Evaluation of a rapid screening method for detection of antimicrobial resistance in the commensal microbiota of the gut

Prevalence, Characteristics, and Clonal Distribution of Escherichia coli Carrying Mobilized Colistin Resistance Gene mcr-1.1 in Swine Farms and Their Differences According to Swine Production Stages

Global spread of Escherichia coli strains carrying the mobilized colistin resistance gene mcr-1.1 (MCR1-EC) poses serious threats to public health. Colistin has been generally prescribed for swine colibacillosis, having made swine farms as major reservoirs of MCR1-EC. The present study aimed to understand characteristic differences of MCR1-EC, including prevalence, antimicrobial resistance, and virulence, according to swine production stages. In addition, genetic relatedness was evaluated between MCR1-EC isolated from this study as well as pig-, human-, and chicken-derived strains published in the National Center for Biotechnology Information (NCBI), based on the multi-locus sequence types (MLSTs) and whole-genome sequences (WGS). Individual fecal samples (n = 331) were collected from asymptomatic weaning-piglets, growers, finishers, and sows from 10 farrow-to-finishing farms in South Korea between 2017 and 2019. The weighted prevalence of MCR1-EC was 11.6% (95% CI: 8.9%–15.0%, 55/331), with the highest prevalence at weaning stage. The 96.2% of MCR1-EC showed multi-drug resistance. Notably, weaning stage-derived MCR1-EC showed higher resistance rates (e.g., against extended-spectrum β-lactams or quinolones) than those from other stages. MCR1-EC with virulence advantages (e.g., intestinal/extraintestinal pathogenic E. coli or robust biofilm formation) were identified from all pig stages, accounting for nearly half of the total strains. WGS-based in-depth characterization showed that intestinal pathogenic MCR1-EC harbored multi-drug resistance and multiple virulence factors, which were highly shared between strains isolated from pigs of different stages. The clonal distribution of MCR1-EC was shared within swine farms but rarely across farms. The major clonal type of MCR1-EC from swine farms and NCBI database was ST10-A. Core genomes of MCR1-EC isolated from individuals within closed environments (same farms or human hospitals) were highly shared (genetic distance < 0.01), suggesting a high probability of clonal expansion of MCR1-EC within closed environments such as livestock husbandry. To the best of our knowledge, this is the first study to analyze the differences in the characteristics and clonal distribution of MCR1-EC according to production stages in swine farms, an important reservoir of MCR1-EC. Our results highlight the need to establish MCR1-EC control plans in swine farms based on an in-depth understanding of MCR1-EC characteristics according to swine production stages, focusing especially on the weaning stages.

High Prevalence of blaCTX-M in Fecal Commensal Escherichia coli from Healthy Children

Background

Antibiotic-resistant Escherichia coli can colonize the intestinal tract of healthy children, causing concern when antibiotic resistance is related to the presence of transferable mechanisms, such as extended-spectrum β-lactamases (ESBLs).

Materials and Methods

Fecal samples from 41 healthy children from two villages of rural Peru were cultured on ceftriaxone-disks. ESBL production was confirmed with double disk synergy. In all ESBL-produced isolates, antibiotic susceptibility to 12 antibacterial agents was established by disk diffusion, while clonal relationships were determined by repetitive extragenic palindromic-polymerase chain reaction (REP-PCR). Presence of ST131 was determined using PCR.

Results

Ceftriaxone-resistant microorganisms were recovered from 39 samples belonging to 22 out of 41 children (53.7%). Of these, 80 ceftriaxone-resistant and two ceftriaxone-intermediate E. coli from inside ceftriaxone-halos were confirmed as ESBL-producers. All isolates were multidrug-resistant. In 79/80 (98.8%) ceftriaxone-resistant isolates, the presence of bla_CTX-M was detected alone (58 isolates, or together with other β-lactamase (bla_TEM, 17 isolates; bla_OXA-1-like, 3 isolates; bla_TEM + bla_OXA-1-like, 1 isolate), while in one isolate no such ESBL was identified. The two ceftriaxone-intermediate isolates recovered from the same sample, carried a bla_TEM and bla_SHV respectively. Thirty-four different clones were identified, with 4 clones being recovered from different samples from the same child. Twelve clones were disseminated among different children, including 5 clones disseminated between both villages. Two clones, accounting for 3 isolates and both recovered from the same children, belonged to E. coli ST131.

Conclusion

This study demonstrates high prevalence of ESBL-carriers among healthy children living in a rural area of Peru, stressing the need for continuous surveillance and search for public health control measures.

Evidence of Another Anthropic Impact on Iguana delicatissima from the Lesser Antilles: The Presence of Antibiotic Resistant Enterobacteria

The improper use of antibiotics by humans may promote the dissemination of resistance in wildlife. The persistence and spread of acquired antibiotic resistance and human-associated bacteria in the environment, while representing a threat to wildlife, can also be exploited as a tool to monitor the extent of human impact, particularly on endangered animal species. Hence, we investigated both the associated enterobacterial species and the presence of acquired resistance traits in the cloacal microbiota of the critically endangered lesser Antillean iguana (Iguana delicatissima), by comparing two separate populations living in similar climatic conditions but exposed to different anthropic pressures. A combination of techniques, including direct plating, DNA sequencing and antimicrobial susceptibility testing allowed us to characterize the dominant enterobacterial populations, the antibiotic resistant strains and their profiles. A higher frequency of Escherichia coli was found in the samples from the more anthropized site, where multi-drug resistant strains were also isolated. These results confirm how human-associated bacteria as well as their antibiotic-resistance determinants may be transferred to wildlife, which, in turn, may act as a reservoir of antibiotic resistance.

Antimicrobial Resistance Creates Threat to Chimpanzee Health and Conservation in the Wild

Infectious disease is recognized as the greatest threat to the endangered chimpanzees made famous by the groundbreaking work of Dr. Jane Goodall at Gombe National Park (GNP), Tanzania. The permeable boundary of this small protected area allows for regular wildlife–human and wildlife–domestic animal overlap, which may facilitate cross-species transmission of pathogens and antimicrobial resistance. Few studies have examined the prevalence of antimicrobial resistance in wild ape populations. We used molecular techniques to investigate the presence of genes conferring resistance to sulfonamides (often used to treat diarrheal illness in human settings in this region) and tetracycline (used in the past—though much less so now) in fecal specimens from humans, domestic animals, chimpanzees, and baboons in and around GNP. We also tested stream water used by these groups. Sulfonamide resistance was common in humans (74%), non-human primates (43%), and domestic animals (17%). Tetracycline resistance was less common in all groups: humans (14%), non-human primates (3%), and domestic animals (6%). Sul resistance genes were detected from 4/22 (18%) of streams sampled. Differences in sul gene frequencies did not vary by location in humans nor in chimpanzees.

The Pattern of Antibiotic Prescription and Antimicrobial Resistance of Gut Flora Escherichia coli at Aisyiyah Hospital, Bojonegoro

Antimicrobial resistance (AMR) is the failure of antibiotic to kill bacteria and becomes ineffective in therapeutic purpose. The AMR bacteria is a major health problem worldwide and Indonesia is not exception. AMR is increased by two factors, higher antibiotic use and low compliance in infection control and prevention.  WHO has recommended 7 bacterial indicators as point of view in surveillance, one of these bacteria is Escherichia coli. This study aimed to analyze the correlation between antibiotic use and resistance pattern of gut flora Escherichia coli. The study was conducted at Aisyiyah Hospital, Bojonegoro from June to October 2017. Total 101 patients from internal medicine and surgery department in this hospital were included in this study. Bacterial gut flora were tested against 12 antibiotics by disk diffusion test at the Department of Clinical Microbiology, Universitas Airlangga.. The results showed that the highest quantity of antibiotic use in internal medicine service was cefepime (40,50 DDD) and the highest resistance rate was ciprofloxacin, whereas in the surgical service it was ceftriaxone (132,75 DDD) with the highest E. coli resistance to amoxicillin-clavulanic acid. The antibiotics use has significant correlation against E. coli resistance on cefotaxime (p=0.046), ceftazidime (p=0.046), ceftriaxone (p=0.017), aztreonam (p=0.024), and cefepime (p=0.010).

Antibiotic Resistance of Gram-Negative Bacteria from Wild Captured Loggerhead Sea Turtles

Sea turtles have been proposed as health indicators of marine habitats and carriers of antibiotic-resistant bacterial strains, for their longevity and migratory lifestyle. Up to now, a few studies evaluated the antibacterial resistant flora of Mediterranean loggerhead sea turtles (Caretta caretta) and most of them were carried out on stranded or recovered animals. In this study, the isolation and the antibiotic resistance profile of 90 Gram negative bacteria from cloacal swabs of 33 Mediterranean wild captured loggerhead sea turtles are described. Among sea turtles found in their foraging sites, 23 were in good health and 10 needed recovery for different health problems (hereafter named weak). Isolated cloacal bacteria belonged mainly to Enterobacteriaceae (59%), Shewanellaceae (31%) and Vibrionaceae families (5%). Although slight differences in the bacterial composition, healthy and weak sea turtles shared antibiotic-resistant strains. In total, 74 strains were endowed with one or multi resistance (up to five different drugs) phenotypes, mainly towards ampicillin (~70%) or sulfamethoxazole/trimethoprim (more than 30%). Hence, our results confirmed the presence of antibiotic-resistant strains also in healthy marine animals and the role of the loggerhead sea turtles in spreading antibiotic-resistant bacteria.

Routine antibiotic therapy in dogs increases the detection of antimicrobial-resistant faecal Escherichia coli

Background

Antimicrobial resistance (AMR) is a critical health problem, with systemic antimicrobial therapy driving development of AMR across the host spectrum.

Objectives

This study compares longitudinal carriage, at multiple timepoints, of AMR faecal Escherichia coli in dogs undergoing routine antimicrobial treatment.

Methods

Faecal samples (n = 457) from dogs (n = 127) were examined pretreatment, immediately after treatment and 1 month and 3 months post-treatment with one of five antimicrobials. Isolates were tested for susceptibility to a range of antimicrobials using disc diffusion for each treatment group at different timepoints; the presence/absence of corresponding resistance genes was investigated using PCR assays. The impact of treatment group/timepoint and other risk factors on the presence of resistance [MDR, fluoroquinolone resistance, third-generation cephalosporin resistance (3GCR) and ESBL and AmpC production] was investigated using multilevel modelling. Samples with at least one AMR E. coli from selective/non-selective agar were classed as positive. Resistance was also assessed at the isolate level, determining the abundance of AMR from non-selective culture.

Results

Treatment with β-lactams or fluoroquinolones was significantly associated with the detection of 3GCR, AmpC-producing, MDR and/or fluoroquinolone-resistant E. coli, but not ESBL-producing E. coli, immediately after treatment. However, 1 month post-treatment, only amoxicillin/clavulanate was significantly associated with the detection of 3GCR; there was no significant difference at 3 months post-treatment for any antimicrobial compared with pretreatment samples.

Conclusions

Our findings demonstrated that β-lactam and fluoroquinolone antibiotic usage is associated with increased detection of important phenotypic and genotypic AMR faecal E. coli following routine therapy in vet-visiting dogs. This has important implications for veterinary and public health in terms of antimicrobial prescribing and biosecurity protocols, and dog waste disposal.

Carriage and population genetics of extended spectrum β-lactamase-producing Escherichia coli in cats and dogs in New Zealand

The incidence of infections with extended spectrum β-lactamase producing Escherichia coli (ESBL-E) is increasing both in humans and animals. There is a paucity of data about the rate of faecal carriage of ESBL-E in pets. In this study, faecal swabs collected from 586 pets (225 cats; 361 dogs) in Auckland, New Zealand, were analysed for the presence of ESBL-E by culture, and a questionnaire was delivered to the owners. The ESBL-E were characterised and data elicited by the questionnaires were used for a multivariable analysis, to investigate the factors associated with faecal ESBL-E carriage. The prevalence of ESBL-E in faecal swabs was 6.4%. The β-lactamase genes detected in the ESBL-E were the blaCTX-M-14 (n = 2) and blaCMY-2 (n = 34). Several isolates displayed multilocus sequence types (ST) associated with human and animal infections. Multiple isolates sharing the same ST displayed different antibiograms and β-lactamase genes, reflecting horizontal gene transfer between and within ST. Variables independently associated with increased odds of ESBL-E carriage were: animal received systemic antimicrobial treatment in the six months before the sampling; presence of household members working in veterinary clinics; presence of household members travelling overseas in the six months before the sampling. We conclude that pets are colonised by ESBL-E which are genotypically similar to the bacteria found to infect humans and animals. The statistical analysis suggested a number of eco-epidemiological factors associated with ESBL-E carriage. In particular, they suggest veterinary clinics may represent hot-spots of antimicrobial resistance.

Antimicrobial-resistant Escherichia coli in hospitalised companion animals and their hospital environment

INTRODUCTION

Antimicrobial resistance is a growing concern with implications for animal health. This study investigated the prevalence of antimicrobial resistance among commensal and environmental Escherichia coli isolated from animals sampled in referral hospitals in the UK.

MATERIALS AND METHODS

Resistant Escherichia coli isolated from animal faeces and practice environments were tested for susceptibility to antimicrobial agents. PCR and sequencing techniques were used to identify extended spectrum beta-lactamase and AmpC-producer genotypes.

RESULTS

In total, 333 faecal and 257 environmental samples were collected. Multi-drug resistant Escherichia coli were found in 13·1% of faecal and 8·9% of environmental samples. Extended spectrum beta-lactamase and AmpC genes were identified 14% and 7·7% of faecal samples and 8·6% and 8·6% of environmental samples, respectively. The most common extended spectrum beta-lactamase gene type detected was blaCTX-M -15 , although blaTEM-158 was detected in faecal and environmental samples from one practice.

CLINICAL SIGNIFICANCE

Escherichia coli resistant to key antimicrobials were isolated from hospitalised animals and the practice environment. We identified the emergence of the inhibitor resistant and extended spectrum beta-lactamase blaTEM-158 in companion animals. Further investigation to determine risk factors for colonisation with antimicrobial-resistant bacteria is needed to provide evidence for antimicrobial stewardship and infection control programmes.

A novel Direct MIC-gradient Strip Method to screen for antibiotic-resistant faecal Enterobacteriaceae

A novel method to detect resistant faecal Enterobacteriaceae was developed by applying MIC-gradient strips directly onto agar plates inoculated with faeces. The method provided the susceptibility pattern (MICs) of the dominant bacterial population directly on the plates and also detected smaller resistant subpopulations with a sensitivity of 1/10(5).

Antimicrobial resistance risk factors and characterisation of faecal E. coli isolated from healthy Labrador retrievers in the United Kingdom

Antimicrobial resistant bacteria are increasingly detected from canine samples but few studies have examined commensal isolates in healthy community dogs. We aimed to characterise faecal Escherichia coli from 73 healthy non-veterinarian-visiting and non-antimicrobial treated Labrador retrievers, recruited from dog shows in the North West United Kingdom between November 2010 and June 2011. Each enrolled dog provided one faecal sample for our study. E. coli were isolated from 72/73 (99%) faecal samples. Disc diffusion susceptibility tests were determined for a range of antimicrobials, including phenotypic extended-spectrum beta-lactamase (ESBL) and AmpC-production. PCR assay detected phylogenetic groups and resistance genes (blaCTX-M, blaSHV, blaTEM, blaOXA, blaCIT, qnr), and conjugation experiments were performed to investigate potential transfer of mobile genetic elements. Multivariable logistic regression examined potential risk factors from owner-questionnaires for the presence of antimicrobial resistant faecal E. coli. Antimicrobial resistant, multi-drug resistant (≥3 antimicrobial classes; MDR) and AmpC-producing E. coli were detected in 63%, 30% and 16% of samples, respectively. ESBL-producing E. coli was detected from only one sample and conjugation experiments found that blaCTX-M and blaCIT were transferred from commensal E. coli to a recipient strain. Most isolates were phylogenetic groups B1 and A. Group B2 isolates were associated with lower prevalence of resistance to at least one antimicrobial (P<0.001) and MDR (P<0.001). Significant at P<0.003, was the consumption of raw meat for clavulanate-amoxicillin (OR: 9.57; 95% CI: 2.0-45.7) and third generation cephalosporin resistance (3GCR) (OR: 10.9; 95% CI: 2.2-54.0). AMR E. coli were surprisingly prevalent in this group of non-antimicrobial treated and non-veterinarian-visiting dogs and consumption of raw meat was a significant risk factor for antimicrobial resistance. These findings are of concern due to the increasing popularity of raw-meat canine diets, and the potential for opportunistic infection, zoonotic transmission and transmission of antimicrobial resistant determinants from commensal isolates to potential pathogenic bacteria.

Quinolone resistance in absence of selective pressure: the experience of a very remote community in the Amazon forest

BACKGROUND

Quinolones are potent broad-spectrum bactericidal agents increasingly employed also in resource-limited countries. Resistance to quinolones is an increasing problem, known to be strongly associated with quinolone exposure. We report on the emergence of quinolone resistance in a very remote community in the Amazon forest, where quinolones have never been used and quinolone resistance was absent in 2002.

METHODS

The community exhibited a considerable level of geographical isolation, limited contact with the exterior and minimal antibiotic use (not including quinolones). In December 2009, fecal carriage of antibiotic resistant Escherichia coli was investigated in 120 of the 140 inhabitants, and in 48 animals reared in the community. All fluoroquinolone-resistant isolates were genotyped and characterized for the mechanisms of plasmid- and chromosomal-mediated quinolone resistance.

PRINCIPAL FINDINGS

Despite the characteristics of the community remained substantially unchanged during the period 2002-2009, carriage of quinolone-resistant E. coli was found to be common in 2009 both in humans (45% nalidixic acid, 14% ciprofloxacin) and animals (54% nalidixic acid, 23% ciprofloxacin). Ciprofloxacin-resistant isolates of human and animal origin showed multidrug resistance phenotypes, a high level of genetic heterogeneity, and a combination of GyrA (Ser83Leu and Asp87Asn) and ParC (Ser80Ile) substitutions commonly observed in fluoroquinolone-resistant clinical isolates of E. coli.

CONCLUSIONS

Remoteness and absence of antibiotic selective pressure did not protect the community from the remarkable emergence of quinolone resistance in E. coli. Introduction of the resistant strains from antibiotic-exposed settings is the most likely source, while persistence and dissemination in the absence of quinolone exposure is likely mostly related with poor sanitation. Interventions aimed at reducing the spreading of resistant isolates (by improving sanitation and water/food safety) are urgently needed to preserve the efficacy of quinolones in resource-limited countries, as control strategies based only on antibiotic restriction policies are unlikely to succeed in those settings.

Are subinhibitory concentrations of antibiotics the only culprit of antibiotic resistance?

Evaluation of: Gullberg E, Cao S, Berg OG et al. Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathog. 7(7), e1002158 (2011). Subinhibitory concentrations of antibiotics and antifungals promote resistance. Antibiotic consumption including hospital use, and country use, including patients self-medications is one of the major drivers of antibiotic or antifungal resistance. However, consumption of antibiotics should be distinguished between the hospital and community. Hospital consumption, poor hospital hygiene and intrahospital transfer have been determined as major risk factors for development of resistance. The correlation between resistance and consumption in the community is not so clear. Therefore consumption of antibiotics and antifungals alone cannot explain the selection of resistant bacterial and fungal mutants and other factors have to be investigated.

Cross-sectional study of antimicrobial-resistant bacteria in horses. Part 1: Prevalence of antimicrobial-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus

REASONS FOR PERFORMING STUDY

The increasing prevalence of antimicrobial-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) and antimicrobial-resistant Escherichia coli represents a significant problem. However, the carriage of such bacteria by horses in the UK has not been well characterised.

OBJECTIVES

To estimate the prevalence of nasal carriage of MRSA and faecal carriage of antimicrobial-resistant E. coli amongst horses in the general equine community of the mainland UK.

METHODS

A cross-sectional study of horses recruited by 65 randomly selected equine veterinary practices was conducted, with nasal swabs and faecal samples collected. Faecal samples were cultured for antimicrobial-resistant E. coli. Nasal swabs were cultured for staphylococcal species; methicillin-resistant isolates identified as S. aureus were characterised by SCCmec and spa gene typing. Multilevel logistic regression models were used to calculate prevalence estimates with adjustment for clustering at practice and premises levels. Spatial variation in risk of antimicrobial resistance was also examined.

RESULTS

In total, 650 faecal samples and 678 nasal swabs were collected from 692 horses located on 525 premises. The prevalence of faecal carriage of E. coli with resistance to any antimicrobial was 69.5% (95% CI 65.9-73.1%) and the prevalence of extended-spectrum β-lactamase (ESBL)-producing E. coli was 6.3% (95% CI 4.1-9.6%). The prevalence of nasal carriage of MRSA was 0.6% (95% CI 0.2-1.5%). Spatial analysis indicated variation across the UK for risk of carriage of resistant and multidrug-resistant (resistant to more than 3 antimicrobial classes) E. coli.

CONCLUSIONS AND POTENTIAL RELEVANCE

Carriage of MRSA by horses in the community appears rare, but the prevalence of antimicrobial-resistant E. coli (including ESBL-producing E. coli) is higher. A high prevalence of antimicrobial-resistant bacteria could have significant health implications for the horse population of the UK.

Carriage of antibiotic-resistant Escherichia coli among healthy children and home-raised chickens: a household study in a resource-limited setting

We have previously observed high rates of acquired antibiotic resistance in commensal Escherichia coli from healthy children living in urban areas of Bolivia and Peru, including resistance to tetracycline and quinolones, which are not routinely used in childhood. In this work we investigated acquired resistance in commensal E. coli from healthy children and home-raised chickens in 12 households from one of the previously surveyed urban area in Bolivia, to ascertain the possibility of human-animal exchange of resistant strains in similar settings. The resistance rates to ampicillin, tetracycline, chloramphenicol, streptomycin, and trimethoprim-sulphametoxazole were overall high (≥50%) and comparable between children and chickens, whereas those to quinolones were significantly higher in chickens (81% vs. 29% for nalidixic acid; 43% vs. 10% for ciprofloxacin). Molecular characterization of tetracycline- and quinolone-resistant isolates (n = 66) from children and chickens of three selected households revealed a remarkable clonal diversity and, in some cases, the presence of the same resistant strains among children or among chickens living in the same household, but not between children and chickens. Several resistance plasmids were characterized, but inter-clonal plasmid dissemination was not detected. Overall, the results from the present study suggested that cross-transmission between children and home-raised chickens could not represent a major spreading mechanism for resistant E. coli in households of resource-limited settings with high human-animal promiscuity.

Prevalence of antimicrobial-resistant Escherichia coli in dogs in a cross-sectional, community-based study

The prevalence of carriage of antimicrobial-resistant (AMR) and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli was determined in 183 healthy dogs from a semi-rural community in Cheshire. Isolates were tested against a panel of antimicrobials and by PCR to detect resistance genes. In the suspected ESBL-producing isolates, the presence of bla(SHV), bla(TEM), bla(CTX-M) and bla(AmpC) genes was determined by PCR and sequencing. A total of 53 (29 per cent, 95 per cent confidence interval [CI] 22.4 to 35.5 per cent) dogs carried at least one AMR E coli isolate. Twenty-four per cent (95 per cent CI 17.9 to 30.2 per cent) of dogs carried isolates resistant to ampicillin, 19.7 per cent (95 per cent CI 13.9 to 25.4 per cent) to tetracycline and 16.9 per cent (95 per cent CI 11.5 to 22.4 per cent) to trimethoprim. A bla(TEM) gene was detected in 39 of 54 ampicillin-resistant isolates, a tet(B) gene in 12 of 45 tetracycline-resistant isolates, and a dfr gene in 22 of 33 trimethoprim-resistant isolates. Multidrug-resistant isolates were demonstrated in 15 per cent (28 of 183; 95 per cent CI 10.1 to 20.5 per cent) of dogs. Nine suspected ESBL-producing E coli were isolated, of which only one was confirmed by double disc diffusion testing. Two of these isolates carried the bla(TEM-1) gene and seven carried the bla(CMY-2) gene.

Longitudinal study of antimicrobial-resistant commensal Escherichia coli in the faeces of horses in an equine hospital

The increasing prevalence of antimicrobial resistance in bacteria represents a considerable problem for human and veterinary medicine, causing complications in the treatment of infections. Resistance in Escherichia coli from horses has been documented in commensal and pathogenic strains, but little information exists regarding the prevalence of such bacteria in hospitalised horses or associated risk factors. A longitudinal cohort study was conducted of 103 horses admitted to a referral equine hospital for more than 48 h, with faecal samples collected on hospital admission and subsequently every two days until discharge. Horses undergoing radioactive gamma scintigraphic examination, un-weaned foals and mares with un-weaned foals were excluded. Data were collected from enrolled animals, including antimicrobial treatment history and hospitalisation details. Samples were cultured for resistant E. coli; isolates had their antimicrobial resistance profile determined. High sample prevalence for resistant E. coli was identified for all antimicrobials examined except co-amoxiclav. The prevalence of resistance was consistently lower at admission, rising to a peak 4 days post-admission. Risk factors were analysed using multilevel, multivariable modelling, which identified significant clustering of resistance outcomes within horses. For all outcomes except trimethoprim resistance, the day the sample was obtained was significant, with increased risk of resistance for samples taken on day 2 or later. Antimicrobial treatment in the previous seven days and increased total daily dosages of cotrimoxazole prescribed in the hospital in the previous 24-48 h were associated with increased risk. Location within the hospital and admission reason were significant risk factors for some resistance outcomes. High levels of multidrug-resistant E. coli (47.7% of samples) and extended spectrum β-lactamase-producing E. coli (27.3% of samples) were recovered; such bacteria could significantly complicate treatment if they were the cause of infection and may represent a risk to personnel in close contact with hospitalised horses.

Surveillance of antimicrobial resistance in resource-constrained settings - experience from five pilot projects

OBJECTIVE

The rapid increase in antimicrobial resistance (AMR) among bacteria is a major public health concern. The WHO Global Strategy for Containment of Antimicrobial Resistance proposed that model systems be developed for AMR surveillance and for monitoring antimicrobial use.

METHODS

Pilot projects were established in three sites in India and two in South Africa to collect monthly AMR data on target bacteria for at least 12 months. Escherichia coli was used as the target bacterium in four sites (three in India, one in South Africa). One South African site used Streptococcus pneumoniae and Haemophilus influenzae. Each site sought to obtain at least 960 isolates per year. Resistance was determined by disc diffusion or minimum inhibitory concentration (MIC) methods.

RESULTS

Data were collected for 12 and 16 months respectively in the South African sites and for 14 months in one Indian site and 24 months in the other two. All sites found difficulty collecting the required number of isolates, with three sites failing to do so. Escherichia coli isolates were more easily obtained and two sites developed methods to increase their yield. Disc diffusion testing provided more timely and reliable AMR data than did MIC determinations. Although methodological issues limit the comparability of data, high AMR rates were observed at all five sites.

CONCLUSION

All five pilot sites provided data on AMR, but also raised several issues related to logistics of long-term surveillance in settings under resource constraints. For surveillance of AMR in such settings, E. coli is probably the best indicator bacterium.

Tracking acquired antibiotic resistance in commensal bacteria of Galápagos land iguanas: no man, no resistance

Background

Antibiotic resistance, evolving and spreading among bacterial pathogens, poses a serious threat to human health. Antibiotic use for clinical, veterinary and agricultural practices provides the major selective pressure for emergence and persistence of acquired resistance determinants. However, resistance has also been found in the absence of antibiotic exposure, such as in bacteria from wildlife, raising a question about the mechanisms of emergence and persistence of resistant strains under similar conditions, and the implications for resistance control strategies. Since previous studies yielded some contrasting results, possibly due to differences in the ecological landscapes of the studied wildlife, we further investigated this issue in wildlife from a remote setting of the Galapagos archipelago.

Methodology/Principal Findings

Screening for acquired antibiotic resistance was carried out in commensal enterobacteria from Conolophus pallidus, the terrestrial iguana of Isla Santa Fe, where: i) the abiotic conditions ensure to microbes good survival possibilities in the environment; ii) the animal density and their habits favour microbial circulation between individuals; and iii) there is no history of antibiotic exposure and the impact of humans and introduced animal species is minimal except for restricted areas. Results revealed that acquired antibiotic resistance traits were exceedingly rare among bacteria, occurring only as non-dominant strains from an area of minor human impact.

Conclusions/Significance

Where both the exposure to antibiotics and the anthropic pressure are minimal, acquired antibiotic resistance traits are not normally found in bacteria from wildlife, even if the ecological landscape is highly favourable to bacterial circulation among animals. Monitoring antibiotic resistance in wildlife from remote areas could also be a useful tool to evaluate the impact of anthropic pressure.

Socioeconomic factors and antibiotic use in relation to antimicrobial resistance in the Amazonian area of Peru

Our objective was to correlate antibiotic resistance in gut E. coli flora of children, aged 6-72 months, with use of antibiotics, socioeconomic status (SES) and household characteristics in the urban communities of Yurimaguas and Moyobamba in the Amazonian area of Peru. Caregivers of 1598 children were interviewed using a structured questionnaire in a cross-sectional survey. Faecal samples were collected from the children and the antimicrobial susceptibility of E. coli was analysed by a rapid resistance screening method. Significantly higher odds for resistance were seen for children who had used antibiotics, both during the last 2 weeks and the last 6 months. Children from wealthier families had significantly higher odds for resistance to a number of antibiotics than children from the least wealthy families (Yurimaguas: nalidixic acid, OR = 2.13; ciprofloxacin, OR = 2.09; chloramphenicol, OR = 1.98. Moyobamba: nalidixic acid, OR = 1.59; ciprofloxacin, OR = 1.69). Thus, the children of wealthier families had a significantly increased odds ratio for resistance, also when controlling for the family's antibiotic use. Unknown factors related to socioeconomic status seem to contribute to the results seen in the study area.

Risk factors for antibiotic-resistant E. coli in children in a rural area

We surveyed antimicrobial susceptibility in faecal Escherichia coli in primary schoolchildren in rural Tamil Nadu, India. Resistance profiles of E. coli samples from local water sources were also obtained. We investigated sociodemographic characteristics as risk factors for resistance and local paediatric prescription patterns. In 119 stool samples, carriage of resistance to 1 antibiotic was 63% and multiple drug resistance was 32%. Resistance outcomes were associated with school of attendance, having a sibling attend the same school, younger age, and less crowded households. Eight of nine water samples were resistant to > or =1 antibiotic. Recent history of medication use was not associated with resistance carriage. Resistance patterns may have been influenced by local paediatric prescription patterns and veterinary antibiotic use. Frequent, low-cost surveillance of commensal resistance can guide development of locally appropriate treatment guidelines. School-based hygiene programmes should be considered as means of limiting the spread of antibiotic resistance.

Antibiotic resistance in a very remote Amazonas community

In a very remote human community of the Peruvian Amazonas with minimal antibiotic exposure, high levels of acquired resistance to the oldest antibiotics (ampicillin, tetracycline, trimethoprim/sulfamethoxazole, streptomycin and chloramphenicol) were detected in commensal Escherichia coli, with remarkable diversity of resistant clones and of resistance genes and plasmids. This pattern was similar overall to that previously observed in a very remote community of Bolivia. It was also similar to that observed in the nearest urban area, except for a lower dominance of resistant isolates and the absolute lack of quinolone resistance in the remote community. Present findings suggest that antibiotic resistance observed in remote communities with minimal antibiotic exposure is a general phenomenon contributed by complex mechanisms and provide new insights into the mechanisms involved in this phenomenon.

Multidrug-resistant commensal Escherichia coli in children, Peru and Bolivia

Healthy children in urban areas have a high prevalence of fecal carriage of drug-resistant E. coli.

Using a rapid screening method, we investigated the prevalence of fecal carriage of antimicrobial drug–resistant Escherichia coli in 3,174 healthy children from 4 urban settings in Peru and Bolivia. High resistance rates were observed for ampicillin (95%), trimethoprim-sulfamethoxazole (94%), tetracycline (93%), streptomycin (82%), and chloramphenicol (70%). Lower resistance rates were observed for nalidixic acid (35%), kanamycin (28%), gentamicin (21%), and ciprofloxacin (18%); resistance to ceftriaxone and amikacin was uncommon (<0.5%). In a random sample of 1,080 resistant E. coli isolates, 90% exhibited a multidrug-resistance (MDR) phenotype. The 2 most common MDR phenotypes (ampicillin/tetracycline/trimethoprim-sulfamethoxazole and ampicillin/tetracycline/trimethoprim-sulfamethoxazole/chloramphenicol) could be transferred en bloc in conjugation experiments. The most common acquired resistance genes were bla_TEM, tet(A), tet(B), drfA8, sul1, sul2, and catI. These findings underscore the magnitude of the problem of antimicrobial drug resistance in low-resource settings and the urgent need for surveillance and control of this phenomenon.

Extended antimicrobial resistance screening of the dominant faecal Escherichia coli and of rare resistant clones

Fifty faecal samples from healthy adults were grown on MacConkey agar and three pink colonies were subcultured, identified to species level and their antimicrobial susceptibility determined. Forty-seven samples yielded 141 isolates of Escherichia coli that were susceptible to most antimicrobials. Resistance was noted for ampicillin (30.5%), chloramphenicol (12.1%), tetracycline (23.4%), trimethoprim (24.8%) and co-trimoxazole (22.7%). A direct faecal plating method was used for extended resistance screening with E. coli as the indicator organism. Zone breakpoints were determined using normalised resistance interpretation and gave similar susceptibility results. Eighty-eight isolates of E. coli from within the zones of inhibition revealed four times more antimicrobial resistance. Extended antimicrobial resistance screening both provides the susceptibility profile of the dominant E. coli isolate and detects greater resistance in rare isolates.