Epidemiology of plasmid-mediated beta-lactamases in enterobacteria Swedish neonatal wards and relation to antimicrobial therapy

Antimicrobial Resistance in Nepal

Antimicrobial resistance (AMR) is a global problem to animal and public health. It has drawn the attention of public health experts, stakeholders, and medical science due to the substantial economic loss that it causes to individuals and nation as a whole. Various cross-sectional studies and some national surveys in developing countries have shown increase in the burden of antimicrobial resistance. Nepal is one of the major contributors to the growing burden of AMR due to widespread irrational use of antibiotics along with poor health care systems poor infection control and prevention measures. This review was conducted to summarize the situation of AMR in Nepal, determinants of AMR, current government intervention strategies and the way forward to reduce the AMR burden in Nepal. Available cross sectional reports warn that bacterial pathogens are becoming highly resistant to most first- and some second-line antibiotics. The irrational and injudicious use of high doses of antibiotics for therapy and sub-optimal doses as growth promoters are leading causes of AMR in Nepal. Establishment of a surveillance programme and a national plan for containment of AMR, following the National Antibiotics Treatment Guideline 2014 and generation of awareness among veterinarians, technicians, and medical physicians on prudent use of antimicrobial drugs in Nepal could reduce the burden of AMR. In addition, there is a need to develop a national laboratory strategic plan to provide guidance and governance to national laboratories.

Antibiotic therapy in neonates and impact on gut microbiota and antibiotic resistance development: a systematic review

Objectives

To systematically review the impact of antibiotic therapy in the neonatal period on changes in the gut microbiota and/or antibiotic resistance development.

Methods

Data sources were PubMed, Embase, Medline and the Cochrane Database, supplemented by manual searches of reference lists. Randomized controlled trials (RCTs) and observational studies were included if they provided data on different categories of antibiotic treatment (yes versus no, long versus short duration and/or broad- versus narrow-spectrum regimens) and subsequent changes in the gut microbiota and/or antibiotic resistance development. We evaluated risk of bias using the Cochrane Handbook, adapted to include observational studies. When appropriate, we used the vote-counting method to perform semi-quantitative meta-analyses. We applied the Grades of Recommendation, Assessment, Development and Evaluation approach to rate the quality of evidence (QoE). Study protocol registration: PROSPERO CRD42015026743.

Results

We included 48 studies, comprising 3 RCTs and 45 observational studies. Prolonged antibiotic treatment was associated with reduced gut microbial diversity in all three studies investigating this outcome (very low QoE). Antibiotic treatment was associated with reduced colonization rates of protective commensal anaerobic bacteria in four of five studies (very low QoE). However, all three categories of antibiotic treatment were associated with an increased risk of antibiotic resistance development, in particular MDR in Gram-negative bacteria, and we graded the QoE for these outcomes as moderate.

Conclusions

We are moderately confident that antibiotic treatment leads to antibiotic resistance development in neonates and it may also induce potentially disease-promoting gut microbiota alterations. Our findings emphasize the need to reduce unnecessary antibiotic treatment in neonates.

Impact of extensive antibiotic treatment on faecal carriage of antibiotic-resistant enterobacteria in children in a low resistance prevalence setting

We prospectively studied the consequences of extensive antibiotic treatment on faecal carriage of antibiotic-resistant enterobacteria in a cohort of children with cystic fibrosis (CF) and a cohort of children with cancer compared to healthy children with no or low antibiotic exposure. The study was conducted in Norway in a low resistance prevalence setting. Sixty longitudinally collected faecal samples from children with CF (n = 32), 88 samples from children with cancer (n = 45) and 127 samples from healthy children (n = 70) were examined. A direct MIC-gradient strip method was used to detect resistant Enterobacteriaceae by applying Etest strips directly onto agar-plates swabbed with faecal samples. Whole genome sequencing (WGS) data were analysed to identify resistance mechanisms in 28 multidrug-resistant Escherichia coli isolates. The prevalence of resistance to third-generation cephalosporins, gentamicin and ciprofloxacin was low in all the study groups. At inclusion the prevalence of ampicillin-resistant E. coli and trimethoprim-sulfamethoxazole-resistant E. coli in the CF group compared to healthy controls was 58.6% vs. 28.4% (p = 0.005) and 48.3% vs. 14.9% (p = 0.001), respectively, with a similar prevalence at the end of the study. The prevalence of resistant enterobacteria was not significantly different in the children with cancer compared to the healthy children, not even at the end of the study when the children with cancer had been treated with repeated courses of broad-spectrum antibiotics. Children with cancer were mainly treated with intravenous antibiotics, while the CF group mainly received peroral treatment. Our observations indicate that the mode of administration of antibiotics and the general level of antimicrobial resistance in the community may have an impact on emergence of resistance in intestinal enterobacteria during antibiotic treatment. The WGS analyses detected acquired resistance genes and/or chromosomal mutations that explained the observed phenotypic resistance in all 28 multidrug-resistant E. coli isolates examined.

Generalized additive model demonstrates fluoroquinolone use/resistance relationships for Staphylococcus aureus

Mathematical models currently used to study the relationship between the prevalence of the resistance to an antibiotic and the amount of drug may not be adequate because they do not integrate temporal and area analyses simultaneously. Furthermore, the forms of such relationship are unknown. We applied the Generalized Additive Model (GAM) to study fluoroquinolone use and the incidence of fluoroquinolone-resistance in Staphylococcus aureus in our institution over a 3-year period. Overall institution and individual hospital unitrestricted analyses were performed. Relative risk (RR) observed for increasing fluoroquinolone use with a 4-month lag from the 25th percentile to the 75th percentile was 1.27 (95% CI: 1.13-1.42). In the surgery units, RR was 1.23 (95% CI: 1.01-1.50) for fluoroquinolone use with a 2-months lag. GAM enabled us to observe for the first time a significant temporal relationship between fluoroquinolone use and the incidence of fluoroquinolone-resistant nosocomial S. aureus isolates.

Beta-lactamases in ampicillin-resistant Escherichia coli isolates from foods, humans, and healthy animals

TEM-, SHV-, and OXA-type beta-lactamases were studied by PCR with 124 ampicillin-resistant (AMP(r)) Escherichia coli isolates recovered from foods of animal origin (n = 20) and feces of humans (n = 49) and healthy animals (n = 55). PCR showed that 103 isolates were positive for TEM and negative for SHV and OXA. Three E. coli isolates showed a positive reaction for OXA, and one showed a positive reaction for SHV. The remaining 17 E. coli isolates were negative for the three enzymes by PCR. Fifty-seven of the 103 bla(TEM) amplicons were sequenced. Different molecular variants of bla(TEM-1) were found in 52 isolates: bla(TEM-1a) (n = 9), bla(TEM-1b) (n = 36), bla(TEM-1c) (n = 6), and bla(TEM-1f) (n = 1). Four inhibitor-resistant TEM (IRT) beta-lactamase-encoding genes were also detected: bla(TEM-30c) (IRT-2), bla(TEM-34b) (IRT-6), bla(TEM-40b) (IRT-11), and bla(TEM-51a) (IRT-15). A new bla(TEM) gene, named bla(TEM-95b), which showed a mutation in amino acid 145 (P-->A) was detected. It was found in a food isolate of chicken origin (AMP(r), amoxicillin-clavulanic acid susceptible). The promoter region in 24 bla(TEM) amplicons was analyzed, and the weak P3 promoter was found in 23 of them (bla(TEM-1) in 20 amplicons and bla(TEM-51a), bla(TEM-30c), and bla(TEM-95b) in 1 amplicon each). The strong Pa/Pb promoter was found only in the bla(TEM-34b) gene. No extended-spectrum beta-lactamases were detected. Mutations at position -42 or -32 in the ampC gene promoter were demonstrated in 4 of 10 E. coli isolates for which the cefoxitin MIC was >/=16 micro g/ml. Different variants of bla(TEM-1) and IRT bla(TEM) genes were found among the AMP(r) E. coli isolates from foods and the feces of humans and healthy animals, and a new gene, bla(TEM-95b) (P3), was detected.

Clinical assay of N-duopropenide alcohol solution on hand application in newborn and pediatric intensive care units: control of an outbreak of multiresistant Klebsiella pneumoniae in a newborn intensive care unit with this measure

Outbreaks of gram-negative colonization (generally by antibiotic-resistant enterobacteria) are common in newborn intensive care units (NICUs), and control methods are not always effective. We studied the effectiveness of an alcohol solution of N-duopropenide (NDP) in vivo (germicidal effect on flora of teams in the NICU and the pediatric intensive care unit vs handwashing with nonantiseptic soap) and its effect on the control of a multiresistant (MR) Klebsiella pneumoniae outbreak in our NICU that had persisted for 13 months, despite the use of classic control measures. For educational purposes, we also performed 4 prevalence studies of microbial hand flora in NICU staff (two before and two after introducing NDP). The alcohol solution of NDP was highly germicidal in vivo, destroying microorganisms better than classic handwashing on the hands of 69 health care staff of our NICU and PICU. The flora in both units was reduced from an average of 63% to an average of 95%. Application of this disinfectant to the hands of health care workers after handling newborns helped to eliminate the MR Klebsiella strain in our NICU, (relative risk compared with the period preceding use of the disinfectant: 8.6, with 95% confidence intervals, 4.8-145.5). Four prevalence studies of hand microbial contamination, before and after NDP introduction in the NICU, showed a significant reduction of enterobacteriaceae, mainly MR K pneumoniae, in health care workers. In conclusion, NDP in alcohol was very effective in vivo. It proved to be a useful complementary measure to handwashing and reduced exogenous microorganism transmission in a unit with a heavy patient-care workload.

beta-lactamases in Shigella flexneri isolates from Hong Kong and Shanghai and a novel OXA-1-like beta-lactamase, OXA-30

Ninety-one ampicillin-resistant Shigella flexneri strains from Hong Kong and Shanghai were studied for production of beta-lactamases. TEM-1-like and OXA-1-like enzymes were identified in 21 and 79% of the strains, respectively, by isoelectric focusing (IEF). No difference in the pattern of beta-lactamase production was found between strains from Hong Kong and Shanghai. Four ribotypes were detected. Over 88% of OXA-producing strains had the same ribotype. All TEM-1-like strains harbored a plasmid which hybridized positively with the bla(TEM) probe. Total DNA from OXA-1-like strains failed to hybridize or only hybridized weakly with an OXA probe. The OXA resistance was not transferable. OXA-1-like enzymes exhibited substrate and inhibition profiles similar to that of OXA-1 and were shown to have a pI of 7.3 by further IEF using a narrow-range ampholine gel. The gene encoding the OXA-1-like enzyme from one isolate (CH-07) was cloned, sequenced, and found to differ from bla(OXA-1) at codon 131 (AGA-->GGA; Arg to Gly), resulting in the novel designation OXA-30. The predominance of OXA-type enzymes in ampicillin-resistant S. flexneri suggests host preference for specific beta-lactamases.

The relationship between the volume of antimicrobial consumption in human communities and the frequency of resistance

The threat to human health posed by antibiotic resistance is of growing concern. Many commensal and pathogenic organisms have developed resistance to well established and newer antibiotics. The major selection pressure driving changes in the frequency of antibiotic resistance is the volume of drug use. However, establishing a quantitative relationship between the frequency of resistance and volume of drug use has proved difficult. Using population genetic methods and epidemiological observations, we report an analysis of the influence of the selective pressure imposed by the volume of drug use on temporal changes in resistance. Analytical expressions are derived to delineate key relationships between resistance and drug consumption. The analyses indicate that the time scale for emergence of resistance under a constant selective pressure is typically much shorter than the decay time after cessation or decline in the volume of drug use and that significant reductions in resistance require equally significant reductions in drug consumption. These results highlight the need for early intervention once resistance is detected.

An allelic variant of the chromosomal gene for class A beta-lactamase K2, specific for Klebsiella pneumoniae, is the ancestor of SHV-1

Fecal Klebsiella isolates from neonates in 22 Swedish special care units were examined by a PCR we developed for detection of the SHV-1 beta-lactamase gene. All 105 K. pneumoniae isolates and all 11 K. pneumoniae reference strains (including the K. pneumoniae subsp. pneumoniae, ozaenae, and rhinoscleromatis type strains) tested were positive, whereas all 67 K. oxytoca isolates and the K. oxytoca, K. planticola, and K. terrigena type strains tested were negative. Resistance to beta-lactams in K. pneumoniae was not transferable by conjugation, and the beta-lactamase gene was never found on a plasmid. Southern blot analysis showed that the gene had a defined chromosomal location. Isoelectric focusing and sequencing of 231-bp PCR amplicons from different isolates revealed many variants of the enzyme, with the two main groups being SHV-1 like (pI 7.6; 68 isolates) and LEN-1 like (pI 7.1; 14 isolates). Clavulanic acid markedly reduced the MICs of ampicillin for all the K. pneumoniae isolates tested. This fact, MIC profiles (penicillin rather than cephalosporin resistance), pIs, and sequence data showed that the chromosomal beta-lactamase of K. pneumoniae is a class A, group 2 enzyme distinct from the chromosomal AmpC enzymes found in several other gram-negative bacteria and from the chromosomal beta-lactamase K1 of K. oxytoca. We propose that the chromosomal beta-lactamase of K. pneumoniae be designated K2 and suggest that an allelic pI 7.6 variant of this enzyme is the ancestor of the SHV family of plasmid-mediated beta-lactamases.

The transmission dynamics of antibiotic-resistant bacteria: the relationship between resistance in commensal organisms and antibiotic consumption

We propose a mathematical model of the transmission dynamics of colonization by commensal bacteria within a human community subject to varying levels of antibiotic use designed to control morbidity induced by pathogenic strains of the normally commensal organisms. Colonization is assumed not to induce morbidity in the majority of cases, and antibiotic use is assumed to be related to the arrival and growth of pathogenic strains that give rise to infections including clinical symptoms of disease. In the absence of antibiotic resistance, the model shows how the pattern of antibiotic prescription and use can eliminate the non-pathogenic commensal strains from the host community if the fraction of people taking antibiotics with a defined efficacy exceeds some critical level. The model is extended to take account of the evolution of antibiotic resistance in the commensal population. We assume resistance may be either plasmid-mediated or conferred by selection of low-level pre-existing mutants, and that resistant organisms may experience reduced reproductive fitness. Invasion of the host community by drug-resistant commensals is possible if certain antibiotic prescribing patterns pertain. We calculate these conditions in terms of the transmission parameter of the organism and the level of antibiotic prescription and use. The model is employed to address the issues of how best to use antibiotics in populations harbouring resistant organisms, and when resistant bacteria will out-compete sensitive strains.

Antimicrobial and mercury resistance in aerobic gram-negative bacilli in fecal flora among persons with and without dental amalgam fillings

Antimicrobial resistance is more widespread than can be accounted for as being a consequence of the selection pressure caused by the use of antibiotics alone. In this study, we tested the hypothesis that a high mercury content in feces might select for mercury-resistant bacteria and thus for antimicrobial resistance linked to mercury resistance. Three subject groups with different exposures to dental amalgam fillings were compared. None of the subjects had taken antimicrobial agents during the three preceding months or longer. The group exposed to dental amalgam (n = 92) had 13 times more mercury in feces than the group that had never been exposed to amalgam (n = 43) and the group whose amalgam fillings had been removed (n = 56). No significant differences in either mercury resistance or antibiotic resistance in the fecal aerobic gram-negative flora of these subject groups were seen. The following antimicrobial resistance frequencies were detected with a replica plating method: > or = 1% resistance was seen in 40% of the subjects for ampicillin, 14% of the subjects for cefuroxime, 6% of the subjects for nalidixic acid, 14% of the subjects for trimethoprim, 19% of the subjects for sulfamethoxazole, and 25% of the subjects for tetracycline. The amount of mercury in feces derived from amalgam was not selective for any resistance factors in aerobic gram-negative bacteria, but antimicrobial resistance was widespread even among healthy subjects with no recent exposure to antibiotics.

beta-Lactamases in laboratory and clinical resistance

beta-Lactamases are the commonest single cause of bacterial resistance to beta-lactam antibiotics. Numerous chromosomal and plasmid-mediated types are known and may be classified by their sequences or phenotypic properties. The ability of a beta-lactamase to cause resistance varies with its activity, quantity, and cellular location and, for gram-negative organisms, the permeability of the producer strain. beta-Lactamases sometimes cause obvious resistance to substrate drugs in routine tests; often, however, these enzymes reduce susceptibility without causing resistance at current, pharmacologically chosen breakpoints. This review considers the ability of the prevalent beta-lactamases to cause resistance to widely used beta-lactams, whether resistance is accurately reflected in routine tests, and the extent to which the antibiogram for an organism can be used to predict the type of beta-lactamase that it produces.