Emergence of a Potent Multidrug Efflux Pump Variant That Enhances Campylobacter Resistance to Multiple Antibiotics

Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella

Salmonella is an important genus of Gram-negative pathogens, treatment of which has become problematic due to increases in antimicrobial resistance. This is partly attributable to the overexpression of tripartite efflux pumps, particularly the constitutively expressed AcrAB-TolC. Despite its clinical importance, the structure of the Salmonella AcrB transporter remained unknown to-date, with much of our structural understanding coming from the Escherichia coli orthologue. Here, by taking advantage of the styrene maleic acid (SMA) technology to isolate membrane proteins with closely associated lipids, we report the very first experimental structure of Salmonella AcrB transporter. Furthermore, this novel structure provides additional insight into mechanisms of drug efflux as it bears the mutation (G288D), originating from a clinical isolate of Salmonella Typhimurium presenting an increased resistance to fluoroquinolones. Experimental data are complemented by state-of-the-art molecular dynamics (MD) simulations on both the wild type and G288D variant of Salmonella AcrB. Together, these reveal several important differences with respect to the E. coli protein, providing insights into the role of the G288D mutation in increasing drug efflux and extending our understanding of the mechanisms underlying antibiotic resistance.

Antimicrobial Resistance Determinants Circulating among Thermophilic Campylobacter Isolates Recovered from Broilers in Ireland Over a One-Year Period

Campylobacteriosis is the leading cause of human bacterial gastroenteritis, very often associated with poultry consumption. Thermophilic Campylobacter (Campylobacter jejuni and Campylobacter coli) isolates (n = 158) recovered from broiler neck skin and caecal contents in Ireland over a one-year period, resistant to at least one of three clinically relevant antimicrobial classes, were screened for resistance determinants. All ciprofloxacin-resistant isolates (n = 99) harboured the C257T nucleotide mutation (conferring the Thr-86-Ile substitution) in conjunction with other synonymous and nonsynonymous mutations, which may have epidemiological value. The A2075G nucleotide mutation and amino acid substitutions in L4 and L22 were detected in all erythromycin-resistant isolates (n = 5). The tetO gene was detected in 100% (n = 119) of tetracycline-resistant isolates and three of which were found to harbour the mosaic tetracycline resistance gene tetO/32/O. Two streptomycin-resistant C. jejuni isolates (isolated from the same flock) harboured ant(6)-Ib, located in a multidrug resistance genomic island, containing aminoglycoside, streptothricin (satA) and tetracycline resistance genes (truncated tetO and mosaic tetO/32/O). The ant(6)-Ie gene was identified in two streptomycin-resistant C. coli isolates. This study highlights the widespread acquisition of antimicrobial resistance determinants among chicken-associated Campylobacter isolates, through horizontal gene transfer or clonal expansion of resistant lineages. The stability of such resistance determinants is compounded by the fluidity of mobile genetic element.

Insights Into the Resistome of Bovine Clinical Mastitis Microbiome, a Key Factor in Disease Complication

Bovine clinical mastitis (CM) is one of the most prevalent diseases caused by a wide range of resident microbes. The emergence of antimicrobial resistance in CM bacteria is well-known, however, the genomic resistance composition (the resistome) at the microbiome-level is not well characterized. In this study, we applied whole metagenome sequencing (WMS) to characterize the resistome of the CM microbiome, focusing on antibiotics and metals resistance, biofilm formation (BF), and quorum sensing (QS) along with in vitro resistance assays of six selected pathogens isolated from the same CM samples. The WMS generated an average of 21.13 million reads (post-processing) from 25 CM samples that mapped to 519 bacterial strains, of which 30.06% were previously unreported. We found a significant (P = 0.001) association between the resistomes and microbiome composition with no association with cattle breed, despite significant differences in microbiome diversity among breeds. The in vitro investigation determined that 76.2% of six selected pathogens considered "biofilm formers" actually formed biofilms and were also highly resistant to tetracycline, doxycycline, nalidixic acid, ampicillin, and chloramphenicol and remained sensitive to metals (Cr, Co, Ni, Cu, Zn) at varying concentrations. We also found bacterial flagellar movement and chemotaxis, regulation and cell signaling, and oxidative stress to be significantly associated with the pathophysiology of CM. Thus, identifying CM microbiomes, and analyzing their resistomes and genomic potentials will help improve the optimization of therapeutic schemes involving antibiotics and/or metals usage in the prevention and control of bovine CM.

Detection of the enterococcal oxazolidinone/phenicol resistance gene optrA in Campylobacter coli

The transferable optrA gene encodes an ABC-F protein which confers resistance to oxazolidinones and phenicols, and has so far been detected exclusively in Gram-positive bacteria, including enterococci, staphylococci and streptococci. Here, we identified for the first time the presence of optrA in naturally occurring Gram-negative bacteria. Seven optrA-positive Campylobacter coli were identified from 563 Campylobacter isolates of animal origin from Guangdong (n = 1, chicken) and Shandong (n = 6, duck) provinces of China in 2017-2018. The detected optrA genes were functionally active and mediated resistance or elevated minimal inhibitory concentrations of linezolid, florfenicol and chloramphenicol in the respective C. coli isolates. The optrA gene, together with other transferable resistance genes, such as fexA, catA9, tet(O), tet(L), erm(A)-like, spc, or aadE, was located in two different chromosome-borne multidrug resistance genomic islands (MDRGIs). In both MDRGIs, complete or truncated copies of the insertion sequence IS1216E were present in the vicinity of optrA. The IS1216E-bracketed genetic environment of optrA was almost identical to the optrA regions on enterococcal plasmids, suggesting that the optrA in Campylobacter probably originated from Enterococcus spp.. Moreover, the formation of an optrA-carrying translocatable unit by recombination of IS1216E indicated that this IS element may play an important role in the horizontal transfer of optrA in Campylobacter. Although optrA was only found in a small number of C. coli isolates, enhanced surveillance is needed to monitor the distribution and the potential emergence of optrA in Campylobacter.

Molecular Characterization and Antimicrobial Susceptibility of C. jejuni Isolates from Italian Wild Bird Populations

Poultry is considered a major reservoir of human campylobacteriosis. It also been reported that not only poultry, but also wild birds, are capable of carrying C. jejuni, thus demonstrating to be a risk of spreading the bacteria in the environment. To gain insight into the population structure and investigate the antimicrobial resistance genotypes and phenotypes, we analyzed a collection of 135 C. jejuni from 15 species of wild birds in Italy. MLST revealed the presence of 41 sequence types (STs) and 13 clonal complexes (CCs). ST-179 complex and the generalist ST-45 complex were the most prevalent. Core genome MLST revealed that C. jejuni from ST-45 complex clustered according to the bird species, unlike the ST-179 complex which featured 3 different species in the same cluster. Overall we found a moderate prevalence of resistance to tetracycline (12.5%), ciprofloxacin and nalidixic acid (10%). The novel ST isolated from one pigeon showed resistance to all the antibiotics tested. The ST-179 complex (33.3%) was identified with significantly higher nalidixic acid resistance relative to other tested STs. Nine AMR genes (tet(O), cmeA, cmeB, cmeC, cmeR, aad, blaOXA-61, blaOXA-184 and erm(B)) and 23S rRNA and gyrA-associated point mutations were also described, indicating a concordance level between genotypic and phenotypic resistance of 23.3%, 23.4% and of 37.5% for streptomycin, tetracycline and quinolones/fluoroquinolones, respectively. We recommend that particular attention should be given to wild birds as key sentinel animals for the ecosystem contamination surveillance.

The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice

Background

Emergence of antibiotic resistance is a global public health concern. The relationships between antibiotic use, the gut community composition, normal physiology and metabolism, and individual and public health are still being defined. Shifts in composition of bacteria, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) after antibiotic treatment are not well-understood.

Methods

This project used next-generation sequencing, custom-built metagenomics pipeline and differential abundance analysis to study the effect of antibiotic monotherapy on resistome and taxonomic composition in the gut of Balb/c mice infected with E. coli via transurethral catheterization to investigate the evolution and emergence of antibiotic resistance.

Results

There is a longitudinal decrease of gut microbiota diversity after antibiotic treatment. Various ARGs are enriched within the gut microbiota despite an overall reduction of the diversity and total amount of bacteria after antibiotic treatment. Sometimes treatment with a specific class of antibiotics selected for ARGs that resist antibiotics of a completely different class (e.g. treatment of ciprofloxacin or fosfomycin selected for cepA that resists ampicillin). Relative abundance of some MGEs increased substantially after antibiotic treatment (e.g. transposases in the ciprofloxacin group).

Conclusions

Antibiotic treatment caused a remarkable reduction in diversity of gut bacterial microbiota but enrichment of certain types of ARGs and MGEs. These results demonstrate an emergence of cross-resistance as well as a profound change in the gut resistome following oral treatment of antibiotics.

Point Deletion or Insertion in CmeR-Box, A2075G Substitution in 23S rRNA, and Presence of erm(B) Are Key Factors of Erythromycin Resistance in Campylobacter jejuni and Campylobacter coli Isolated From Central China

Campylobacter jejuni and Campylobacter coli are major food-borne pathogens that cause bacterial gastroenteritis in humans, and poultry is considered as their most important reservoir. Macrolides, such as erythromycin, are the first-line choice for treatment of campylobacteriosis. In this study, of the 143 Campylobacter isolates recovered from poultry in central China during 2015–2017, 25.2% were erythromycin resistant. A2075G substitution in 23S ribosomal RNA (rRNA) and ribosomal methylase encoded by erm(B) were found in 4.2 and 4.9% isolates, respectively, and correlated with erythromycin resistance. The polymorphisms of CmeR-Box were also analyzed in our isolates. Among them, 9.1% isolates harbored a point deletion or insertion within the CmeR-Box, and we first showed that point deletion or insertion, but not substitution, in CmeR-Box led to high expression of cmeABC, which was significantly associated with erythromycin resistance (p < 0.05). These results suggest that point deletion or insertion in CmeR-Box, A2075G substitution in 23S rRNA, and presence of erm(B) are three main factors to erythromycin resistance in C. jejuni and C. coli.

The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2017/2018

Data on antimicrobial resistance (AMR) in zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs), jointly analysed by EFSA and ECDC and reported in a yearly EU Summary Report. The annual monitoring of AMR in animals and food within the EU is targeted at selected animal species corresponding to the reporting year. The 2017 monitoring specifically focussed on pigs and calves under 1 year of age, as well as their derived carcases/meat, while the monitoring performed in 2018 specifically focussed on poultry and their derived carcases/meat. Monitoring and reporting of AMR in 2017/2018 included data regarding Salmonella, Campylobacter and indicator Escherichia coli isolates, as well as data obtained from the specific monitoring of ESBL-/AmpC-/carbapenemase-producing E. coli isolates. Additionally, some MSs reported voluntary data on the occurrence of meticillin-resistant Staphylococcus aureus in animals and food, with some countries also providing data on antimicrobial susceptibility. This report provides, for the first time, an overview of the main findings of the 2017/2018 harmonised AMR monitoring in the main food-producing animal populations monitored, in related carcase/meat samples and in humans. Where available, data monitoring obtained from pigs, calves/cattle, broilers, laying hens and turkeys, as well as from carcase/meat samples and humans were combined and compared at the EU level, with particular emphasis on multiple drug resistance, complete susceptibility and combined resistance patterns to critically important antimicrobials, as well as Salmonella and E. coli isolates exhibiting presumptive ESBL-/AmpC-/carbapenemase-producing phenotypes. The outcome indicators for AMR in food-producing animals, such as complete susceptibility to the harmonised panel of antimicrobials in E. coli and the prevalence of ESBL-/AmpC-producing E. coli have been also specifically analysed over the period 2014-2018.

Comparative Genomic Analysis of a Multidrug-Resistant Campylobacter jejuni Strain YH002 Isolated from Retail Beef Liver

Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide. In this study, we report the comparative genomic and functional characteristics of C. jejuni YH002 recently isolated from retail beef liver. Whole-genome sequencing and annotation of the strain revealed novel genetic features, including an integrated intact phage element, multiple antimicrobial resistance (AMR) genes, virulence factors, and a Phd-Doc type toxin-antitoxin (TA) system. Phenotypic tests of AMR showed that C. jejuni YH002 was resistant to amoxicillin and tetracycline, which correlates with the AMR genes found in the strain. Comparative analysis of cell motility at genotypic and phenotypic levels identified discernible patterns of amino acid changes, which could explain the variations of motility among C. jejuni strains. Together, these results provide important clues to the genetic mechanisms of AMR and cell motility in C. jejuni. The finding of a Phd-Doc TA system in the genome of C. jejuni YH002 is the first report of this TA system in Campylobacter spp.

RND efflux pumps in Gram-negative bacteria; regulation, structure and role in antibiotic resistance

Rresistance-nodulation-division (RND) efflux pumps in Gram-negative bacteria remove multiple, structurally distinct classes of antimicrobials from inside bacterial cells therefore directly contributing to multidrug resistance. There is also emerging evidence that many other mechanisms of antibiotic resistance rely on the intrinsic resistance conferred by RND efflux. In addition to their role in antibiotic resistance, new information has become available about the natural role of RND pumps including their established role in virulence of many Gram-negative organisms. This review also discusses the recent advances in understanding the regulation and structure of RND efflux pumps.

Acinetobacter baumannii Efflux Pumps and Antibiotic Resistance

Acinetobacter baumannii is a nosocomial pathogen and gram-negative coccobacillus that is responsible for opportunistic infections, pneumonia, and infections of the urinary tract, bloodstream, skin, and soft tissue. This bacterium poses a major public health problem due to inducing resistance to several drugs, isolates, multidrug treatment, and occasionally pan drugs. Drug resistance is not only a major concern caused by A. baumannii but also is considered as the main challenge in many other pathogens. Several factors such as the efflux pump are associated with antibiotic resistance, biofilm production, and genetic mutations. In this review, A. baumannii is introduced in then some of the practical works conducted on the existing efflux pump are reviewed. The importance of the efflux pump is considered in this paper in relation to the antibiotic resistance and mechanisms developed for the inhibition of these pumps as well.

Molecular and phenotypical investigation of ciprofloxacin resistance among Campylobacter jejuni strains of human origin: high prevalence of resistance in Turkey

Campylobacteriosis is one of the most frequently reported zoonoses worldwide. The well-documented increase in the ciprofloxacin resistance has increased the importance of rapid detection of the resistance. The incidence of ciprofloxacin resistance was investigated using real-time PCR. Identification of one hundred and fifty-eight strains was performed by PCR. Minimum inhibitory concentration (MIC) of ciprofloxacin was determined by Epsilometer test. Following the confirmation of the efficiencies of singleplex real-time PCR methods using two different probes, a cytosine to thymine point mutation at codon 86 was detected by allelic discrimination. Of the 158 strains, 114 (72.2%) were determined to be resistant to ciprofloxacin. The MIC₅₀ and the MIC₉₀ of ciprofloxacin were found to be 8 and ≥32 mg/L, respectively. By real-time PCR, the presence of the mutation was confirmed in all, but one, resistant strains and the absence of the mutation was demonstrated in all, but one, susceptible strains. The rate of resistance is high among C. jejuni strains and ciprofloxacin should not be used in the treatment of such infections in Turkey. A cytosine to thymine mutation is the most frequently detected mechanism for the resistance. Real-time PCR can be used for the quick screening of the resistance.

Multidrug efflux pumps: structure, function and regulation

Infections arising from multidrug-resistant pathogenic bacteria are spreading rapidly throughout the world and threaten to become untreatable. The origins of resistance are numerous and complex, but one underlying factor is the capacity of bacteria to rapidly export drugs through the intrinsic activity of efflux pumps. In this Review, we describe recent advances that have increased our understanding of the structures and molecular mechanisms of multidrug efflux pumps in bacteria. Clinical and laboratory data indicate that efflux pumps function not only in the drug extrusion process but also in virulence and the adaptive responses that contribute to antimicrobial resistance during infection. The emerging picture of the structure, function and regulation of efflux pumps suggests opportunities for countering their activities.

Ashworth A, Ricke SC. A Historical Review on Antibiotic Resistance of Foodborne Campylobacter

Campylobacter is one of the most commonly reported foodborne human bacterial gastrointestinal pathogens. Campylobacter is the etiological agent of campylobacteriosis, which is generally a self-limited illness and therefore does not require treatment. However, when patients are immunocompromised or have other co-morbidities, antimicrobial treatment may be necessary for clinical treatment of campylobacteriosis, macrolides and fluoroquinolones are the drugs of choices. However, the increase in antimicrobial resistance of Campylobacter to clinically important antibiotics may become insurmountable. Because of the transmission between poultry and humans, the poultry industry must now allocate resources to address the problem by reducing Campylobacter as well as antimicrobial use, which may reduce resistance. This review will focus on the incidence of antibiotic-resistant Campylobacter in poultry, the clinical consequences of this resistance, and the mechanisms of antibiotic resistance associated with Campylobacter.

Emerging erm(B)-Mediated Macrolide Resistance Associated with Novel Multidrug Resistance Genomic Islands in Campylobacter

The rapid dissemination of the macrolide resistance gene erm(B) will likely compromise the efficacy of macrolides as the treatment of choice for campylobacteriosis. More importantly, erm(B) is always associated with several multidrug resistance genomic islands (MDRGIs), which confer resistance to multiple other antimicrobials. Continuous monitoring of the emergence of erm(B) and analysis of its associated genetic environments are crucial for our understanding of macrolide resistance in Campylobacter In this study, 290 Campylobacter isolates (216 Campylobacter coli isolates and 74 Campylobacter jejuni isolates) were obtained from 1,039 fecal samples collected in 2016 from pigs and chickens from three regions of China (344 samples from Guangdong, 335 samples from Shanghai, and 360 samples from Shandong). Overall, 74 isolates (72 C. coli isolates and 2 C. jejuni isolates) were PCR positive for erm(B). Combined with data from previous years, we observed a trend of increasing prevalence of erm(B) in C. coli Pulsed-field gel electrophoresis analyses suggested that both clonal expansion and horizontal transmission were involved in the dissemination of erm(B) in C. coli, and three novel types of erm(B)-associated MDRGIs were identified among the isolates. Furthermore, 2 erm(B)-harboring C. jejuni isolates also contained an aminoglycoside resistance genomic island and a multidrug-resistance-enhancing efflux pump, encoded by RE-cmeABC Antimicrobial susceptibility testing showed that most of the isolates were resistant to all clinically important antimicrobial agents used for the treatment of campylobacteriosis. These findings suggest that the increasing prevalence of erm(B)-associated MDRGIs might further limit treatment options for campylobacteriosis.

Technical specifications on harmonised monitoring of antimicrobial resistance in zoonotic and indicator bacteria from food-producing animals and food

Proposals to update the harmonised monitoring and reporting of antimicrobial resistance (AMR) from a public health perspective in Salmonella, Campylobacter coli, Campylobacter jejuni, Escherichia coli, Enterococcus faecalis, Enterococcus faecium and methicillin-resistant Staphylococcus aureus (MRSA) from food-producing animals and derived meat in the EU are presented in this report, accounting for recent trends in AMR, data collection needs and new scientific developments. Phenotypic monitoring of AMR in bacterial isolates, using microdilution methods for testing susceptibility and interpreting resistance using epidemiological cut-off values is reinforced, including further characterisation of those isolates of E. coli and Salmonella showing resistance to extended-spectrum cephalosporins and carbapenems, as well as the specific monitoring of ESBL/AmpC/carbapenemase-producing E. coli. Combinations of bacterial species, food-producing animals and meat, as well as antimicrobial panels have been reviewed and adapted, where deemed necessary. Considering differing sample sizes, numerical simulations have been performed to evaluate the related statistical power available for assessing occurrence and temporal trends in resistance, with a predetermined accuracy, to support the choice of harmonised sample size. Randomised sampling procedures, based on a generic proportionate stratified sampling process, have been reviewed and reinforced. Proposals to improve the harmonisation of monitoring of prevalence, genetic diversity and AMR in MRSA are presented. It is suggested to complement routine monitoring with specific cross-sectional surveys on MRSA in pigs and on AMR in bacteria from seafood and the environment. Whole genome sequencing (WGS) of isolates obtained from the specific monitoring of ESBL/AmpC/carbapenemase-producing E. coli is strongly advocated to be implemented, on a voluntary basis, over the validity period of the next legislation, with possible mandatory implementation by the end of the period; the gene sequences encoding for ESBL/AmpC/carbapenemases being reported to EFSA. Harmonised protocols for WGS analysis/interpretation and external quality assurance programmes are planned to be provided by the EU-Reference Laboratory on AMR.

The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2017

The data on antimicrobial resistance in zoonotic and indicator bacteria in 2017, submitted by 28 EU Member States (MSs), were jointly analysed by EFSA and ECDC. Resistance in zoonotic Salmonella and Campylobacter from humans, animals and food, and resistance in indicator Escherichia coli as well as meticillin‐resistant Staphylococcus aureus in animals and food were addressed, and temporal trends assessed. ‘Microbiological’ resistance was assessed using epidemiological cut‐off (ECOFF) values; for some countries, qualitative data on human isolates were interpreted in a way which corresponds closely to the ECOFF‐defined ‘microbiological’ resistance. In Salmonella from humans, as well as in Salmonella and E. coli isolates from fattening pigs and calves of less than 1 year of age, high proportions of isolates were resistant to ampicillin, sulfonamides and tetracyclines, whereas resistance to third‐generation cephalosporins was uncommon. Varying occurrence/prevalence rates of presumptive extended‐spectrum beta‐lactamase (ESBL)/AmpC producers in Salmonella and E. coli monitored in meat (pork and beef), fattening pigs and calves, and Salmonella monitored in humans, were observed between countries. Carbapenemase‐producing E. coli were detected in one single sample from fattening pigs in one MS. Resistance to colistin was observed at low levels in Salmonella and E. coli from fattening pigs and calves and meat thereof and in Salmonella from humans. In Campylobacter from humans, high to extremely high proportions of isolates were resistant to ciprofloxacin and tetracyclines, particularly in Campylobacter coli. In five countries, high to very high proportions of C. coli from humans were resistant also to erythromycin, leaving few options for treatment of severe Campylobacter infections. High resistance to ciprofloxacin and tetracyclines was observed in C. coli isolates from fattening pigs, whereas much lower levels were recorded for erythromycin. Combined resistance to critically important antimicrobials in both human and animal isolates was generally uncommon but very high to extremely high multidrug resistance levels were observed in S. Typhimurium and its monophasic variant in both humans and animals. S. Kentucky from humans exhibited high‐level resistance to ciprofloxacin, in addition to a high prevalence of ESBL.

Nonribosomal antibacterial peptides that target multidrug-resistant bacteria

This review summarizes the development of nonribosomal antibacterial peptides from untapped sources that target multidrug-resistant bacteria.

Antimicrobial Resistance in Campylobacter spp

Campylobacter is a major foodborne pathogen and has become increasingly resistant to clinically important antimicrobials. To cope with the selection pressure from antimicrobial use in both veterinary and human medicine, Campylobacter has developed multiple mechanisms for antibiotic resistance, including modification or mutation of antimicrobial targets, modification or inactivation of antibiotics, and reduced drug accumulation by drug efflux pumps. Some of these mechanisms confer resistance to a specific class of antimicrobials, while others give rise to multidrug resistance. Notably, new antibiotic resistance mechanisms continuously emerge in Campylobacter, and some examples include the recently discovered multidrug resistance genomic islands harboring multiple genes involved in the resistance to aminoglycosides and macrolides, a novel Cfr(C) conferring resistance to phenicols and other drugs, and a potent multidrug efflux pump CmeABC variant (RE-CmeABC) that shows a significantly enhanced function in multidrug resistance and is associated with exceedingly high-level resistance to fluoroquinolones. These newly emerged resistance mechanisms are horizontally transferable and greatly facilitate the adaptation of Campylobacter in the food-producing environments where antibiotics are frequently used. In this article, we will discuss how Campylobacter resists the action of various classes of antimicrobials, with an emphasis on newly discovered mechanisms.

Antimicrobial susceptibility of clinical isolates of Campylobacter jejuni from New South Wales, Australia

OBJECTIVES

The aim of this study was to investigate the prevalence of resistance to commonly used antimicrobials in Campylobacter jejuni isolates from clinical faecal samples in New South Wales (NSW), Australia.

METHODS

A total of 117 C. jejuni isolates from human faecal samples from regional and metropolitan NSW were examined for antimicrobial resistance.

RESULTS

Of the 117 isolates tested, 15.4% were resistant to ampicillin, 5.1% to tetracycline and 13.7% to ciprofloxacin. Most of the isolates were susceptible to erythromycin, except for three that showed intermediate resistance. Furthermore, 9.4% of isolates were resistant (or intermediate-resistant) to more than one antimicrobial agent. Isolates that were resistant to ampicillin and tetracycline harboured the bla_OXA-61 and tet(O) genes, respectively. A mutation in the gyrA gene, resulting in the T86I substitution, was identified in the majority of ciprofloxacin-resistant isolates.

CONCLUSION

The data obtained in the current study demonstrate that the majority of C. jejuni isolates evaluated were susceptible to one or more antimicrobials tested. Apart from three isolates that demonstrated intermediate resistance, all of the isolates were susceptible to erythromycin, which is the drug of choice for treating Campylobacter infections.

Structure and mechanism of bacterial tripartite efflux pumps

Efflux pumps are membrane proteins which contribute to multi-drug resistance. In Gram-negative bacteria, some of these pumps form complex tripartite assemblies in association with an outer membrane channel and a periplasmic membrane fusion protein. These tripartite machineries span both membranes and the periplasmic space, and they extrude from the bacterium chemically diverse toxic substrates. In this chapter, we summarise current understanding of the structural architecture, functionality, and regulation of tripartite multi-drug efflux assemblies.

The Molecular Mechanisms of Ciprofloxacin Resistance in Clinical Campylobacter jejuni and Their Genotyping Characteristics in Beijing, China

We assessed the susceptibility of 182 Campylobacter jejuni isolates from patients with diarrhea to eight antibiotics and analyzed the molecular mechanisms of ciprofloxacin resistance as well as the genetic characteristics based on multilocus sequence typing (MLST). The C257T mutation was found on the quinolone resistance-determining region (QRDR) of the gyrA gene in all ciprofloxacin-resistant strains. Mutations on the QRDR of the gyrB gene were silent. A total of 74 strains had 7 inverted repeat (IR) (a 16-bp IR on the intergenic region between cmeR and cmeABC) mutation polymorphisms. Compared with strains without the IR mutations, strains with the IR mutations had higher resistance rates to ciprofloxacin (94.6% vs. 83.3%), nalidixic acid (94.6% vs. 83.3%), tetracycline (98.6% vs. 85.2%), doxycycline (91.9% vs. 71.3%), florfenicol (59.5% vs. 17.6%), chloramphenicol (25.7% vs. 4.6%), gentamicin (16.2% vs. 3.7%), and multidrug resistance than those without IR mutations (all p < 0.05). With C257T mutation alone, 89.9% strains with minimum inhibitory concentration (MIC) values focused on 16, 32, and 64 μg/mL, whereas strains with C257T mutation in combination with the IR mutations had a higher ciprofloxacin resistance level with 88.6% MIC values focused on 64, 128, and 512 μg/mL (p < 0.0001). The strains in this study showed a high genetic variability based on MLST with 117 sequence types (STs), 37 of which were novel. CC-21 was the most common clonal complex (CC) followed by CC-353 and CC-45. No association was found between STs and ciprofloxacin resistance. In conclusion, the C257T mutation on gyrA was the major mechanism for ciprofloxacin resistance, and the C257T mutation in combination with the IR mutations might result in more severe ciprofloxacin resistance to C. jejuni.

The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2016

The data on antimicrobial resistance in zoonotic and indicator bacteria in 2016, submitted by 28 EU Member States (MSs), were jointly analysed by the EFSA and ECDC. Resistance in bacterial isolates of zoonotic Salmonella and Campylobacter from humans, animals and food, and resistance in indicator Escherichia coli as well as in meticillin-resistant Staphylococcus aureus from animals and food were addressed. 'Microbiological' resistance was assessed using epidemiological cut-off (ECOFF) values; for some countries, qualitative data on isolates from humans were interpreted in a way that corresponds closely to ECOFF-defined 'microbiological' resistance. In Salmonella from humans, the occurrence of resistance to ampicillin, sulfonamides and tetracyclines was high, whereas resistance to third-generation cephalosporins was low. In Salmonella and E. coli isolates from broilers, fattening turkeys and their meat, resistance to ampicillin, (fluoro)quinolones, tetracyclines and sulfonamides was frequently high, whereas resistance to third-generation cephalosporins was rare. The occurrence of ESBL-/AmpC producers was low in Salmonella and E. coli from poultry and in Salmonella from humans. The prevalence of ESBL-/AmpC-producing E. coli, assessed in poultry and its meat for the first time, showed marked variations among MSs. Fourteen presumptive carbapenemase-producing E. coli were detected from broilers and its meat in two MSs. Resistance to colistin was observed at low levels in Salmonella and E. coli from poultry and meat thereof and in Salmonella from humans. In Campylobacter from humans, broilers and broiler meat, resistance to ciprofloxacin and tetracyclines was high to extremely high, whereas resistance to erythromycin was low to moderate. Combined resistance to critically important antimicrobials in isolates from both humans and animals was generally uncommon, but very high to extremely high multidrug resistance levels were observed in certain Salmonella serovars. Specific serovars of Salmonella (notably Kentucky) from both humans and animals exhibited high-level resistance to ciprofloxacin, in addition to findings of ESBL.

Trends in fluoroquinolone resistance in Campylobacter

Members of the genus Campylobacter remain a leading cause of bacterial gastroenteritis worldwide. Infection is usually self-limiting but in severe cases may require antibiotic treatment. In a recent statement by the World Health Organization (WHO) Campylobacter was named as one of the 12 bacteria that pose the greatest threat to human health because they are resistant to antibiotics. In this mini review we describe recent trends in fluoroquinolone (FQ) (particularly ciprofloxacin) resistance in strains of members of the genus Campylobacter isolated from livestock and clinical samples from several countries. Using evidence from phenotyping surveys and putative resistance prediction from DNA sequence data, we discuss the acquisition and spread of FQ resistance and the role of horizontal gene transfer and describe trends in FQ-resistance in samples from livestock and clinical cases. This review emphasises that FQ resistance remains common among isolates of members of the genus Campylobacter from various sources.

Integrated Genomic and Proteomic Analyses of High-level Chloramphenicol Resistance in Campylobacter jejuni

Campylobacter jejuni is a major zoonotic pathogen, and its resistance to antibiotics is of great concern for public health. However, few studies have investigated the global changes of the entire organism with respect to antibiotic resistance. Here, we provide mechanistic insights into high-level resistance to chloramphenicol in C. jejuni, using integrated genomic and proteomic analyses. We identified 27 single nucleotide polymorphisms (SNPs) as well as an efflux pump cmeB mutation that conferred modest resistance. We determined two radical S-adenosylmethionine (SAM) enzymes, one each from an SNP gene and a differentially expressed protein. Validation of major metabolic pathways demonstrated alterations in oxidative phosphorylation and ABC transporters, suggesting energy accumulation and increase in methionine import. Collectively, our data revealed a novel rRNA methylation mechanism by a radical SAM superfamily enzyme, indicating that two resistance mechanisms existed in Campylobacter. This work provided a systems biology perspective on understanding the antibiotic resistance mechanisms in bacteria.

Antibiotic resistance trends and mechanisms in the foodborne pathogen,Campylobacter

Campylobacteris a major foodborne pathogen and is commonly present in food producing animals. This pathogenic organism is highly adaptable and has become increasingly resistant to various antibiotics. Recently, both the Centers for Disease Control and Prevention and the World Health Organization have designated antibiotic-resistantCampylobacteras a serious threat to public health. For the past decade, multiple mechanisms conferring resistance to clinically important antibiotics have been described inCampylobacter, and new resistance mechanisms constantly emerge in the pathogen. Some of the recent examples include theerm(B)gene conferring macrolide resistance, thecfr(C)genes mediating resistance to florfenicol and other antimicrobials, and a functionally enhanced variant of the multidrug resistance efflux pump, CmeABC. The continued emergence of new resistance mechanisms illustrates the extraordinary adaptability ofCampylobacterto antibiotic selection pressure and demonstrate the need for innovative strategies to control antibiotic-resistantCampylobacter. In this review, we will briefly summarize the trends of antibiotic resistance inCampylobacterand discuss the mechanisms of resistance to antibiotics used for animal production and important for clinical therapy in humans. A special emphasis will be given to the newly discovered antibiotic resistance.

CmeABC Multidrug Efflux Pump Contributes to Antibiotic Resistance and Promotes Campylobacter jejuni Survival and Multiplication in Acanthamoeba polyphaga

Campylobacter jejuni is a foodborne pathogen that is recognized as the leading cause of human bacterial gastroenteritis. The widespread use of antibiotics in medicine and in animal husbandry has led to an increased incidence of antibiotic resistance in Campylobacter In addition to a role in multidrug resistance (MDR), the Campylobacter CmeABC resistance-nodulation-division (RND)-type efflux pump may be involved in virulence. As a vehicle for pathogenic microorganisms, the protozoan Acanthamoeba is a good model for investigations of bacterial survival in the environment and the molecular mechanisms of pathogenicity. The interaction between C. jejuni 81-176 and Acanthamoeba polyphaga was investigated in this study by using a modified gentamicin protection assay. In addition, a possible role for the CmeABC MDR pump in this interaction was explored. Here we report that this MDR pump is beneficial for the intracellular survival and multiplication of C. jejuni in A. polyphaga but is dispensable for biofilm formation and motility.IMPORTANCE The endosymbiotic relationship between amoebae and microbial pathogens may contribute to persistence and spreading of the latter in the environment, which has significant implications for human health. In this study, we found that Campylobacter jejuni was able to survive and to multiply inside Acanthamoeba polyphaga; since these microorganisms can coexist in the same environment (e.g., on poultry farms), the latter may increase the risk of infection with Campylobacter Our data suggest that, in addition to its role in antibiotic resistance, the CmeABC MDR efflux pump plays a role in bacterial survival within amoebae. Furthermore, we demonstrated synergistic effects of the CmeABC MDR efflux pump and TetO on bacterial resistance to tetracycline. Due to its role in both the antibiotic resistance and the virulence of C. jejuni, the CmeABC MDR efflux pump could be considered a good target for the development of antibacterial drugs against this pathogen.

Structures and transport dynamics of a Campylobacter jejuni multidrug efflux pump

Resistance-nodulation-cell division efflux pumps are integral membrane proteins that catalyze the export of substrates across cell membranes. Within the hydrophobe-amphiphile efflux subfamily, these resistance-nodulation-cell division proteins largely form trimeric efflux pumps. The drug efflux process has been proposed to entail a synchronized motion between subunits of the trimer to advance the transport cycle, leading to the extrusion of drug molecules. Here we use X-ray crystallography and single-molecule fluorescence resonance energy transfer imaging to elucidate the structures and functional dynamics of the Campylobacter jejuni CmeB multidrug efflux pump. We find that the CmeB trimer displays a very unique conformation. A direct observation of transport dynamics in individual CmeB trimers embedded in membrane vesicles indicates that each CmeB subunit undergoes conformational transitions uncoordinated and independent of each other. On the basis of our findings and analyses, we propose a model for transport mechanism where CmeB protomers function independently within the trimer.

Multidrug efflux pumps significantly contribute for bacteria resistance to antibiotics. Here the authors present the structure of Campylobacter jejuni CmeB pump combined with functional FRET assays to propose a transport mechanism where each CmeB protomers is functionally independent from the trimer.

Correlation between gyrA and CmeR Box Polymorphism and Fluoroquinolone Resistance in Campylobacter jejuni Isolates in China

Sequence analysis of 79 ciprofloxacin-resistant Campylobacter jejuni isolates collected in China showed resistance-related sequence variations in gyrA and CmeR-Box. All the isolates contain an identical Thr-86-Ile substitution in GyrA. Several novel CmeR-Box variations, including point substitutions, deletion, and insertion, were identified. The point insertion or deletion led to dramatically reduced binding of CmeR to the cmeABC promoter, which significantly increases the expression of cmeABC and contributes to the high fluoroquinolone resistance.

The Current State of Macrolide Resistance in Campylobacter spp.: Trends and Impacts of Resistance Mechanisms

Campylobacter spp., especially Campylobacter jejuni and C. coli, are leading bacterial foodborne pathogens worldwide. In the United States, an estimated 0.8 million cases of campylobacteriosis occur annually, mostly involving C. jejuni Campylobacteriosis is generally self-limiting, but in severe cases, treatment with antibiotics may be mandated. The increasing incidence of fluoroquinolone resistance in Campylobacter has rendered macrolides such as erythromycin and azithromycin the drugs of choice for human campylobacteriosis. The prevalence of macrolide resistance in C. jejuni remains low, but macrolide resistance can be common in C. coli Substitutions in the 23S rRNA gene, specifically A2075G, and less frequently A2074C/G, remain the most common mechanism for high-level resistance to macrolides. In C. jejuni, resistance mediated by such substitutions is accompanied by a reduced ability to colonize chickens and other fitness costs, potentially contributing to the low incidence of macrolide resistance. Interestingly, similar fitness impacts have not been noted in C. coli Also noteworthy is a novel mechanism first reported in 2014 for a C. coli isolate from China and mediated by erm(B) harbored on multidrug resistance genomic islands. The incidence of erm(B) appears to reflect clonal expansion of certain strains, and whole-genome sequencing has been critical to the elucidation of erm(B)-associated macrolide resistance in Campylobacter spp. With the exception of one report from Spain, erm(B)-mediated macrolide resistance has been restricted to Campylobacter spp., mostly C. coli, of animal and human origin from China. If erm(B)-mediated macrolide resistance does not confer fitness costs in C. jejuni, the range of this gene may expand in C. jejuni, threatening to compromise treatment effectiveness for severe campylobacteriosis cases.

High Prevalence and Predominance of the aph(2″)-If Gene Conferring Aminoglycoside Resistance in Campylobacter

Campylobacter is a major foodborne pathogen, and previous studies revealed that Campylobacter isolates from food-producing animals are increasingly resistant to gentamicin in China. The molecular epidemiology and genetic mechanisms responsible for gentamicin resistance in China have not been well understood. In this study, 607 Campylobacter isolates of chicken and swine origins collected in 2014 were analyzed, revealing that 15.6% (25/160) of the Campylobacter jejuni isolates and 79.9% (357/447) of the Campylobacter coli isolates were resistant to gentamicin. PCR detection of the gentamicin resistance genes indicated that aph(2″)-If was more prevalent than the previously identified aacA/aphD gene and has become the dominant gentamicin resistance determinant in Campylobacter Transformation and whole-genome sequencing as well as long-range PCR discovered that aph(2″)-If was located on a chromosomal segment inserted between two conserved genes, Cj0299 and panB Cloning of aph(2″)-If into gentamicin-susceptible C. jejuni NCTC 11168 confirmed its function in conferring high-level resistance to gentamicin and kanamycin. Molecular typing by pulsed-field gel electrophoresis suggested that both regional expansion of a particular clone and horizontal transmission were involved in the dissemination of the aph(2″)-If gene in Campylobacter To our knowledge, this is the first report describing the high prevalence of a chromosomally encoded aph(2″)-If gene in Campylobacter The high prevalence and predominance of this gene might be driven by the use of aminoglycoside antibiotics in food animal production in China and potentially compromise the usefulness of gentamicin as a therapeutic agent for Campylobacter-associated systemic infection.

Rising fluoroquinolone resistance in Campylobacter isolated from feedlot cattle in the United States

Antibiotic resistance, particularly to fluoroquinolones and macrolides, in the major foodborne pathogen Campylobacter is considered a serious threat to public health. Although ruminant animals serve as a significant reservoir for Campylobacter, limited information is available on antibiotic-resistant Campylobacter of bovine origin. Here, we analyzed the antimicrobial susceptibilities of 320 C. jejuni and 115 C. coli isolates obtained from feedlot cattle farms in multiple states in the U.S. The results indicate that fluoroquinolone resistance reached to 35.4% in C. jejuni and 74.4% in C. coli, which are significantly higher than those previously reported in the U.S. While all fluoroquinolone resistant (FQ^R) C. coli isolates examined in this study harbored the single Thr-86-Ile mutation in GyrA, FQ^RC. jejuni isolates had other mutations in GyrA in addition to the Thr-86-Ile change. Notably, most of the analyzed FQ^RC. coli isolates had similar PFGE (pulsed field gel electrophoresis) patterns and the same MLST (multilocus sequence typing) sequence type (ST-1068) regardless of their geographic sources and time of isolation, while the analyzed C. jejuni isolates were genetically diverse, suggesting that clonal expansion is involved in dissemination of FQ^RC. coli but not C. jejuni. These findings reveal the rising prevalence of FQ^RCampylobacter in the U.S. and provide novel information on the epidemiology of antibiotic-resistant Campylobacter in the ruminant reservoir.