Variations in antibiotic resistance profile in Enterobacteriaceae isolated from wild Australian mammals

European Wild Carnivores and Antibiotic Resistant Bacteria: A Review

Antibiotic resistance is a global concern that affects not only human health but also the health of wildlife and the environment. Wildlife can serve as reservoirs for antibiotic-resistant bacteria, and antibiotics in veterinary medicine and agriculture can contribute to the development of resistance in these populations. Several European carnivore species, such as wolves, foxes, otters, and bears, can be exposed to antibiotics by consuming contaminated food, water, or other resources in their habitats. These animals can also be indirectly exposed to antibiotics through interactions with domestic animals and human activities in their environment. Antibiotic resistance in wildlife can harm ecosystem health and also impact human health indirectly through various pathways, including zoonotic disease transmission. Moreover, the spread of resistant bacteria in wildlife can complicate conservation efforts, as it can threaten already endangered species. This review aims to describe the presence of antibiotic-resistant bacteria in wild carnivores in Europe.

Antimicrobial Resistance in Physiological and Potentially Pathogenic Bacteria Isolated in Southern Italian Bats

The spread of antimicrobial resistance is one of the major health emergencies of recent decades. Antimicrobial-resistant bacteria threaten not only humans but also populations of domestic and wild animals. The purpose of this study was to evaluate the distribution of antibiotic resistance (AMR) and multidrug resistance (MDR) in bacterial strains isolated from six Southern-Italian bat populations. Using the disk diffusion method, we evaluated the antimicrobial susceptibility of 413 strains of Gram-negative bacteria and 183 strains of Gram-positive bacteria isolated from rectal (R), oral (O) and conjunctival (C) swabs of 189 bats belonging to 4 insectivorous species (Myotis capaccinii, Myotis myotis, Miniopterus schreibersii and Rhinolophus hipposideros). In all bat species and locations, numerous bacterial strains showed high AMR levels for some of the molecules tested. In both Gram-negative and Gram-positive strains, the resistance patterns ranged from one to thirteen. MDR patterns varied significantly across sites, with Grotta dei Pipistrelli in Pantalica displaying the highest levels of MDR (77.2% of isolates). No significant differences were found across different bat species. Monitoring antibiotic resistance in wildlife is a useful method of evaluating the impact of anthropic pressure and environmental pollution. Our analysis reveals that anthropic contamination may have contributed to the spread of the antibiotic resistance phenomenon among the subjects we examined.

High Prevalence of Beta-Lactam-Resistant Escherichia coli in South Australian Grey-Headed Flying Fox Pups (Pteropus poliocephalus)

The emergence of antimicrobial-resistant Escherichia coli in wildlife is concerning-especially resistance to clinically important beta-lactam antibiotics. Wildlife in closer proximity to humans, including in captivity and in rescue/rehabilitation centres, typically have a higher prevalence of antimicrobial-resistant E. coli compared to their free-living counterparts. Each year, several thousand Australian fruit bat pups, including the grey-headed flying fox (GHFF; Pteropus poliocephalus), require rescuing and are taken into care by wildlife rescue and rehabilitation groups. To determine the prevalence of beta-lactam-resistant E. coli in rescued GHFF pups from South Australia, faecal samples were collected from 53 pups in care. A combination of selective culture, PCR, antimicrobial susceptibility testing, whole-genome sequencing, and phylogenetic analysis was used to identify and genetically characterise beta-lactam-resistant E. coli isolates. The prevalence of amoxicillin-, amoxicillin-plus-clavulanic-acid-, and cephalosporin-resistant E. coli in the 53 pups was 77.4% (n = 41), 24.5% (n = 13), and 11.3% (n = 6), respectively. GHFF beta-lactam-resistant E. coli also carried resistance genes to aminoglycosides, trimethoprim plus sulphonamide, and tetracyclines in 37.7% (n = 20), 35.8% (n = 19), and 26.4% (n = 14) of the 53 GHFF pups, respectively, and 50.9% (n = 27) of pups carried multidrug-resistant E. coli. Twelve E. coli strain types were identified from the 53 pups, with six strains having extraintestinal pathogenic traits, indicating that they have the potential to cause blood, lung, or wound infections in GHFFs. Two lineages-E. coli ST963 and ST58 O8:H25-were associated with human extraintestinal infections. Phylogenetic analyses determined that all 12 strains were lineages associated with humans and/or domestic animals. This study demonstrates high transmission of anthropogenic-associated beta-lactam-resistant E. coli to GHFF pups entering care. Importantly, we identified potential health risks to GHFF pups and zoonotic risks for their carers, highlighting the need for improved antibiotic stewardship and biosafety measures for GHFF pups entering care.

Occurrence of Salmonella enterica in grey-headed flying foxes from New South Wales

Salmonella enterica and Campylobacter jejuni are significant foodborne zoonotic pathogens causing gastroenteritis in humans. Domestic animals are commonly implicated as reservoirs of S. enterica and C. jejuni, but both are also detected in wild animals. Salmonella enterica serovar Typhimurium is the most common cause of human salmonellosis in Australia; however, Salmonella enterica serovar Wangata is associated with sporadic human outbreaks in New South Wales and wild animals may be a potential reservoir. To determine if wild grey-headed flying foxes (GHFF; Pteropus poliocephalus) are reservoirs of Salmonella and Campylobacter, faecal samples were collected from three GHFF colonies in New South Wales and cultured for the presence of Salmonella and Campylobacter. One Salmonella isolate was cultured from 254 GHFF faecal samples (0.39%). Whole genome sequencing was used to genetically characterise the Salmonella isolate and perform phylogenetic analysis. The GHFF isolate was determined to be Salmonella Typhimurium ST19. The GHFF isolate carried a virulence plasmid and other virulence factors, but did not exhibit antimicrobial resistance. Phylogenetic analysis determined that the GHFF isolate was most closely related to a cluster of six isolates: four from human salmonellosis cases in Queensland and two from Australian livestock. Neither Campylobacter nor Salmonella Wangata were cultured from the 254 GHFF faecal samples. This study concluded that wild GHFF in New South Wales are not major reservoirs for Salmonella, and the zoonotic risks associated with S. enterica carriage by urban GHFF are low for the general public.

Characterization of beta-lactam-resistant Escherichia coli from Australian fruit bats indicates anthropogenic origins

Antimicrobial-resistant Escherichia coli, particularly those resistant to critically important antimicrobials, are increasingly reported in wildlife. The dissemination of antimicrobial-resistant bacteria to wildlife indicates the far-reaching impact of selective pressures imposed by humans on bacteria through misuse of antimicrobials. The grey-headed flying fox (GHFF; Pteropus poliocephalus), a fruit bat endemic to eastern Australia, commonly inhabits urban environments and encounters human microbial pollution. To determine if GHFF have acquired human-associated bacteria, faecal samples from wild GHFF (n=287) and captive GHFF undergoing rehabilitation following illness or injury (n=31) were cultured to detect beta-lactam-resistant E. coli. Antimicrobial susceptibility testing, PCR and whole genome sequencing were used to determine phenotypic and genotypic antimicrobial resistance profiles, strain type and virulence factor profiles. Overall, 3.8 % of GHFF carried amoxicillin-resistant E. coli (wild 3.5 % and captive 6.5 %), with 38.5 % of the 13 GHFF E. coli isolates exhibiting multidrug resistance. Carbapenem (blaNDM-5) and fluoroquinolone resistance were detected in one E. coli isolate, and two isolates were resistant to third-generation cephalosporins (blaCTX-M-27 and ampC). Resistance to tetracycline and trimethoprim plus sulfamethoxazole were detected in 69.2% and 30.8 % of isolates respectively. Class 1 integrons, a genetic determinant of resistance, were detected in 38.5 % of isolates. Nine of the GHFF isolates (69.2 %) harboured extraintestinal virulence factors. Phylogenetic analysis placed the 13 GHFF isolates in lineages associated with humans and/or domestic animals. Three isolates were human-associated extraintestinal pathogenic E. coli (ST10 O89:H9, ST73 and ST394) and seven isolates belonged to lineages associated with extraintestinal disease in both humans and domestic animals (ST88, ST117, ST131, ST155 complex, ST398 and ST1850). This study provides evidence of anthropogenic multidrug-resistant and pathogenic E. coli transmission to wildlife, further demonstrating the necessity for incorporating wildlife surveillance within the One Health approach to managing antimicrobial resistance.

Characterization of ESBL-Producing Enterobacteria from Fruit Bats in an Unprotected Area of Makokou, Gabon

In Gabon, terrestrial mammals of protected areas have been identified as a possible source of antibiotic-resistant bacteria. Some studies on antibiotic resistance in bats have already been carried out. The main goal of our study was to detect extended-spectrum beta-lactamases (ESBLs) that are produced by enterobacteria from bats in the Makokou region in Gabon. Sixty-eight fecal samples were obtained from 68 bats caught in the forests located 1 km from the little town of Makokou. After culture and isolation, 66 Gram-negative bacterial colonies were obtained. The double-disk diffusion test confirmed the presence of ESBLs in six (20.69%) Escherichia coli isolates, four (13.79%) Klebsiella pneumoniae isolates, and one (3.45%) Enterobacter cloacae isolate. The analysis based on the nucleotide sequences of the ESBL resistance genes showed that all cefotaximase-Munichs (CTX-Ms) were CTX-M-15 and that all sulfhydryl variables (SHVs) were SHV-11: 41.67% CTX-M-15-producing E. coli, 16.67% CTX-M-15+SHV-11-producing E. coli, 8.33% CTX-M-15-producing K. pneumoniae, 25% CTX-M-15+SHV-11-producing K. pneumoniae, and 8.33% CTX-M-15-produced E. cloacae. This study shows for the first time the presence of multiresistant ESBL-producing enterobacteria in fruit bats in Makokou.

Salmonella enterica isolates from Western Australian rangeland goats remain susceptible to critically important antimicrobials

This study investigated faecal carriage and antimicrobial resistance (AMR) of Salmonella enterica recovered from rangeland goats. Faecal samples (n = 400) were collected at slaughter from four consignments of goats (n = 100 samples per consignment), each from one of four localities in Western Australia. Carriage of Salmonella spp. was detected in 106 samples (26.5%; 95% CI 22.4-31.0%). The rate of faecal carriage for each consignment ranged between 23-30%. PCR assays targeting the STM2755 and STM4497 genes revealed 84.9% (90/106) of the isolates were of serovar Typhimurium. Salmonella Chester (11/106, 10.4%) and S. Saintpaul (5/106, 4.7%) were characterised at invA and ompF genes. Antimicrobial susceptibility testing demonstrated that 84.0% of isolates were susceptible to all tested (n = 13) antimicrobials. Resistance was identified to azithromycin (14.2%), tetracycline (10.4%), ampicillin (5.7%), amoxicillin-clavulanate and cefoxitin (3.8%), trimethoprim/sulfamethoxazole (1.9%), gentamicin and streptomycin (0.9%). No isolate was resistant to four or more antimicrobials, or to critically important antimicrobials such as fluoroquinolones and extended spectrum cephalosporins. This is the first study reporting AMR in Salmonella isolates from Australian rangeland goats. The rate of detection of AMR was very low, some resistance to low-importance drugs was present in the Salmonella population, despite the absence of active selection pressure.

Bacteria richness and antibiotic-resistance in bats from a protected area in the Atlantic Forest of Southeastern Brazil

Bats play key ecological roles, also hosting many zoonotic pathogens. Neotropical bat microbiota is still poorly known. We speculate that their dietary habits strongly influence their microbiota richness and antibiotic-resistance patterns, which represent growing and serious public health and environmental issue. Here we describe the aerobic microbiota richness of bats from an Atlantic Forest remnant in Southeastern Brazil, and the antibiotic-resistance patterns of bacteria of clinical importance. Oral and rectal cavities of 113 bats from Carlos Botelho State Park were swabbed. Samples were plated on 5% sheep blood and MacConkey agar and identified by the MALDI-TOF technique. Antibiotic susceptibility tests were performed using Kirby-Bauer’s antibiotic disc diffusion technique.We identified 596 isolates at the genus level and tentatively to the species level. Proteobacteria was the most abundant phylum in all the dietary guilds, representing 87% of the total identified samples. The most common bacteria within bat individuals were Escherichia coli, Klebsiella oxytoca and Serratia marcescens, and within bat species were Serratia marcescens, Pseudomonas sp. and Staphylococcus sp. Frugivores presented the most diverse microbiota. In general, the antibiogram results indicated a low occurrence of resistance on eigth potentially pathogenic bacteria species. The resistance to antibiotics found on our samples was related mostly to the intrinsic resistance of the tested species.The low occurrence of resistant bacteria in our samples could be related to the well preserved environment where bats were caught. Once the major causes of resistance-acquiring are related to anthropic activites, the controlled access of tourists on certain regions of the Park seems to be effectively protecting the environment.

Temporal variations in patterns of Escherichia coli strain diversity and antimicrobial resistance in the migrant Egyptian vulture

Aims: Multiple antimicrobial resistance in Escherichia coli of wild vertebrates is a global concern with scarce assessments on the subject from developing countries that have high human-wild species interactions. We studied the ecology of E. coli in a wintering population of Egyptian Vultures in India to understand temporal changes in both E. coli strains and patterns of antimicrobial resistance. Methods and Results: We ribotyped E. coli strains and assessed antimicrobial resistance from wintering vultures at a highly synanthropic carcass dump in north-west India. Both E. coli occurence (90.32%) and resistance to multiple antimicrobials (71.43%) were very high. Clear temporal patterns were apparent. Diversity of strains changed and homogenized at the end of the Vultures' wintering period, while the resistance pattern showed significantly difference inter-annually, as well as between arrival and departing individuals within a wintering cycle. Significance of study: The carcass dump environment altered both E. coli strains and multiple antimicrobial resistance in migratory Egyptian Vultures within a season. Long-distance migratory species could therefore disseminate resistant E. coli strains across broad geographical scales rendering regional mitigation strategies to control multiple antimicrobial resistance in bacteria ineffective.

Highly diverse and antimicrobial susceptible Escherichia coli display a naïve bacterial population in fruit bats from the Republic of Congo

Bats are suspected to be a reservoir of several bacterial and viral pathogens relevant to animal and human health, but studies on Escherichia coli in these animals are sparse. We investigated the presence of E. coli in tissue samples (liver, lung and intestines) collected from 50 fruit bats of five different species (Eidolon helvum, Epomops franqueti, Hypsignathus monstrosus, Myonycteris torquata, Rousettus aegyptiacus) of two different areas in the Republic of Congo between 2009 and 2010. To assess E. coli pathotypes and phylogenetic relationships, we determined the presence of 59 virulence associated genes and multilocus sequence types (STs). Isolates were further tested for their susceptibility to several antimicrobial substances by agar disk diffusion test and for the presence of an Extended-Spectrum Beta-Lactamase phenotype. E. coli was detected in 60% of the bats analysed. The diversity of E. coli strains was very high, with 37 different STs within 40 isolates. Occasionally, we detected sequence types (e.g. ST69, ST127, and ST131) and pathotypes (e.g. ExPEC, EPEC and atypical EPEC), which are known pathogens in human and/or animal infections. Although the majority of strains were assigned to phylogenetic group B2 (46.2%), which is linked with the ExPEC pathovar, occurrence of virulence-associated genes in these strains were unexpectedly low. Due to this, and as only few of the E. coli isolates showed intermediate resistance to certain antimicrobial substances, we assume a rather naïve E. coli population, lacking contact to humans or domestic animals. Future studies featuring in depth comparative whole genome sequence analyses will provide insights into the microevolution of this interesting strain collection.

The prevalence of antimicrobial-resistant Escherichia coli in sympatric wild rodents varies by season and host

AIMS

  To investigate the prevalence and temporal patterns of antimicrobial resistance in wild rodents with no apparent exposure to antimicrobials.

METHODS AND RESULTS

  Two sympatric populations of bank voles and wood mice were trapped and individually monitored over a 2- year period for faecal carriage of antimicrobial-resistant Escherichia coli. High prevalences of ampicillin-, chloramphenicol-, tetracycline- and trimethoprim-resistant E. coli were observed. A markedly higher prevalence of antimicrobial-resistant E. coli was found in wood mice than in bank voles, with the prevalence in both increasing over time. Superimposed on this trend was a seasonal cycle with a peak prevalence of resistant E. coli in mice in early- to mid-summer and in voles in late summer and early autumn.

CONCLUSIONS

  These sympatric rodent species had no obvious contact with antimicrobials, and the difference in resistance profiles between rodent species and seasons suggests that factors present in their environment are unlikely to be drivers of such resistance.

SIGNIFICANCE AND IMPACT OF THE STUDY

  These findings suggest that rodents may represent a reservoir of antimicrobial-resistant bacteria, transmissible to livestock and man. Furthermore, such findings have implications for human and veterinary medicine regarding antimicrobial usage and subsequent selection of antimicrobial-resistant organisms.

Lyme Borreliosis: Is there a preexisting (natural) variation in antimicrobial susceptibility among Borrelia burgdorferi strains?

The development of antibiotics changed the world of medicine and has saved countless human and animal lives. Bacterial resistance/tolerance to antibiotics have spread silently across the world and has emerged as a major public health concern. The recent emergence of pan-resistant bacteria can overcome virtually any antibiotic and poses a major problem for their successful control. Selection for antibiotic resistance may take place where an antibiotic is present: in the skin, gut, and other tissues of humans and animals and in the environment. Borrelia burgdorferi, the etiological agents of Lyme borreliosis, evades host immunity and establishes persistent infections in its mammalian hosts. The persistent infection poses a challenge to the effective antibiotic treatment, as demonstrated in various animal models. An increasingly heterogeneous subpopulation of replicatively attenuated spirochetes arises following treatment, and these persistent antimicrobial tolerant/resistant spirochetes are non-cultivable. The non-cultivable spirochetes resurge in multiple tissues at 12 months after treatment, with B. burgdorferi-specific DNA copy levels nearly equivalent to those found in shame-treated experimental animals. These attenuated spirochetes remain viable, but divide slowly, thereby being tolerant to antibiotics. Despite the continued non-cultivable state, RNA transcription of multiple B. burgdorferi genes was detected in host tissues, spirochetes were acquired by xenodiagnostic ticks, and spirochetal forms could be visualized within ticks and mouse tissues. A number of host cytokines were up- or down-regulated in tissues of both shame- and antibiotic-treated mice in the absence of histopathology, indicating a lack of host response to the presence of antimicrobial tolerant/resistant spirochetes.

Acquired antibiotic resistance among wild animals: the case of Iberian Lynx (Lynx pardinus)

The selective pressure generated by the clinical misuse of antibiotics has been the major driving force leading to the emergence of antibiotic resistance among bacteria. Antibiotics or even resistant bacteria are released into the environment and contaminate the surrounding areas. Human and animal populations in contact with these sources are able to become reservoirs of these resistant organisms. Then, due to the convergence between habitats, the contact of wild animals with other animals, humans, or human sources is now more common and this leads to an increase in the exchange of resistance determinants between their microbiota. Indeed, it seems that wildlife populations living in closer proximity to humans have higher levels of antibiotic resistance. Now, the Iberian Lynx (Lynx pardinus) is a part of this issue, being suggested as natural reservoir of acquired resistant bacteria. The emerging public health concern regarding microbial resistance to antibiotics is becoming true: the bacteria are evolving and are now affecting unintentional hosts.

Potential impact of antimicrobial resistance in wildlife, environment and human health

Given the significant spatial and temporal heterogeneity in antimicrobial resistance distribution and the factors that affect its evolution, dissemination, and persistence, it is important to highlight that antimicrobial resistance must be viewed as an ecological problem. Monitoring the resistance prevalence of indicator bacteria such as Escherichia coli and enterococci in wild animals makes it possible to show that wildlife has the potential to serve as an environmental reservoir and melting pot of bacterial resistance. These researchers address the issue of antimicrobial-resistant microorganism proliferation in the environment and the related potential human health and environmental impact.

Into the wild: dissemination of antibiotic resistance determinants via a species recovery program

Management strategies associated with captive breeding of endangered species can establish opportunities for transfer of pathogens and genetic elements between human and animal microbiomes. The class 1 integron is a mobile genetic element associated with clinical antibiotic resistance in gram-negative bacteria. We examined the gut microbiota of endangered brush-tail rock wallabies Petrogale penicillata to determine if they carried class 1 integrons. No integrons were detected in 65 animals from five wild populations. In contrast, class 1 integrons were detected in 48% of fecal samples from captive wallabies. The integrons contained diverse cassette arrays that encoded resistance to streptomycin, spectinomycin, and trimethoprim. Evidence suggested that captive wallabies had acquired typical class 1 integrons on a number of independent occasions, and had done so in the absence of strong selection afforded by antibiotic therapy. Sufficient numbers of bacteria containing diverse class 1 integrons must have been present in the general environment occupied by the wallabies to account for this acquisition. The captive wallabies have now been released, in an attempt to bolster wild populations of the species. Consequently, they can potentially spread resistance integrons into wild wallabies and into new environments. This finding highlights the potential for genes and pathogens from human sources to be acquired during captive breeding and to be unwittingly spread to other populations.

Characterization of Antibiotic Resistance E. Coli and Antibiotic Resistance Genes in Aquatic Environment of Taihu Lake, China

The aims of this study are to evaluate multiple antibiotic resistant Escherichia coli isolated from surface water and to investigate the presence and distribution antibiotic resistance genes (ARGs) in sediments of Taihu Lake. The results show that the presentence of four ARGs concentrations in the sediments of the lake was in sequence: strB>qnrB>strA>qnrS, as determined by realtime-PCR technique. The southwest and east areas of Taihu Lake were polluted seriously than other areas from all kinds of antibiotics. The screening Escherichia coli had a higher resistance to streptomycin, tetracycline and ampicillin than other four antibiotics, and had a lowest resistance to levofloxacin.

Bats and bacterial pathogens: a review

The occurrence of emerging infectious diseases and their relevance to human health has increased the interest in bats as potential reservoir hosts and vectors of zoonotic pathogens. But while previous and ongoing research activities predominantly focused on viral agents, the prevalence of pathogenic bacteria in bats and their impact on bat mortality have largely neglected. Enteric pathogens found in bats are often considered to originate from the bats' diet and foraging habitats, despite the fact that little is known about the actual ecological context or even transmission cycles involving bats, humans and other animals like pets and livestock. For some bacterial pathogens common in human and animal diseases (e.g. Pasteurella, Salmonella, Escherichia and Yersinia spp.), the pathogenic potential has been confirmed for bats. Other bacterial pathogens (e.g. Bartonella, Borrelia and Leptospira spp.) provide evidence for novel species that seem to be specific for bat hosts but might also be of disease importance in humans and other animals. The purpose of this review is to summarize the current knowledge of bacterial pathogens identified in bats and to consider factors that might influence the exposure and susceptibility of bats to bacterial infection but could also affect bacterial transmission rates between bats, humans and other animals.

Extended-Spectrum Beta-Lactamases Producing E. coli in Wildlife, yet Another Form of Environmental Pollution?

Wildlife is normally not exposed to clinically used antimicrobial agents but can acquire antimicrobial resistant bacteria through contact with humans, domesticated animals and the environment, where water polluted with feces seems to be the most important vector. Escherichia coli, an ubiquitous commensal bacterial species colonizing the intestinal tract of mammals and birds, is also found in the environment. Extended-spectrum beta-lactamases producing E. coli (ESBL-E. coli) represent a major problem in human and veterinary medicine, particular in nosocomial infections. Additionally an onset of community-acquired ESBL-E. coli infections and an emergence in livestock farming has been observed in recent years, suggesting a successful transmission as well as persistence of ESBL-E. coli strains outside clinical settings. Another parallel worldwide phenomenon is the spread of ESBL-E. coli into the environment beyond human and domesticated animal populations, and this seems to be directly influenced by antibiotic practice. This might be a collateral consequence of the community-onset of ESBL-E. coli infections but can result (a) in a subsequent colonization of wild animal populations which can turn into an infectious source or even a reservoir of ESBL-E. coli, (b) in a contribution of wildlife to the spread and transmission of ESBL-E. coli into fragile environmental niches, (c) in new putative infection cycles between wildlife, domesticated animals and humans, and (d) in problems in the medical treatment of wildlife. This review aims to summarize the current knowledge on ESBL-E. coli in wildlife, in turn underlining the need for more large scale investigations, in particular sentinel studies to monitor the impact of multiresistant bacteria on wildlife.

Frequency of Detection of Escherichia coli, Salmonella spp., and Campylobacter spp. in the Faeces of Wild Rats (Rattus spp.) in Trinidad and Tobago

The study was conducted to determine the frequency of isolation of Salmonella, Campylobacter and E. coli O157 in the faecal samples of rats trapped across the regional corporations in Trinidad and to assess their resistance to antimicrobial agents. A total of 204 rats were trapped for the detection of selected bacteria. Standard methods were used to isolate Salmonella, Campylobacter and E. coli O157. Characterization of E. coli was done on sorbitol MacConkey agar to determine non-sorbitol fermentation, blood agar to determine haemolytic and mucoid colonies and by using E. coli O157 antiserum to determine O157 strain. The disc diffusion method was used to determine resistance to nine antimicrobial agents. Of the 204 rats, 4 (2.0%), 7 (3.4%) and 171 (83.8%) were positive for Salmonella spp., Campylobacter spp. and E. coli, respectively. Of the 171 isolates of E. coli tested 0 (0.0%), 25 (14.6%) and 19 (11.1%) were haemolytic, mucoid and non-sorbitol fermenters, respectively. All isolates were negative for the O157 strain. The frequency of resistance to the 9 antimicrobial agents tested was 75% (3 of 4) for Salmonella, 85.7% (6 of 7) of Campylobacter spp. and 36.3% (62 of 171) for E. coli (P < .05; χ(2)).

Biofilm formation by and thermal niche and virulence characteristics of Escherichia spp

In order to better understand the ecological and virulence characteristics of the various clades of Escherichia, in vitro and in vivo experiments were undertaken. Members of the recently described cryptic clades of Escherichia (clades III, IV, and V) were found to have an enhanced ability to form biofilms compared to strains of Escherichia coli, E. fergusonii, or E. albertii. Members of the cryptic clades were also able to replicate at a lower temperature (5°C versus 11°C) than strains of the named species of Escherichia. Neither a strain's maximal growth rate nor its optimal temperature for growth varied with respect to the strain's phylogenetic affiliation. Escherichia strains not belonging to the species E. coli were positive for a mix of traits thought to enhance a strain's ability to cause either intestinal or extraintestinal disease. However, no non-E. coli Escherichia strain was virulent in a mouse model of extraintestinal infection. The frequency of resistance to antibiotics was low, and none of the strains tested harbored class 1, 2, or 3 integrons. The results of these experiments support the hypothesis that members of the cryptic Escherichia clades may be better able to persist in the external environment compared to E. coli, E. fergusonii, or E. albertii, isolates.

Highly variable patterns of antimicrobial resistance in commensal Escherichia coli isolates from pigs, sympatric rodents, and flies

Antimicrobial-resistant Escherichia coli strains from pigs, sympatric rodents, and flies from two large farms in the Czech Republic with different antibiotic exposure histories were characterized based on antimicrobial resistance genes, integrons, and macrorestriction DNA profiles. Isolates of E. coli were tested for susceptibility to 12 antimicrobial agents according to the standard disk diffusion method. In resistant isolates, polymerase chain reaction was used to detect antibiotic resistance genes, integrase genes, and gene cassettes. Pulsed-field gel electrophoresis (PFGE) was used for molecular subtyping of E. coli. In farm A (long-term use of amoxicillin only), 75% (n = 198), 65% (n = 49), 11% (n = 139), and 82% (n = 177) of E. coli isolates from piglets, sows, sympatric rodents, and flies, respectively, were antibiotic resistant. In farm B (various antibiotics commonly used), 53% (n = 154), 69% (n = 98), and 54% (n = 74) of E. coli isolates from piglets, sows, and sympatric rodents, respectively, were antibiotic resistant. In both farms, the highest resistance prevalence was to tetracycline, and resistance patterns of isolates were greatly variable. Isolates with the same resistance phenotype, genes, and PFGE profile were found in pigs and flies. Isolates from rodents showed unique PFGE profiles. Close contact of sympatric rodents and flies with pigs or their products was associated with colonization of rodents and flies with resistant bacteria or transfer of resistance genes found in pig intestinal flora.

Antimicrobial-resistant faecal Escherichia coli in wild mammals in central Europe: multiresistant Escherichia coli producing extended-spectrum beta-lactamases in wild boars

AIMS

To determine the presence of antibiotic-resistant faecal Escherichia coli in populations of wild mammals in the Czech Republic and Slovakia.

METHODS AND RESULTS

Rectal swabs or faeces collected during 2006-2008 from wild mammals were spread on MacConkey agar and MacConkey agar containing 2 mg l(-1) of cefotaxime. From plates with positive growth, one isolate was recovered and identified as E. coli. Susceptibility to 12 antibiotics was tested using the disk diffusion method. Resistance genes, class 1 and 2 integrons and gene cassettes were detected in resistant isolates by polymerase chain reaction (PCR). Extended-spectrum beta-lactamases (ESBL) were further characterized by DNA sequencing, macrorestriction profiling and determination of plasmid sizes. Plasmid DNA was subjected to EcoRV digestion, transferability by conjugation and incompatibility grouping by multiplex PCR. The prevalence of resistant isolates was 2% in small terrestrial mammals (rodents and insectivores, n(E. coli) = 242), 12% in wild ruminants and foxes (n(E. coli) = 42), while no resistant isolates were detected in brown bears (n(E. coli) = 16). In wild boars (Sus scrofa) (n(E. coli) = 290), the prevalence of resistant isolates was 6%. Class 1 and 2 integrons with various gene cassettes were recorded in resistant isolates. From wild boars, five (2%, n(rectal smears) = 293) multiresistant isolates producing ESBL were recovered: one isolate with bla(CTX-M-1) + bla(TEM-1), three with bla(CTX-M-1) and one with bla(TEM-52b). The bla(CTX-M-1) genes were carried on approx. 90 kb IncI1 conjugative plasmids.

CONCLUSIONS

Antibiotic-resistant E. coli occurred in populations of wild mammals in various prevalences.

SIGNIFICANCE AND IMPACT OF THE STUDY

Wild mammals are reservoirs of antibiotic-resistant E. coli including ESBL-producing strains which were found in wild boars.

Antibiotic resistance of enterococci in American bison (Bison bison) from a nature preserve compared to that of Enterococci in pastured cattle

Enterococci isolated from a bison population on a native tall-grass prairie preserve in Kansas were characterized and compared to enterococci isolated from pastured cattle. The species diversity was dominated by Enterococcus casseliflavus in bison (62.4%), while Enterococcus hirae was the most common isolate from cattle (39.7%). Enterococcus faecalis was the second most common species isolated from bison (16%). In cattle, E. faecalis and Enterococcus faecium were isolated at lower percentages (3.2% and 1.6%, respectively). No resistance to ampicillin, chloramphenicol, gentamicin, or high levels of vancomycin was detected from either source. Tetracycline and erythromycin resistance phenotypes, encoded by tetO and ermB, respectively, were common in cattle isolates (42.9% and 12.7%, respectively). A significant percentage of bison isolates (8% and 4%, respectively) were also resistant to these two antibiotics. The tetracycline resistance genes from both bison and cattle isolates resided on mobile genetic elements and showed a transfer frequency of 10(-6) per donor, whereas erythromycin resistance was not transferable. Resistance to ciprofloxacin was found to be higher in enterococci from bison (14.4%) than in enterococci isolated from cattle (9.5%). The bison population can serve as a sentinel population for studying the spread and origin of antibiotic resistance.

Coliform dynamics and the implications for source tracking

In many parts of the world, coliform counts in recreational waters are unacceptably high. In an attempt to rectify this problem, programmes are under way to develop methods that will allow the sources of the faecal contamination thought to be responsible for these elevated counts to be identified. The success of these efforts depends on the validity of several assumptions that underlie many of the proposed methods. One of the critical assumptions is that the clonal composition of the coliform species being monitored in a water body reflects the clonal composition of the species in the host populations responsible for the faecal inputs into that water body. To determine the extent to which among-strain variation in a coliform species might invalidate this assumption, a series of simple mathematical models was proposed and analysed. The first series of models assumed that all cells of species were identical. The question posed was - is the density of a coliform species in a body of water linearly related to the rate at which cells of the species enter the water body via faecal production? The results of these models suggest that, over a wide range of conditions, cell densities in the water body are linearly related to the rate at which cells enter the water body as a result of faecal contamination. This outcome occurs whether or not cells are capable of division in the external environment. When the rate of cell division depends on the concentration of available nutrients then, when nutrient input rates are 'high' and rates of faecal contamination are 'low', this linear relationship does not hold. The second series of models assumed that the coliform species consists of different strains and that these strains differ in their performance in the external environment. The results of these multistrain models show that the relative abundance of strains in the external environment is unlikely to reflect their relative abundance in the faecal inputs to the environment. Consequently, statements such as - domestic animals are responsible for 30% and wildlife for 70% of the faecal inputs to a water body - may well be meaningless.

Genetic and ecological structure of Hafnia alvei in Australia

Multilocus enzyme electrophoresis of 161 Hafnia alvei isolates from 158 hosts and 3 water column samples collected in Australia revealed that this species consists of two genetically distinct groups. The two groups of H. alvei differed significantly in their genetic structure and host distribution. The taxonomic class of the host but not geographic locality explained a significant proportion of the observed genetic and biochemical variation among strains within each genetic group.

A molecular phylogeny of enteric bacteria and implications for a bacterial species concept

A molecular phylogeny for seven taxa of enteric bacteria (Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, and Serratia plymuthica) was made from multiple isolates per taxa taken from a collection of environmental enteric bacteria. Sequences from five housekeeping genes (gapA, groEL, gyrA, ompA, and pgi) and the 16S rRNA gene were used to infer individual gene trees and were concatenated to infer a composite molecular phylogeny for the species. The isolates from each taxa formed tight species clusters in the individual gene trees, suggesting the existence of 'genotypic' clusters that correspond to traditional species designations. These sequence data and the resulting gene trees and consensus tree provide the first data set with which to assess the utility of the recently proposed core genome hypothesis (CGH). The CGH provides a genetically based approach to applying the biological species concept to bacteria.

Antimicrobial resistance in livestock

Antimicrobial resistance may become a major problem in veterinary medicine as a consequence of the intensive use and misuse of antimicrobial drugs. Related problems are now arising in human medicine, such as the appearance of multi-resistant food-borne pathogens. Product characteristics, dose, treatment interval and duration of treatment influence the selection pressure for antimicrobial drug resistance. There are theoretical, experimental and clinical indications that the emergence of de novo resistance in a pathogenic population can be prevented by minimizing the time that suboptimal drug levels are present in the infected tissue compartment. Until recently, attention has been focused on target pathogens. However, it should be kept in mind that when antimicrobial drugs are used in an individual, resistance selection mainly affects the normal body flora. In the long term, this is at least equally important as resistance selection in the target pathogens, as the horizontal transfer of resistance genes converts almost all pathogenic bacteria into potential recipients for antimicrobial resistance. Other factors contributing to the epidemiology of antimicrobial resistance are the localization and size of the microbial population, and the age, immunity and contact intensity of the host. In livestock, dynamic herd-related resistance patterns have been observed in different animal species.

11: Antibiotic resistance

Antibiotic resistance is a consequence of antibiotic use - we need to use antibiotics less and to use them prudently. Plans to combat antibiotic resistance were recently proposed by the World Health Organization, a United States interagency taskforce and the Australian Joint Expert Technical Advisory Committee on Antibiotic Resistance. Prudent antibiotic use includes not using antibiotics when benefit is minimal (eg, in many respiratory tract infections), using narrow-spectrum antibiotics whenever possible and using optimal dosages and regimens. The need for antibiotic therapy can be reduced by preventing infections through vaccination, infection control measures and improved sanitation. Surveillance of antibiotic resistance is needed to target interventions for minimising antibiotic use. More research is needed into new antibiotics and regimens and into improving medical devices and protocols to prevent infection. Some simple changes to practice could reduce development and spread of antibiotic resistance

Antibiotic resistance in bacteria from magpies (Pica pica) and rabbits (Oryctolagus cuniculus) from west Wales

The prevalence of antibiotic-resistant bacteria in wild animal and bird populations is largely unknown, with little consistency among the few published reports. We therefore examined intestinal bacteria from magpies (Pica pica) and rabbits (Oryctolagus cuniculus) collected in rural west Wales. Escherichia coli isolates resistant to multiple antibiotics were grown from eight of 20 magpies trapped in spring, 1999 and one of 17 in spring, 2000; the most prevalent resistance trait among these isolates was to tetracycline, but resistances to ampicillin, chloramphenicol, kanamycin, sulphonamide, tetracycline and trimethoprim were also found. Tetracycline-resistant Enterococcus spp. were found in one of 20 magpies in 1999 and three of 17 in 2000. Only one resistant E. coli isolate was detected among gut bacteria from 13 rabbits, and this strain was resistant only to tetracycline. Differences in the prevalence of resistance between bacteria from rabbits and magpies may reflect differences in diet: rabbits graze field edges, whereas magpies are omnivorous and opportunistic. The resistance genes found in E. coli isolates from magpies mostly corresponded to those common among human isolates, but those conferring tetracycline resistance were unique.