhea and pelvic inflammatory diseases in those geographic areas in which fluoroquinolone resistance rates and/or ESBL production is high. Fluoroquinolone resistance has been selected among the commensal flora colonizing the gut, nose, oropharynx, and skin, so that horizontal gene transfer between the commensal flora and the offending pathogen as well as inter- and intraspecies recombinations contribute to the emergence and spread of fluoroquinolone resistance among pathogenic streptococci. Although interspecies recombinations are not yet the major cause for the emergence of fluoroquinolone resistance, its existence indicates that a large reservoir of fluoroquinolone resistance exists. Thus, a scenario resembling that of a worldwide spread of β-lactam resistance in pneumococci is conceivable. However, many resistance surveillance studies suffer from inaccuracies like the sampling of a selected patient population, restricted geographical sampling, and undefined requirements of the user, so that the results are biased. The number of national centers is most often limited with one to two participating laboratories, so that such studies are point prevalence but not surveillance studies. Selected samples are analyzed predominantly as either hospitalized patients or patients at risk or those in whom therapy failed are sampled; however, fluoroquinolones are most frequently prescribed by the general practitioner. Selected sampling results in a significant over-estimation of fluoroquinolone resistance in outpatients. Furthermore, the requirements of the users are often not met; the prescribing physician, the microbiologist, the infection control specialist, public health and regulatory authorities, and the pharmaceutical industry have diverse interests, which, however, are not addressed by different designs of a surveillance study. Tools should be developed to provide customer-specific datasets.

CONCLUSION

Consequently, most surveillance studies suffer from well recognized but uncorrected biases or inaccuracies. Nevertheless, they provide important information that allows the identification of trends in pathogen incidence and antimicrobial resistance.

Functional metagenomic investigations of the human intestinal microbiota

The human intestinal microbiota encode multiple critical functions impacting human health, including metabolism of dietary substrate, prevention of pathogen invasion, immune system modulation, and provision of a reservoir of antibiotic resistance genes accessible to pathogens. The complexity of this microbial community, its recalcitrance to standard cultivation, and the immense diversity of its encoded genes has necessitated the development of novel molecular, microbiological, and genomic tools. Functional metagenomics is one such culture-independent technique, used for decades to study environmental microorganisms, but relatively recently applied to the study of the human commensal microbiota. Metagenomic functional screens characterize the functional capacity of a microbial community, independent of identity to known genes, by subjecting the metagenome to functional assays in a genetically tractable host. Here we highlight recent work applying this technique to study the functional diversity of the intestinal microbiota, and discuss how an approach combining high-throughput sequencing, cultivation, and metagenomic functional screens can improve our understanding of interactions between this complex community and its human host.

The use of systemic and topical fluoroquinolones

Appropriate prescribing practices for fluoroquinolones are essential as evolving resistance patterns are considered, additional treatment indications are identified, and the toxicity profile of fluoroquinolones in children becomes better defined. Earlier recommendations for systemic therapy remain; expanded uses of fluoroquinolones for the treatment of certain infections are outlined in this report. Although fluoroquinolones are reasonably safe in children, clinicians should be aware of the specific adverse reactions. Use of fluoroquinolones in children should continue to be limited to treatment of infections for which no safe and effective alternative exists.

Within-household sharing of a fluoroquinolone-resistant Escherichia coli sequence type ST131 strain causing pediatric osteoarticular infection

A fluoroquinolone-resistant Escherichia coli strain of sequence type ST131 caused severe septic arthritis and contiguous osteomyelitis in an 8-month-old girl, and colonized the girl's healthy mother, who shared a different fecal E. coli strain with the father. Within-household transmission can contribute to the dissemination of the emerging, multidrug-resistant ST131 clonal group, which has evident invasive potential for otherwise-healthy children.

The clinical consequences of antimicrobial resistance

The continued evolution of antimicrobial resistance in the hospital and more recently in the community threatens to seriously compromise our ability to treat serious infections. The major success of the seven-valent Streptococcus pneumoniae vaccine at reducing both infection and resistance has been followed by the emergence of previously minor serotypes that express multiresistance. The almost universal activity of cephalosporins and fluoroquinolones against community Escherichia coli strains has been compromised by the spread of CTX-M beta-lactamase-producing, fluoroquinolone-resistant strains, and the emergence of community-onset methicillin-resistant Staphylococcus aureus, particularly in the United States, has forced us to re-think our empirical treatment guidelines for skin and soft-tissue infections. Finally, our most potent and reliable class of antibiotics, the carbapenems, is compromised by the growth, primarily in intensive care units, of multiresistant Klebsiella pneumoniae, Acinetobacter baumanni, and Pseudomonas aeruginosa. The lack of a robust pipeline of new agents, particularly against resistant Gram-negative bacteria, emphasizes the importance of optimizing our use of current antimicrobials and promoting strict adherence to established infection control practices.

Increased fluoroquinolone resistance with time in Escherichia coli from >17,000 patients at a large county hospital as a function of culture site, age, sex, and location

Background

Escherichia coli infections are common and often treated with fluoroquinolones. Fluoroquinolone resistance is of worldwide importance and is monitored by national and international surveillance networks. In this study, we analyzed the effects of time, culture site, and patient age, sex, and location on fluoroquinolone resistance in E. coli clinical isolates.

Methods

To understand how patient factors and time influenced fluoroquinolone resistance and to determine how well data from surveillance networks predict trends at Ben Taub General Hospital in Houston, TX, we used Perl to parse and MySQL to house data from antibiograms (n ≅ 21,000) for E. coli isolated between 1999 to 2004 using Chi Square, Bonferroni, and Multiple Linear Regression methods.

Results

Fluoroquinolone resistance (i) increased with time; (ii) exceeded national averages by 2- to 4-fold; (iii) was higher in males than females, largely because of urinary isolates from male outpatients; (iv) increased with patient age; (v) was 3% in pediatric patients; (vi) was higher in hospitalized patients than outpatients; (vii) was higher in sputum samples, particularly from inpatients, than all other culture sites, including blood and urine, regardless of patient location; and (viii) was lowest in genital isolates than all other culture sites. Additionally, the data suggest that, with regard to susceptibility or resistance by the Dade Behring MicroScan system, a single fluoroquinolone suffices as a "surrogate marker" for all of the fluoroquinolone tested.

Conclusion

Large surveillance programs often did not predict E. coli fluoroquinolone resistance trends at a large, urban hospital with a largely indigent, ethnically diverse patient population or its affiliated community clinics.

Virulence factors in urinary Escherichia coli strains: phylogenetic background and quinolone and fluoroquinolone resistance

Quinolone- and fluoroquinolone-resistant Escherichia coli strains harbor fewer virulence factors than susceptible strains. The reasons underlying this correlation are incompletely understood. We investigated the phylogenetic background, the presence of the papC, hlyA, and cnf1 (pathogenicity island II(J96)-associated), fimA, iss, and iutA genes, and the presence of type 1 fimbriae, P fimbriae, and hemolysin in 243 urinary E. coli isolates resistant only to quinolones (8%), resistant to both quinolones and fluoroquinolones (51%), or susceptible to both drugs (41%). Group B2 accounted for 56% of the isolates, showing a significantly higher prevalence among fluoroquinolone-susceptible strains than among resistant strains (65% versus 50% [P = 0.03]). hly and cnf1 were significantly more associated with susceptibility (P < 0.001) and with group B2 (P < 0.001 for group B2 versus groups A and D). However, within group B2, fluoroquinolone-resistant strains showed lower prevalences of papC, hlyA, and cnf1 than their susceptible counterparts (P < 0.001). In contrast, the incidence of iutA appeared higher for refractory isolates, including group B2, than for susceptible isolates (P < 0.001). Only in group B2 did fluoroquinolone-resistant strains reveal a lesser ability to agglutinate Saccharomyces cerevisiae (7%) than quinolone-resistant (87%) and susceptible (80%) isolates, despite uniform possession of fimA genes. No similar contrast emerged for expression of hemolysin and P fimbriae. Mutations conferring quinolone and fluoroquinolone resistance may thus require a particular genetic background, not strictly correlated with phylogenetic groups. More interestingly, the mutational event itself can affect the expression of type 1 fimbriae, at least in the prevalent and complex B2 strains.

Pediatric uses of fluoroquinolone antibiotics

Current data, although incomplete, suggest that pediatric administration of a fluoroquinolone, especially the best-studied ciprofloxacin, is safe. However, many experts have raised concerns regarding the emergence of fluoroquinolone-resistant pathogens such as pneumococcus if more children are treated with fluoroquinolones. Examination of the available data suggests that these concerns remain valid. Therefore, most experts continue to advise against expanded pediatric use of fluoroquinolones, except in those selected clinical situations where the benefits clearly outweigh the risks of therapy and there are few other antibiotic choices.