Enhanced in vivo fitness of fluoroquinolone-resistant Campylobacter jejuni in the absence of antibiotic selection pressure

Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world

Foodborne illnesses pose a substantial health and economic burden, presenting challenges in prevention due to the diverse microbial hazards that can enter and spread within food systems. Various factors, including natural, political and commercial drivers, influence food production and distribution. The risks of foodborne illness will continue to evolve in step with these drivers and with changes to food systems. For example, climate impacts on water availability for agriculture, changes in food sustainability targets and evolving customer preferences can all have an impact on the ecology of foodborne pathogens and the agrifood niches that can carry microorganisms. Whole-genome and metagenome sequencing, combined with microbial surveillance schemes and insights from the food system, can provide authorities and businesses with transformative information to address risks and implement new food safety interventions across the food chain. In this Review, we describe how genome-based approaches have advanced our understanding of the evolution and spread of enduring bacterial foodborne hazards as well as their role in identifying emerging foodborne hazards. Furthermore, foodborne hazards exist in complex microbial communities across the entire food chain, and consideration of these co-existing organisms is essential to understanding the entire ecology supporting pathogen persistence and transmission in an evolving food system.

Transmission rates of veterinary and clinically important antibiotic resistant Escherichia coli: A meta- ANALYSIS

The transmission rate per hour between hosts is a key parameter for simulating transmission dynamics of antibiotic-resistant bacteria, and might differ for antibiotic resistance genes, animal species, and antibiotic usage. We conducted a Bayesian meta-analysis of resistant Escherichia coli (E. coli) transmission in broilers and piglets to obtain insight in factors determining the transmission rate, infectious period, and reproduction ratio. We included blaCTX-M-1, blaCTX-M-2, blaOXA-162, catA1, mcr-1, and fluoroquinolone resistant E. coli. The Maximum a Posteriori (MAP) transmission rate in broilers without antibiotic treatment ranged from 0.4∙10-3 to 2.5∙10-3 depending on type of broiler (SPF vs conventional) and inoculation strains. For piglets, the MAP in groups without antibiotic treatment were between 0.7∙10-3 and 0.8∙10-3, increasing to 0.9∙10-3 in the group with antibiotic treatment. In groups without antibiotic treatment, the transmission rate of resistant E. coli in broilers was almost twice the transmission rate in piglets. Amoxicillin increased the transmission rate of E. coli carrying blaCTX-M-2 by three-fold. The MAP infectious period of resistant E. coli in piglets with and without antibiotics is between 971 and 1065 hours (40 - 43 days). The MAP infectious period of resistant E. coli in broiler without antibiotics is between 475 and 2306 hours (20 - 96 days). The MAP infectious period of resistant E. coli in broiler with antibiotics is between 2702 and 3462 hours (113 - 144 days) which means a lifelong colonization. The MAP basic reproduction ratio in piglets of infection with resistant E. coli when using antibiotics is 27.70, which is higher than MAP in piglets without antibiotics between 15.65 and 18.19. The MAP basic reproduction ratio in broilers ranges between 3.46 and 92.38. We consider three possible explanations for our finding that in the absence of antibiotics the transmission rate is higher among broilers than among piglets: i) due to the gut microbiome of animals, ii) fitness costs of bacteria, and iii) differences in experimental set-up between the studies. Regarding infectious period and reproduction ratio, the effect of the resistance gene, antibiotic treatment, and animal species are inconclusive due to limited data.

Unveiling a novel mechanism for competitive advantage of ciprofloxacin-resistant bacteria in the environment through bacterial membrane vesicles

Ciprofloxacin (CIP) is a prevalent environmental contaminant that poses a high risk of antibiotic resistance. High concentrations of antibiotics can lead to the development of resistant bacteria with high fitness costs, which often face a competitive disadvantage. However, it is unclear whether low-cost resistant bacteria formed by exposure to sub-MIC CIP in the environment can evolve competitive mechanisms against sensitive Escherichia coli (SEN) other than stronger resistance to CIP. Our study exposed E. coli to sub-MIC CIP levels, resulting in the development of CIP-resistant E. coli (CIPr). In antibiotic-free co-culture assays, CIPr outcompeted SEN. This indicates that CIPr is very likely to continue to develop and spread in antibiotic-free environments such as drinking water and affect human health. Further mechanism investigation revealed that bacterial membrane vesicles (BMVs) in CIPr, functioning as substance delivery couriers, mediated a cleavage effect on SEN. Proteomic analysis identified Entericidin B (EcnB) within CIPr-BMVs as a key factor in this competitive interaction. RT-qPCR analysis showed that the transcription of its negative regulator ompR/envZ was down-regulated. Moreover, EcnB plays a crucial role in the development of CIP resistance, and some resistance-related proteins and pathways have also been discovered. Metabolomics analysis highlighted the ability of CIPr-BMVs to acidify SEN, increasing the lytic efficiency of EcnB through cationization. Overall, our study reveals the importance of BMVs in mediating bacterial resistance and competition, suggesting that regulating BMVs production may be a new strategy for controlling the spread of drug-resistant bacteria.

Surveillance of antimicrobial resistance in Escherichia coli, Salmonella, and Campylobacter recovered from laying hens, their environment and products in Canada indicated a stable level of resistance to critically important antimicrobials, in varying time periods between 2007 and 2021

The study objective was to determine the occurrence and antimicrobial resistance (AMR) attributes of select foodborne bacteria recovered from egg-producing (layer) chickens between 2007 and 2021 using different sample matrices (Study 1: liquid whole eggs, Study 2: spent hen cecal samples, Study 3: environmental sponge swabs and fecal samples from layer chicken barns, and Study 4: fecal samples from layer chicken barns). Samples from each study were submitted for the culture of Escherichia coli and Salmonella. In addition, samples from layer chicken barns were submitted for the culture of Campylobacter. Isolates were tested by microbroth dilution and interpreted using both clinical breakpoints and epidemiological cut-offs (ECOFFs). The ECOFFs were applied to detect non-wild type (NWT) strains. The proportion of resistant, NWT, and distribution of minimum inhibitory concentrations (MIC) were assessed. Ceftriaxone resistance was detected at a low-level in E. coli (< 2 %, all studies) and Salmonella (4.3 %, Study 2). Very low-level ciprofloxacin resistance was detected in E. coli (<1 %, Study 1) but a slightly elevated ciprofloxacin NWT E. coli (1 % to 6 %) observed. Only the farm fecal samples in Studies 2 and 3 were tested for Campylobacter as part of its study design, and moderate level ciprofloxacin resistance (<15 %) was observed. The MIC distribution patterns were similar across the organisms tested/studies and no substantial shifts in the distributions were detected. This analysis demonstrated that resistance to very important antimicrobials in bacteria from layers in Canada remains low, however, the detection of ciprofloxacin-resistant Campylobacter and the implications of this observation to the safety of egg products, and the role of laying flocks (i.e., as reservoir for resistant organisms) needs to be investigated.

Identification of knowledge gaps in whole-genome sequence analysis of multi-resistant thermotolerant Campylobacter spp

BACKGROUND

Campylobacter spp. is the most frequent cause of bacterial food-borne gastroenteritis and a high priority antibiotic resistant bacterium according to the World Health Organization (WHO). European monitoring of thermotolerant Campylobacter spp. does not reflect the global burden of resistances already circulating within the bacterial population worldwide.

METHODS

We systematically compared whole genome sequencing with comprehensive phenotypic antimicrobial susceptibility, analyzing 494 thermotolerant Campylobacter poultry isolates from Vietnam and Germany. Any discrepancy was checked by repeating the wet lab and improving the dry lab part. Selected isolates were additionally analyzed via long-read Oxford Nanopore technology, leading to closed chromosomes and plasmids.

RESULTS

Overall, 22 different resistance genes and gene variants (e. g. erm(B), aph(3')-IIIa, aph(2'')-If, catA, lnu(C), blaOXA, sat4) and point mutations in three distinct genes (gyrA, 23S rRNA, rpsL) associated with AMR were present in the Campylobacter isolates. Two AMR genes were missing in the database and one falsely associated with resistance. Bioinformatic analysis based on short-read data partly failed to identify tet(O) and aadE, when the genes were present as duplicate or homologous gene variants. Intriguingly, isolates also contained different determinants, redundantly conferring resistance to chloramphenicol, gentamicin, kanamycin, lincomycin and streptomycin. We found a novel tet(W) in tetracycline sensitive strains, harboring point mutations. Furthermore, analysis based on assemblies from short-read data was impaired to identify full length phase variable aad9, due to variations of the poly-C tract within the gene. The genetic determinant responsible for gentamicin resistance of one isolate from Germany could not be identified. GyrT86I, presenting the main determinant for (fluoro-)quinolone resistance led to a rare atypical phenotype of ciprofloxacin resistance but nalidixic acid sensitivity. Long-read sequencing predicted AMR genes were mainly located on the chromosome, and rarely on plasmids. Predictions from long- and short-read sequencing, respectively, often differed. AMR genes were often organized in multidrug resistance islands (MDRI) and partially located in proximity to transposase genes, suggesting main mobilization of resistance determinants is via natural transformation and transposition in Campylobacter.

CONCLUSIONS

The results of this study suggest that there is frequent resistance gene duplication, mosaicism, and mutation leading to gene variation and truncation in Campylobacter strains that have not been reported in previous studies and are missing from databases. Furthermore, there is a need for deciphering yet unknown resistance mechanisms and resistance spread in thermotolerant Campylobacter spp. that may pose a challenge to global food safety.

Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes

Bacterial lineages acquire novel traits at diverse rates in part because the genetic background impacts the successful acquisition of novel genes by horizontal transfer. Yet, how horizontal transfer affects the subsequent evolution of core genes remains poorly understood. Here, we studied the evolution of resistance to quinolones in Escherichia coli accounting for population structure. We found 60 groups of genes whose gain or loss induced an increase in the probability of subsequently becoming resistant to quinolones by point mutations in the gyrase and topoisomerase genes. These groups include functions known to be associated with direct mitigation of the effect of quinolones, with metal uptake, cell growth inhibition, biofilm formation, and sugar metabolism. Many of them are encoded in phages or plasmids. Although some of the chronologies may reflect epidemiological trends, many of these groups encoded functions providing latent phenotypes of antibiotic low-level resistance, tolerance, or persistence under quinolone treatment. The mutations providing resistance were frequent and accumulated very quickly. Their emergence was found to increase the rate of acquisition of other antibiotic resistances setting the path for multidrug resistance. Hence, our findings show that horizontal gene transfer shapes the subsequent emergence of adaptive mutations in core genes. In turn, these mutations further affect the subsequent evolution of resistance by horizontal gene transfer. Given the substantial gene flow within bacterial genomes, interactions between horizontal transfer and point mutations in core genes may be a key to the success of adaptation processes.

Nano-Selenium inhibited antibiotic resistance genes and virulence factors by suppressing bacterial selenocompound metabolism and chemotaxis pathways in animal manure

Numerous antibiotic resistance genes (ARGs) and virulence factors (VFs) found in animal manure pose significant risks to human health. However, the effects of graphene sodium selenite (GSSe), a novel chemical nano-Selenium, and biological nano-Selenium (BNSSe), a new bioaugmentation nano-Se, on bacterial Se metabolism, chemotaxis, ARGs, and VFs in animal manure remain unknown. In this study, we investigated the effects of GSSe and BNSSe on ARGs and VFs expression in broiler manure using high-throughput sequencing. Results showed that BNSSe reduced Se pressure during anaerobic fermentation by inhibiting bacterial selenocompound metabolism pathways, thereby lowering manure Selenium pollution. Additionally, the expression levels of ARGs and VFs were lower in the BNSSe group compared to the Sodium Selenite and GSSe groups, as BNSSe inhibited bacterial chemotaxis pathways. Co-occurrence network analysis identified ARGs and VFs within the following phyla Bacteroidetes (genera Butyricimonas, Odoribacter, Paraprevotella, and Rikenella), Firmicutes (genera Lactobacillus, Candidatus_Borkfalkia, Merdimonas, Oscillibacter, Intestinimonas, and Megamonas), and Proteobacteria (genera Desulfovibrio). The expression and abundance of ARGs and VFs genes were found to be associated with ARGs-VFs coexistence. Moreover, BNSSe disruption of bacterial selenocompound metabolism and chemotaxis pathways resulted in less frequent transfer of ARGs and VFs. These findings indicate that BNSSe can reduce ARGs and VFs expression in animal manure by suppressing bacterial selenocompound metabolism and chemotaxis pathways.

Commensal Fitness Advantage May Contribute to the Global Dissemination of Multidrug-Resistant Lineages of Bacteria-The Case of Uropathogenic E. coli

It is widely accepted that favorable fitness in commensal colonization is one of the prime facilitators of clonal dissemination in bacteria. The question arises as to what kind of fitness advantage may be wielded by uropathogenic strains of the two predominant fluoroquinolone- and multidrug-resistant clonal groups of E. coli-ST131-H30 and ST1193, which has permitted their unprecedented pandemic-like global expansion in the last few decades. The colonization-associated genes' content, carriage of low-cost plasmids, and integrons with weak promoters could certainly contribute to the fitness of the pandemic groups, although those genetic factors are common among other clonal groups as well. Also, ST131-H30 and ST1193 strains harbor fluoroquinolone-resistance conferring mutations targeting serine residues in DNA gyrase (GyrA-S83) and topoisomerase IV (ParC-S80) that, in those clonal backgrounds, might result in a commensal fitness benefit, i.e., beyond the antibiotic resistance per se. This fitness gain might have contributed not only to the widespread dissemination of these major clones in the healthcare setting but also to their long-term colonization of healthy individuals and, thus, circulation in the community, even in a low or no fluoroquinolone use environment. This evolutionary shift affecting commensal E. coli, initiated by mutations co-favorable in both antibiotics-treated patients and healthy individuals warrants more in-depth studies to monitor further changes in the epidemiological situation and develop effective measures to reduce the antibiotic resistance spread.

Monitoring within-farm transmission dynamics of antimicrobial-resistant Campylobacter in dairy cattle using broth microdilution and long-read whole genome sequencing

Campylobacter jejuni and Campylobacter coli are important foodborne zoonotic pathogens and cause for concern due to the increasing trend in antimicrobial resistance. A long-run surveillance study was conducted in animals from different age groups in five dairy cattle farms to investigate the within-farm diversity and transmission dynamics of resistant Campylobacter throughout time. The resistance phenotype of the circulating isolates (170 C. jejuni and 37 C. coli) was determined by broth microdilution and a selection of 56 isolates were whole genome sequenced using the Oxford-Nanopore long-fragment sequencing technology resulting in completely resolved and circularized genomes (both chromosomes and plasmids). C. jejuni was isolated from all farms while C. coli was isolated from only two farms, but resistance rates were higher in C. coli than in C. jejuni and in calves than in adult animals. Some genotypes (e.g. ST-48, gyrA_T86I/tet(O)/blaOXA-61 in farm F1; ST-12000, aadE-Cc/tet(O)/blaOXA-489 in F4) persisted throughout the study while others were only sporadically detected. Acquisition of extracellular genes from other isolates and intracellular mutational events were identified as the processes that led to the emergence of the resistant genotypes that spread within the herds. Monitoring with Oxford Nanopore Technologies sequencing helped to decipher the complex molecular epidemiology underlying the within-farm dissemination of resistant Campylobacter.

SVR-flaA typing of erythromycin- and ciprofloxacin-resistant Campylobacter jejuni strains isolated from poultry slaughterhouses in southern Brazil

The emergence of fluoroquinolone and macrolide resistance in C. jejuni, a recognized zoonotic pathogen, has increased worldwide. This study aimed to investigate phenotypic resistance to ciprofloxacin and erythromycin, the molecular mechanisms involved, and the strain of C. jejuni isolated from broiler carcasses. Eighty C. jejuni isolates from broiler carcasses in southern Brazil were investigated for their susceptibility to ciprofloxacin and erythromycin at minimal inhibitory concentrations. Mismatch amplification mutation assay-polymerase chain reaction (MAMA-PCR) was performed to detect substitutions of Thr-86-Ile, A2074C, and A2075G of domain V in the 23S rRNA. The presence of ermB gene and CmeABC operon were investigated by PCR. DNA sequencing was used to detect substitutions in the L4 and L22 proteins of the erythromycin-resistant strains. The Short Variable Region (SVR) of flaA was used to type all the strains resistant to both antimicrobials. Ciprofloxacin and erythromycin resistance were detected in 81.25% and 30.00% of the strains, respectively, and minimal inhibitory concentration values ranged from ≤ 0.125 to 64 µg/mL for ciprofloxacin and 0.5 to > 128 µg/mL for erythromycin. The Thr-86-Ile mutation in gyrA was observed in 100% of the ciprofloxacin-resistant strains. Mutations in both the A2074C and A2075G positions of 23S rRNA were observed in 62.5% of the erythromycin-resistant strains, while 37.5% had only the mutation A2075G. None of the strains harbored CmeABC operon, and ermB was not detected. Using DNA sequencing, the amino acid substitution T177S was detected in L4, and substitutions I65V, A103V, and S109A were detected in L22. Twelve flaA-SVR alleles were identified among the strains, with the most common SVR-flaA allele, type 287, covering 31.03% of ciprofloxacin- and erythromycin-resistant isolates. The present study revealed a high incidence and high levels of resistance to ciprofloxacin and erythromycin, as well as broad molecular diversity in C. jejuni isolates from broiler carcasses.

Different stages of the infection cycle are enriched for Campylobacter strains with distinct phenotypes and levels of fluoroquinolone resistance

Campylobacter species are the leading cause of bacterial diarrhoea worldwide and consumption of contaminated chicken meat is the most common route of infection. Chickens can be infected with multiple strains of Campylobacter and during the infection cycle this pathogen must survive a wide variety of environments. Numerous studies have reported a high degree of genetic variability in this pathogen that can use antigenic and phase variation to alter the expression of key phenotypes. In this study the phenotypic profile of isolates from freshly slaughtered chickens, chicken products in the supermarket and stool samples from infected patients were compared to identify phenotypic changes during the passage of the bacteria through the infection cycle. Isolates from different stages of the infection cycle had altered phenotypic profiles with isolates from human stool samples showing a lower ability to form a biofilm and an increased ability to associate with epithelial cells in vitro. Resistance to fluoroquinolones was found in all cohorts but at a much higher occurrence (94%) in isolates from supermarket chicken. Isolates displaying high levels of resistance to fluoroquinolones also were more likely to display a higher tolerance to growth in the presence of oxygen. In conclusion, isolates with specific phenotypes appear to be overly represented at different stages of the infection cycle suggesting that environmental stresses may be enriched for strains with these phenotypes.

Genomic Characterization of Antibiotic-Resistant Campylobacterales Isolated from Chilean Poultry Meat

Due to the lack of knowledge about Campylobacterales in the Chilean poultry industry, the objective of this research was to know the prevalence, resistance, and genotypes of Campylobacter, Arcobacter and Helicobacter in 382 samples of chicken meat purchased in Valdivia, Chile. The samples were analyzed using three isolation protocols. Resistance to four antibiotics was evaluated by phenotypic methods. Genomic analyses were performed on selected resistant strains to detect resistance determinants and their genotypes. A total of 59.2% of the samples were positive. Arcobacter butzleri (37.4%) was the most prevalent species, followed by Campylobacter jejuni (19.6%), C. coli (11.3%), A. cryaerophilus (3.7%) and A. skirrowii (1.3%). Helicobacter pullorum (14%) was detected by PCR in a subset of samples. Campylobacter jejuni was resistant to ciprofloxacin (37.3%) and tetracycline (20%), while C. coli and A. butzleri were resistant to ciprofloxacin (55.8% and 2.8%), erythromycin (16.3% and 0.7%) and tetracycline (4.7% and 2.8%), respectively. Molecular determinants were consistent with phenotypic resistance. The genotypes of C. jejuni (CC-21, CC-48, CC-49, CC-257, CC-353, CC-443, CC-446 and CC-658) and C. coli (CC-828) coincided with genotypes of Chilean clinical strains. These findings suggest that besides C. jejuni and C. coli, chicken meat could play a role in the transmission of other pathogenic and antibiotic-resistant Campylobacterales.

The relative transmission fitness of multidrug-resistant Mycobacterium tuberculosis in a drug resistance hotspot

Multidrug-resistant tuberculosis (MDR-TB) is among the most frequent causes of death due to antimicrobial resistance. Although only 3% of global TB cases are MDR, geographical hotspots with up to 40% of MDR-TB have been observed in countries of the former Soviet Union. While the quality of TB control and patient-related factors are known contributors to such hotspots, the role of the pathogen remains unclear. Here we show that in the country of Georgia, a known hotspot of MDR-TB, MDR Mycobacterium tuberculosis strains of lineage 4 (L4) transmit less than their drug-susceptible counterparts, whereas most MDR strains of L2 suffer no such defect. Our findings further indicate that the high transmission fitness of these L2 strains results from epistatic interactions between the rifampicin resistance-conferring mutation RpoB S450L, compensatory mutations in the RNA polymerase, and other pre-existing genetic features of L2/Beijing clones that circulate in Georgia. We conclude that the transmission fitness of MDR M. tuberculosis strains is heterogeneous, but can be as high as drug-susceptible forms, and that such highly drug-resistant and transmissible strains contribute to the emergence and maintenance of hotspots of MDR-TB. As these strains successfully overcome the metabolic burden of drug resistance, and given the ongoing rollout of new treatment regimens against MDR-TB, proper surveillance should be implemented to prevent these strains from acquiring resistance to the additional drugs.

Antimicrobial resistance in Campylobacter fetus: emergence and genomic evolution

Campylobacter fetus is a pathogen, which is primarily associated with fertility problems in sheep and cattle. In humans, it can cause severe infections that require antimicrobial treatment. However, knowledge on the development of antimicrobial resistance in C. fetus is limited. Moreover, the lack of epidemiological cut-off values (ECOFFs) and clinical breakpoints for C. fetus hinders consistent reporting about wild-type and non-wild-type susceptibility. The aim of this study was to determine the phenotypic susceptibility pattern of C. fetus and to determine the C. fetus resistome [the collection of all antimicrobial resistance genes (ARGs) and their precursors] to describe the genomic basis of antimicrobial resistance in C. fetus isolates over time. Whole-genome sequences of 295 C. fetus isolates, including isolates that were isolated in the period 1939 till the mid 1940s, before the usage of non-synthetic antimicrobials, were analysed for the presence of resistance markers, and phenotypic antimicrobial susceptibility was obtained for a selection of 47 isolates. C. fetus subspecies fetus (Cff) isolates showed multiple phenotypic antimicrobial resistances compared to C. fetus subspecies venerealis (Cfv) isolates that were only intrinsic resistant to nalidixic acid and trimethoprim. Cff isolates showed elevated minimal inhibitory concentrations for cefotaxime and cefquinome that were observed in isolates from 1943 onwards, and Cff isolates contained gyrA substitutions, which conferred resistance to ciprofloxacin. Resistances to aminoglycosides, tetracycline and phenicols were linked to acquired ARGs on mobile genetic elements. A plasmid-derived tet(O) gene in a bovine Cff isolate in 1999 was the first mobile genetic element observed, followed by detection of mobile elements containing tet(O)-aph(3')-III and tet(44)-ant(6)-Ib genes, and a plasmid from a single human isolate in 2003, carrying aph(3')-III-ant(6)-Ib and a chloramphenicol resistance gene (cat). The presence of ARGs in multiple mobile elements distributed among different Cff lineages highlights the risk for spread and further emergence of AMR in C. fetus. Surveillance for these resistances requires the establishment of ECOFFs for C. fetus.

Campylobacter in aquatic and terrestrial mammals is driven by life traits: A systematic review and meta-analysis

Introduction

Campylobacter spp. infections are responsible for significant diarrheal disease burden across the globe, with prevalence thought to be increasing. Although wild avian species have been studied as reservoirs of Campylobacter spp., our understanding of the role of wild mammalian species in disease transmission and persistence is limited. Host factors influencing infection dynamics in wild mammals have been neglected, particularly life traits, and the role of these factors in zoonotic spillover risk is largely unknown.

Methods

Here, we conducted a systematic literature review, identifying mammalian species that had been tested for Campylobacter spp. infections (molecular and culture based). We used logistic regression to evaluate the relationship between the detection of Campylobacter spp. in feces and host life traits (urban association, trophic level, and sociality).

Results

Our analysis suggest that C. jejuni transmission is associated with urban living and trophic level. The probability of carriage was highest in urban-associated species (p = 0.02793) and the most informative model included trophic level. In contrast, C. coli carriage appears to be strongly influenced by sociality (p = 0.0113) with trophic level still being important. Detection of Campylobacter organisms at the genus level, however, was only associated with trophic level (p = 0.0156), highlighting the importance of this trait in exposure dynamics across host and Campylobacter pathogen systems.

Discussion

While many challenges remain in the detection and characterization of Camploybacter spp., these results suggest that host life traits may have important influence on pathogen exposure and transmission dynamics, providing a useful starting point for more directed surveillance approaches.

The Missing Pieces: The Role of Secretion Systems in Campylobacter jejuni Virulence

Campylobacter jejuni is likely the most common bacterial cause of gastroenteritis worldwide, responsible for millions of cases of inflammatory diarrhea characterized by severe abdominal cramps and blood in the stool. Further, C. jejuni infections are associated with post-infection sequelae in developed countries and malnutrition and growth-stunting in low- and middle-income countries. Despite the increasing prevalence of the disease, campylobacteriosis, and the recognition that this pathogen is a serious health threat, our understanding of C. jejuni pathogenesis remains incomplete. In this review, we focus on the Campylobacter secretion systems proposed to contribute to host-cell interactions and survival in the host. Moreover, we have applied a genomics approach to defining the structural and mechanistic features of C. jejuni type III, IV, and VI secretion systems. Special attention is focused on the flagellar type III secretion system and the prediction of putative effectors, given that the proteins exported via this system are essential for host cell invasion and the inflammatory response. We conclude that C. jejuni does not possess a type IV secretion system and relies on the type III and type VI secretion systems to establish a niche and potentiate disease.

Growth kinetics and fitness of fluoroquinolone resistant and susceptible Campylobacter jejuni strains of cattle origin

Human enterocolitis is frequently caused by the Gram-negative microaerobic bacterium Campylobacter jejuni. Macrolides (e.g., erythromycin) and fluoroquinolones (FQs) (e.g., ciprofloxacin) are the preferred antibiotics for the treatment of human campylobacteriosis. Rapid emergence of FQ-resistant (FQ-R) Campylobacter during treatment with FQ antimicrobials is well known to occur in poultry. Cattle is also an important reservoir of Campylobacter for humans, and FQ-R Campylobacter from cattle has become highly prevalent in recent years. Even though the selection pressure may have contributed to the expansion of FQ-R Campylobacter, the actual impact of this factor appears to be rather low. In this study, we examined the hypothesis that the fitness of FQ-R Campylobacter may have also played a role in the rise seen in FQ-R Campylobacter isolates by employing a series of in vitro experiments in MH broth and bovine fecal extract. First, it was shown that FQ-R and FQ-susceptible (FQ-S) C. jejuni strains of cattle origin had comparable growth rates when individually cultured in both MH broth and the fecal extract with no antibiotic present. Interestingly, FQ-R strains had small but statistically significant increases over FQ-S strains in growth in competition experiments performed in mixed cultures with no antibiotic present. Lastly, it was observed that FQ-S C. jejuni strains developed resistance to ciprofloxacin more readily at high initial bacterial cell density (10⁷ CFU/mL) and when exposed to low levels of the antibiotic (2-4 μg/mL) compared with that at a low level of initial bacterial cell density (10⁵ CFU/mL) and exposure to a high level of ciprofloxacin (20 μg/mL) in both MH broth and the fecal extract. Altogether, these findings indicate that even though FQ-R C. jejuni of cattle origin may have a slightly higher fitness advantage over the FQ-S population, the emergence of FQ-R mutants from susceptible strains is primarily dictated by the bacterial cell density and the antibiotic concentration exposed under in vitro condition. These observation may also provide plausible explanations for the high prevalence of FQ-R C. jejuni in cattle production due to its overall fit nature in the absence of antibiotic selection pressure and for the paucity of development of FQ-R C. jejuni in the cattle intestine in response to FQ-treatment, as observed in our recent studies.

The bile salt deoxycholate induces Campylobacter jejuni genetic point mutations that promote increased antibiotic resistance and fitness

Oxidative damage to DNA is a significant source of mutations in living organisms. While DNA damage must be repaired to maintain the integrity of the genome and cell survival, errors made during DNA repair may contribute to evolution. Previous work has revealed that Campylobacter jejuni growth in the presence of bile salt deoxycholate (DOC) causes an increase in reactive oxygen species and the occurrence of 8-oxo-deoxyguanosine (8-oxo-dG) DNA lesions. The fundamental goal of this project was to determine if C. jejuni growth in a medium containing DOC contributes to DNA mutations that provide a fitness advantage to the bacterium. Co-culture experiments revealed that C. jejuni growth in a DOC-supplemented medium increases the total number of ciprofloxacin-resistant isolates compared to C. jejuni grown in the absence of DOC. We recovered two individual isolates grown in a medium with DOC that had a point mutation in the gene encoding the EptC phosphoethanolamine transferase. Transformants harboring the EptC variant protein showed enhanced resistance to the antimicrobial agent polymyxin B and DOC when compared to an eptC deletion mutant or the isolate complemented with a wild-type copy of the gene. Finally, we found that the base excision repair (BER), homologous recombination repair (HRR), and nucleotide excision repair (NER) are involved in general oxidative damage repair in C. jejuni but that the BER pathway plays the primary role in the repair of the 8-oxo-dG lesion. We postulate that bile salts drive C. jejuni mutations (adaptations) and enhance bacterial fitness in animals.

In-silico analyses provide strong statistical evidence for intra-species recombination events of the gyrA and CmeABC operon loci contributing to the continued emergence of resistance to fluoroquinolones in natural populations of Campylobacter jejuni

OBJECTIVES

The continued emergence of Campylobacter jejuni strains resistant to fluoroquinolones (FQs) has posed a significant threat to global public health, leading frequently to undesirable outcomes of human campylobacteriosis treatment. The molecular genetic mechanisms contributing to the increased retention of resistance to FQs in natural populations of this species, especially in antibiotic-free environments, are not clearly understood. This study aimed to determine whether genetic recombination could be such a mechanism.

METHODS

We applied a large array of algorithms, imbedded in the SplitsTree and RDP4 software packages, to analyse the DNA sequences of the chromosomal loci, including the gyrA gene and the CmeABC operon, to identify events of their genetic recombination between C. jejuni strains.

RESULTS

The SplitsTree analyses of the above genetic loci resulted in several parallelograms with the bootstrap values being in a range of 94.7 to 100, with the high fit estimates being 99.3 to 100. These analyses were further strongly supported by the Phi test results (P ≤ 0.02715) and the RDP4-generated statistics (P ≤ 0.04005). The recombined chromosomal regions, along with the gyrA gene and CmeABC operon loci, were also found to contain the genetic loci that included, but were not limited to, the genes encoding for phosphoribosyltransferase, lipoprotein, outer membrane motility protein, and radical SAM domain protein.

CONCLUSION

These findings strongly suggest that the genetic recombination of the chromosomal regions involving gyrA, CmeABC, and their adjacent loci may be an additional mechanism underlying the constant emergence of epidemiologically successful FQ-resistant strains in natural populations of C. jejuni.

Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens

Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.

Development of Fluoroquinolone Resistance through Antibiotic Tolerance in Campylobacter jejuni

Antibiotic tolerance not only enables bacteria to survive acute antibiotic exposures but also provides bacteria with a window of time in which to develop antibiotic resistance. The increasing prevalence of Campylobacter jejuni isolates resistant to clinically important antibiotics, particularly fluoroquinolones (FQs), is a global public health concern. Currently, little is known about antibiotic tolerance and its effects on resistance development in C. jejuni. Here, we show that exposure to ciprofloxacin or tetracycline at concentrations 10 and 100 times higher than the MIC induces antibiotic tolerance in C. jejuni, whereas gentamicin or erythromycin treatment causes cell death. Interestingly, FQ resistance rapidly develops in C. jejuni after tolerance induction by ciprofloxacin and tetracycline. Furthermore, after tolerance is induced, alkyl hydroperoxide reductase (AhpC) plays a critical role in reducing FQ resistance development by alleviating oxidative stress. Together, these results demonstrate that exposure of C. jejuni to antibiotics can induce antibiotic tolerance and that FQ-resistant (FQR) C. jejuni clones rapidly emerge after tolerance induction. This study elucidates the mechanisms underlying the high prevalence of FQR C. jejuni and provides insights into the effects of antibiotic tolerance on resistance development. IMPORTANCE Antibiotic tolerance compromises the efficacy of antibiotic treatment by extending bacterial survival and facilitating the development of mutations associated with antibiotic resistance. Despite growing public health concerns about antibiotic resistance in C. jejuni, antibiotic tolerance has not yet been investigated in this important zoonotic pathogen. Here, our results show that exposure of C. jejuni to ciprofloxacin or tetracycline leads to antibiotic tolerance development, which subsequently facilitates the emergence of FQR C. jejuni. Importantly, these antibiotics are commonly used in animal agriculture. Moreover, our study suggests that the use of non-FQ drugs in animal agriculture promotes FQ resistance development, which is crucial because antibiotic-resistant C. jejuni is primarily transmitted from animals to humans. Overall, these findings increase our understanding of the mechanisms of resistance development through the induction of antibiotic tolerance.

Novel insights related to the rise of KPC-producing Enterobacter cloacae complex strains within the nosocomial niche

According to the World Health Organization, carbapenem-resistant Enterobacteriaceae (CRE) belong to the highest priority group for the development of new antibiotics. Argentina-WHONET data showed that Gram-negative resistance frequencies to imipenem have been increasing since 2010 mostly in two CRE bacteria: Klebsiella pneumoniae and Enterobacter cloacae Complex (ECC). This scenario is mirrored in our hospital. It is known that K. pneumoniae and the ECC coexist in the human body, but little is known about the outcome of these species producing KPC, and colonizing or infecting a patient. We aimed to contribute to the understanding of the rise of the ECC in Argentina, taking as a biological model both a patient colonized with two KPC-producing strains (one Enterobacter hormaechei and one K. pneumoniae) and in vitro competition assays with prevalent KPC-producing ECC (KPC-ECC) versus KPC-producing K. pneumoniae (KPC-Kp) high-risk clones from our institution. A KPC-producing E. hormaechei and later a KPC-Kp strain that colonized a patient shared an identical novel conjugative IncM1 plasmid harboring blaKPC-2. In addition, a total of 19 KPC-ECC and 58 KPC-Kp strains isolated from nosocomial infections revealed that high-risk clones KPC-ECC ST66 and ST78 as well as KPC-Kp ST11 and ST258 were prevalent and selected for competition assays. The competition assays with KCP-ECC ST45, ST66, and ST78 versus KPC-Kp ST11, ST18, and ST258 strains analyzed here showed no statistically significant difference. These assays evidenced that high-risk clones of KPC-ECC and KPC-Kp can coexist in the same hospital environment including the same patient, which explains from an ecological point of view that both species can exchange and share plasmids. These findings offer hints to explain the worldwide rise of KPC-ECC strains based on the ability of some pandemic clones to compete and occupy a certain niche. Taken together, the presence of the same new plasmid and the fitness results that showed that both strains can coexist within the same patient suggest that horizontal genetic transfer of blaKPC-2 within the patient cannot be ruled out. These findings highlight the constant interaction that these two species can keep in the hospital environment, which, in turn, can be related to the spread of KPC.

Function-based classification of hazardous biological sequences: Demonstration of a new paradigm for biohazard assessments

Bioengineering applies analytical and engineering principles to identify functional biological building blocks for biotechnology applications. While these building blocks are leveraged to improve the human condition, the lack of simplistic, machine-readable definition of biohazards at the function level is creating a gap for biosafety practices. More specifically, traditional safety practices focus on the biohazards of known pathogens at the organism-level and may not accurately consider novel biodesigns with engineered functionalities at the genetic component-level. This gap is motivating the need for a paradigm shift from organism-centric procedures to function-centric biohazard identification and classification practices. To address this challenge, we present a novel methodology for classifying biohazards at the individual sequence level, which we then compiled to distinguish the biohazardous property of pathogenicity at the whole genome level. Our methodology is rooted in compilation of hazardous functions, defined as a set of sequences and associated metadata that describe coarse-level functions associated with pathogens (e.g., adherence, immune subversion). We demonstrate that the resulting database can be used to develop hazardous “fingerprints” based on the functional metadata categories. We verified that these hazardous functions are found at higher levels in pathogens compared to non-pathogens, and hierarchical clustering of the fingerprints can distinguish between these two groups. The methodology presented here defines the hazardous functions associated with bioengineering functional building blocks at the sequence level, which provide a foundational framework for classifying biological hazards at the organism level, thus leading to the improvement and standardization of current biosecurity and biosafety practices.

Survey of Oxolinic Acid-Resistant Erwinia amylovora in Korean Apple and Pear Orchards, and the Fitness Impact of Constructed Mutants

Fire blight caused by Erwinia amylovora (Ea) is a devastating disease in apple and pear trees. Oxolinic acid (OA), a quinolone family antibiotic that inhibits DNA gyrase, has been employed to control fire blight in South Korea since 2015. The continuous use of this bactericide has resulted in the emergence of OA-resistant strains in bacterial pathogens in other countries. To investigate the occurrence of OA-resistant Ea strains in South Korea, we collected a total of 516 Ea isolates from diseased apple and pear trees in 2020-2021 and assessed their sensitivities to OA. We found that all isolates were susceptible to OA. To explore the possibility of emerging OA-resistant Ea by continuous application of OA, we exposed Ea stains to a range of OA concentrations and constructed OA-resistant mutant strains. Resistance was associated with mutations in the GyrA at codons 81 and 83, which result in glycine to cysteine and serine to arginine amino acid substitutions, respectively. The in vitro growth of the mutants in nutrient media and their virulence in immature apple fruits were lower than those of wild-type. Our results suggest that OA-resistance decreases the fitness of Ea. Future work should clarify the mechanisms by which OA-resistance decreases virulence of this plant pathogen. Continuous monitoring of OA-resistance in Ea is required to maintain the efficacy of this potent bactericide.

Metaphenotypes associated with recurrent genomic lineages of Campylobacter jejuni responsible for human infections in Luxembourg

Campylobacter jejuni is a leading cause of foodborne illnesses worldwide. Although considered fragile, this microaerophilic bacterium is able to survive in various challenging environments, which subsequently constitutes multiple sources of transmission for human infection. To test the assumption of acquiring specific features for adaptation and survival, we established a workflow of phenotypic tests related to the survival and the persistence of recurrent and sporadic strains. A representative collection of 83 strains isolated over 13 years from human, mammal, poultry, and environmental sources in Luxembourg, representing different spreading patterns (endemic, epidemic, and sporadic), was screened for survival to oxidative stresses, for acclimating to aerobic conditions (AC), and for persistence on abiotic surfaces. Using the cgMLST Oxford typing scheme for WGS data, the collection was classified into genomic lineages corresponding to host-generalist strains (lineages A and D, CC ST-21), host-specific strains (lineage B, CC ST-257 and lineage C, CC ST-464) and sporadic strains. We established that when a strain survives concentrations beyond 0.25 mM superoxide stress, it is six times more likely to survive hyperoxide stress and that a highly adherent strain is 14 times more likely to develop a biofilm. Surprisingly, more than half of the strains could acclimate to AC but this capacity does not explain the difference between recurrent genomic lineages and sporadic strains and the survival to oxidative stresses, while recurrent strains have a significantly higher adhesion/biofilm formation capacity than sporadic ones. From this work, the genomic lineages with more stable genomes could be characterized by a specific combination of phenotypes, called metaphenotypes. From the functional genomic analyses, the presence of a potentially functional T6SS in the strains of lineage D might explain the propensity of these strains to be strong biofilm producers. Our findings support the hypothesis that phenotypical abilities contribute to the spatio-temporal adaptation and survival of stable genomic lineages. It suggests a selection of better-adapted and persistent strains in challenging stress environments, which could explain the prevalence of these lineages in human infections.

Emerging patterns of fluoroquinolone resistance in Campylobacter jejuni in the UK [1998-2018]

Campylobacter jejuni (C.jejuni) is the most common causative agent of bacterial food poisoning worldwide and is known to be genetically highly diverse. C. jejuni is increasingly resistant to fluoroquinolone antibiotics, but very few studies have investigated variant-specific patterns of resistance across time. Here we use statistical modelling and clustering techniques to investigate patterns of fluoroquinolone resistance amongst 10,359 UK isolates from human disease sampled over 20 years. We observed six distinct patterns of fluoroquinolone sensitivity/resistance in C. jejuni across time, grouping by clonal complex (CC). Some CCs were fully resistant, some shifted from susceptible to resistant following a sigmoidal shape, and some remained susceptible over time. Our findings indicate that the fluoroquinolone resistance patterns of C. jejuni are complicated and cannot be analysed as a single species but divided into variant dynamics so that the factors driving resistance can be thoroughly investigated.

Antimicrobial effect of a drinking water additive comprising four organic acids on Campylobacter load in broilers and monitoring of bacterial susceptibility

Application of organic acids via feed or drinking water is under discussion as a possible intervention strategy to reduce Campylobacter (C.) load in primary poultry production. A previous in vitro study showed that reduced concentrations of sorbic acid, benzoic acid, propionic acid, and acetic acid were required for antibacterial activity against Campylobacter when using a mixture of these 4 acids compared to when using the single acids. The present study aimed at determining the antibacterial efficiency of this combination in vivo as a drinking water additive for reducing shedding and intestinal C. jejuni colonization in broilers. Furthermore, we assessed whether the inoculated C. jejuni strain BfR-CA-14430 adapted in vivo to the applied organic acids. Results of this study showed that adding the organic acids consistently reduced Campylobacter loads in cloacal swabs. While significant reductions were observed within the entire study period, a maximum 2 log reduction occurred at an age of 18 d. However, after dissection at the end of the trial, no significant differences were detected in Campylobacter loads of cecal and colon contents compared to the control group. Susceptibility testing of re-isolates from cloacal swabs and cecal content revealed equal minimum inhibitory concentration (MIC) values compared to the inoculated test strain, suggesting that C. jejuni remained susceptible throughout the trial.

Antibiotic Resistance in Bacteria—A Review

Background: A global problem of multi-drug resistance (MDR) among bacteria is the cause of hundreds of thousands of deaths every year. In response to the significant increase of MDR bacteria, legislative measures have widely been taken to limit or eliminate the use of antibiotics, including in the form of feed additives for livestock, but also in metaphylaxis and its treatment, which was the subject of EU Regulation in 2019/6. Numerous studies have documented that bacteria use both phenotypis and gentic strategies enabling a natural defence against antibiotics and the induction of mechanisms in increasing resistance to the used antibacterial chemicals. The mechanisms presented in this review developed by the bacteria have a significant impact on reducing the ability to combat bacterial infections in humans and animals. Moreover, the high prevalence of multi-resistant strains in the environment and the ease of transmission of drug-resistance genes between the different bacterial species including commensal flora and pathogenic like foodborne pathogens (E. coli, Campylobacter spp., Enterococcus spp., Salmonella spp., Listeria spp., Staphylococcus spp.) favor the rapid spread of multi-resistance among bacteria in humans and animals. Given the global threat posed by the widespread phenomenon of multi-drug resistance among bacteria which are dangerous for humans and animals, the subject of this study is the presentation of the mechanisms of resistance in most frequent bacteria called as “foodborne pathoges” isolated from human and animals. In order to present the significance of the global problem related to multi-drug resistance among selected pathogens, especially those danger to humans, the publication also presents statistical data on the percentage range of occurrence of drug resistance among selected bacteria in various regions of the world. In addition to the phenotypic characteristics of pathogen resistance, this review also presents detailed information on the detection of drug resistance genes for specific groups of antibiotics. It should be emphasized that the manuscript also presents the results of own research i.e., Campylobacter spp., E. coli or Enetrococcus spp. This subject and the presentation of data on the risks of drug resistance among bacteria will contribute to initiating research in implementing the prevention of drug resistance and the development of alternatives for antimicrobials methods of controlling bacteria.

Comparisons of plasma and fecal pharmacokinetics of danofloxacin and enrofloxacin in healthy and Mannheimia haemolytica infected calves

Danofloxacin and enrofloxacin are fluoroquinolones (FQs) used to treat and control bovine respiratory disease (BRD) complex. While low toxicity, high bactericidal activity, and availability in single and multiple dosing regimens make them preferable, the increasing incidence of FQ-resistance in foodborne pathogens and effects on gut microbiota necessitate evaluating their pharmacokinetics (PKs). The objective of this study was to determine the exposure level of gut microbiota to subcutaneously administered FQs and compare their PKs between plasma and feces in healthy and Mannheimia haemolytica infected calves. A single dose of danofloxacin (8 mg/kg), low dose (7.5 mg/kg), or high dose (12.5 mg/kg) of enrofloxacin was administered to calves. Blood and feces were collected from calves under experimental conditions over 48 h, and FQ concentrations were measured using Ultra High-Pressure Liquid Chromatography. While moderate BRD signs were exhibited in most calves in the infected cohorts, the plasma PKs were similar between healthy and sick calves. However, the fecal danofloxacin concentration was lower in the BRD group (area under concentration–time curve [AUC_inf], BRD median = 2627, healthy median = 2941 h*μg/mL, adj.P = 0.005). The dose normalized plasma and fecal danofloxacin concentrations were higher than those of enrofloxacin and its metabolite ciprofloxacin. Further, FQs had several fold higher overall concentrations in feces than in plasma in both groups. In conclusion, parenterally administered FQs expose gut microbiota to high concentrations of the antibiotics.

Proteomic Signatures of Antimicrobial Resistance in Yersinia pestis and Francisella tularensis

Antimicrobial resistance (AMR) is a well-recognized, widespread, and growing issue of concern. With increasing incidence of AMR, the ability to respond quickly to infection with or exposure to an AMR pathogen is critical. Approaches that could accurately and more quickly identify whether a pathogen is AMR also are needed to more rapidly respond to existing and emerging biological threats. We examined proteins associated with paired AMR and antimicrobial susceptible (AMS) strains of Yersinia pestis and Francisella tularensis, causative agents of the diseases plague and tularemia, respectively, to identify whether potential existed to use proteins as signatures of AMR. We found that protein expression was significantly impacted by AMR status. Antimicrobial resistance-conferring proteins were expressed even in the absence of antibiotics in growth media, and the abundance of 10–20% of cellular proteins beyond those that directly confer AMR also were significantly changed in both Y. pestis and F. tularensis. Most strikingly, the abundance of proteins involved in specific metabolic pathways and biological functions was altered in all AMR strains examined, independent of species, resistance mechanism, and affected cellular antimicrobial target. We have identified features that distinguish between AMR and AMS strains, including a subset of features shared across species with different resistance mechanisms, which suggest shared biological signatures of resistance. These features could form the basis of novel approaches to identify AMR phenotypes in unknown strains.

Genomic diversity and antimicrobial resistance of Campylobacter spp. from humans and livestock in Nigeria

Background

Campylobacter spp. are zoonotic pathogens, ubiquitous and are found naturally as commensals in livestock from where they can be transmitted to humans directly or through animal products. The genomic diversity and antimicrobial resistance profile of Campylobacter was investigated with a focus on C. jejuni and C. coli in humans and livestock (poultry and cattle) from Nigeria.

Methods

586 human stool samples and 472 faecal samples from livestock were cultured for thermophilic Campylobacter species on modified charcoal cefoperazone deoxycholate agar (mCCDA). Culture in combination with whole genome sequencing identified and confirmed the presence of Campylobacter in humans and animals from the study area. Further analysis of the sequences was performed to determine multilocus sequence types and genetic determinants of antimicrobial resistance to fluoroquinolone, betalactam, tetracycline and macrolide classes of antimicrobials.

Results

From the human stool samples tested, 50 (9%) were positive of which 33 (66%) were C. jejuni, 14 (28%) were C. coli while 3 (6%) were C. hyointestinalis. In livestock, 132 (28%) were positive. Thirty one (7%) were C. jejuni while 101 (21%) were C. coli. Whole genome sequencing and MLST of the isolates revealed a total of 32 sequence types (STs) identified from 47 human isolates while 48 STs were identified in 124 isolates from livestock indicating a population which was overall, genetically diverse with a few more dominant strains. The antimicrobial resistance profiles of the isolates indicated a higher prevalence of resistance in Campylobacter isolated from livestock than in humans. Generally, resistance was greatest for betalactams (42%) closely followed by fluoroquinolones (41%), tetracyclines (15%) and lastly macrolides (2%). Multidrug resistance to three or more antimicrobials was observed in 24 (13%) isolates from humans (n = 1, 4%) and chicken (n = 23, 96%).

Conclusions

This study has further contributed information about the epidemiology, genetic diversity and antimicrobial resistance profile of thermophilic Campylobacter in Nigeria.

Resistance to Antibiotics in Thermophilic Campylobacters

Campylobacter jejuni (C. jejuni) is one of the most frequent causes of bacterial enterocolitis globally. The disease in human is usually self-limiting, but when complications arise antibiotic therapy is required at a time when resistance to antibiotics is increasing worldwide. Mechanisms of antibiotic resistance in bacteria are diverse depending on antibiotic type and usage and include: enzymatic destruction or drug inactivation; alteration of the target enzyme; alteration of cell membrane permeability; alteration of ribosome structure and alteration of the metabolic pathway(s). Resistance of Campylobacter spp. to antibiotics, especially fluoroquinolones is now a major public health problem in developed and developing countries. In this review the mechanisms of resistance to fluoroquinolones, macrolides, tetracycline, aminoglycoside and the role of integrons in resistance of Campylobacter (especially at the molecular level) are discussed, as well as the mechanisms of resistance to β-lactam antibiotics, sulphonamides and trimethoprim. Multiple drug resistance is an increasing problem for treatment of campylobacter infections and emergence of resistant strains and resistance are important One Health issues.

RND Efflux Systems Contribute to Resistance and Virulence of Aliarcobacter butzleri

Aliarcobacter butzleri is an emergent enteropathogen that can be found in a range of environments. This bacterium presents a vast repertoire of efflux pumps, such as the ones belonging to the resistance nodulation cell division family, which may be associated with bacterial resistance, as well as virulence. Thus, this work aimed to evaluate the contribution of three RND efflux systems, AreABC, AreDEF and AreGHI, in the resistance and virulence of A. butzleri. Mutant strains were constructed by inactivation of the gene that encodes the inner membrane protein of these systems. The bacterial resistance profile of parental and mutant strains to several antimicrobials was assessed, as was the intracellular accumulation of the ethidium bromide dye. Regarding bacterial virulence, the role of these three efflux pumps on growth, strain fitness, motility, biofilm formation ability, survival in adverse conditions (oxidative stress and bile salts) and human serum and in vitro adhesion and invasion to Caco-2 cells was evaluated. We observed that the mutants from the three efflux pumps were more susceptible to several classes of antimicrobials than the parental strain and presented an increase in the accumulation of ethidium bromide, indicating a potential role of the efflux pumps in the extrusion of antimicrobials. The mutant strains had no bacterial growth defects; nonetheless, they presented a reduction in relative fitness. For the three mutants, an increase in the susceptibility to oxidative stress was observed, while only the mutant for AreGHI efflux pump showed a relevant role in bile stress survival. All the mutant strains showed an impairment in biofilm formation ability, were more susceptible to human serum and were less adherent to intestinal epithelial cells. Overall, the results support the contribution of the efflux pumps AreABC, AreDEF and AreGHI of A. butzleri to antimicrobial resistance, as well as to bacterial virulence.

Epidemiologic Associations Vary Between Tetracycline and Fluoroquinolone Resistant Campylobacter jejuni Infections

Campylobacter jejuni is the leading cause of bacterial gastroenteritis and antibiotic resistant C. jejuni are a serious threat to public health. Herein, we sought to evaluate trends in C. jejuni infections, quantify resistance frequencies, and identify epidemiological factors associated with infection. Campylobacter jejuni isolates (n = 214) were collected from patients via an active surveillance system at four metropolitan hospitals in Michigan between 2011 and 2014. The minimum inhibitory concentration for nine antibiotics was determined using microbroth dilution, while demographic and clinical data were used for the univariate and multivariate analyses. Over the 4-year period, a significant increase in the recovery of C. jejuni was observed (p ≤ 0.0001). Differences in infection rates were observed by hospital and several factors were linked to more severe disease. Patients residing in urban areas, for instance, were significantly more likely to be hospitalized than rural residents as were patients over 40 years of age and those self-identifying as non-White, highlighting potential disparities in disease outcomes. Among the 214 C. jejuni isolates, 135 (63.1%) were resistant to at least one antibiotic. Resistance was observed for all nine antibiotics tested yielding 11 distinct resistance phenotypes. Tetracycline resistance predominated (n = 120; 56.1%) followed by resistance to ciprofloxacin (n = 49; 22.9%), which increased from 15.6% in 2011 to 25.0% in 2014. Resistance to two antibiotic classes was observed in 38 (17.8%) isolates, while multidrug resistance, or resistance to three or more classes, was observed in four (1.9%). Notably, patients with ciprofloxacin resistant infections were more likely to report traveling in the past month (Odds Ratio (OR): 3.0; 95% confidence interval (CI): 1.37, 6.68) and international travel (OR: 9.8; 95% CI: 3.69, 26.09). Relative to patients with only tetracycline resistant infections, those with ciprofloxacin resistance were more likely to travel internationally, be hospitalized and have an infection during the fall or summer. Together, these findings show increasing rates of infection and resistance and highlight specific factors that impact both outcomes. Enhancing understanding of factors linked to C. jejuni resistance and more severe infections is critical for disease prevention, particularly since many clinical laboratories have switched to the use of culture-independent tests for the detection of Campylobacter.

Highly Prevalent Multidrug-Resistant Campylobacter spp. Isolated From a Yellow-Feathered Broiler Slaughterhouse in South China

The purpose of this study was to investigate the prevalence, antimicrobial resistance, virulence genes, and genetic diversity of Campylobacter spp. along the yellow-feathered broiler slaughtering line in Southern China from December 2018 to June 2019. A total of 157 Campylobacter spp. isolates were identified from 1,102 samples (including 53.6% (75/140) of live chicken anal swab samples, 27.5% (44/160) of defeathering samples, 18.1% (29/160) of evisceration samples, 2.1% (3/140) of washing samples, 1.4% (2/140) of chilling samples, and 1.1% (4/362) of environmental samples). The prevalence of Campylobacter spp. was 14.2%, including 43.9% Campylobacter jejuni, 53.5% Campylobacter coli, and 2.5% other Campylobacter species. The highest antimicrobial resistance rate was found to be against sulfamethoxazole (138/157, 87.9%), and 90.4% (142/157) of the isolates were multidrug resistant (MDR). Examination of resistance-related genes revealed the double base mutated Thr-86-Ile, which informed ACA-TTA, with an Arg-79-Lys substitution in gyrA. Eleven virulence-associated genes (cadF, cdtA, cdtB, ciaB, flaA, imaA, dnaJ, plaA, virB11, racR, and cdtC) were also detected by a polymerase chain reaction (PCR) analysis, and cadF (81.5%) was the most prevalent. Based on an analysis of pulsed-field gel electrophoresis (PFGE) results, we found that Campylobacter spp. could be cross-contaminated throughout the entire slaughtering line. These results show that it is imperative to study the Campylobacter spp. from the yellow-feathered broiler along the slaughtering line in China to develop preventative and treatment measures for the poultry industry, as well as food safety and public health.

Antimicrobial use, biosecurity, herd characteristics, and antimicrobial resistance in indicator Escherichia coli in ten Finnish pig farms

We investigated connections between antimicrobial use (AMU), biosecurity, and the numbers of pigs and staff in ten Finnish farrow-to-finish herds. Data on AMU in each herd were collected for 12 months. AMU was quantified as treatment incidences per 1000 days at risk (TI) using the consensus defined daily dose calculation. Biosecurity was scored using the Biocheck.UGent™ system. We also examined antimicrobial resistance patterns of indicator E. coli isolated from faeces of selected pigs. In each herd, two groups of five pigs were formed: 1) antimicrobial treatment group (ANT: at least one pig in the litter was identified as sick and treated with antimicrobials) and 2) non-antimicrobial treatment group (NON: the litter was not medicated). Faecal samples were taken from these pigs at 5 and 22 weeks of age, cultured, and indicator E. coli isolates were tested for antimicrobial susceptibilities. The AMU varied considerably between the herds. Altogether, most of the antimicrobial treatment courses were assigned to weaned piglets. When AMU was quantified as TIs, suckling piglets had the highest TI (mean 46.6), which was significantly higher (P < 0.05) than TIs in fatteners and breeders (9.3 and 7.3, respectively). The difference between TI in suckling and TI in weaned piglets (19.1) was not statistically significant. There was a tendency for a negative correlation between the TI in breeders and the number of sows (r = -0.56, P = 0.09). Larger herds had higher external biosecurity scores than smaller herds (LS-means; 72 vs. 66, P < 0.05). The proportions of E. coli isolates resistant to at least one antimicrobial were higher in pigs at 5 weeks than in pigs at 22 weeks of age (Binomial proportion means; 40.5 % vs. 15.5 %, P < 0.05); as well as proportions of isolates resistant to at least three antimicrobial classes (23.0 % vs. 3.7 %, P < 0.01). These proportions did not differ between the ANT and NON groups at either 5 or 22 weeks of age (P> 0.05). We found few connections: enhanced external biosecurity levels found in the large herds co-occurred with lower use of antimicrobials and herds with low biosecurity scores - especially in the internal subcategories - appeared to have higher proportions of resistant isolates. Conclusively, we suggest that enhancing internal biosecurity might contribute to a reduction in the spreading of antimicrobial resistance in pig herds.

Association of Antimicrobial Resistance in Campylobacter spp. in Broilers and Turkeys with Antimicrobial Use

We investigated trends in antimicrobial resistance (AMR) in Campylobacter&nbsp;jejuni and Campylobacter&nbsp;coli in poultry between 2010 and 2016 in Germany and their association with antimicrobial use. Campylobacter had been isolated from the caeca of broilers and turkeys at slaughter by regional laboratories according to current ISO methods in the framework of a national monitoring program. Isolates were submitted to the National Reference Laboratory for Campylobacter and tested for AMR using broth microdilution methods. Minimum inhibitory concentrations were evaluated according to epidemiological cut-off values. Antimicrobial use (AMU) data from 2014 to 2016 were taken from a government report. AMR was higher in C. coli than in C. jejuni and higher in turkeys than in broilers. AMR was highest to tetracycline and the tested (fluoro)quinolones while it was rare to gentamicin in both bacterial species, infrequent to erythromycin in C. jejuni, and moderate in C. coli. AMR to tetracycline and erythromycin decreased over time while it increased to (fluoro)quinolones. An association of AMU and AMR was observed for resistance to tetracycline and erythromycin, while it was not observed for the aminoglycosides. Resistance to nalidixic acid and ciprofloxacin increased despite a decrease of fluoroquinolone use between 2014 and 2016, indicating that other factors have a strong influence on resistance to (fluoro)quinolones in Campylobacter.

Drug resistance, fitness and compensatory mutations in Mycobacterium tuberculosis

For tuberculosis to be eradicated, the transmission of Multi-Drug-Resistant and eXtensively Drug Resistant strains of Mycobacterium tuberculosis (MDR and XDR-TB) must be considerably reduced. Drug resistant strains were initially thought to have reduced fitness, and the majority of resistant strains may actually have compromised fitness because they are found in only one or a few patients. In contrast, some MDR/XDR-TB strains are highly transmitted and cause large outbreaks. Most antibiotics target essential bacterial functions and the mutations that confer resistance to anti-TB drugs can incur fitness costs manifested as slower growth and reduced viability. The fitness costs vary with different resistance mutations and the bacilli can also accumulate secondary mutations that compensate for the compromised functions and partially or fully restore lost fitness. The compensatory mutations (CM) are different for each antibiotic, as they mitigate the deleterious effects of the specific functions compromised by the resistance mutations. CM are generally more common in strains with resistance mutations incurring the greatest fitness costs, but for RIF resistance, CM are most frequent in strains with the mutation carrying the least fitness cost, Ser450Leu. Here, we review what is known about fitness costs, CM and mechanisms of resistance to the drugs that define a strain as MDR or XDR-TB. The relative fitness costs of the resistance mutations and the mitigating effects of CM largely explain why certain mutations are frequently found in highly transmitted clusters while others are less frequently, rarely or never found in clinical isolates. The CM illustrate how drug resistance affects bacteria and how bacteria evolve to overcome the effects of the antibiotics, and thus a paradigm for how mycobacteria can evolve in response to stress.

Antibiotic resistance: Time of synthesis in a post-genomic age

Antibiotic resistance has been highlighted by international organizations, including World Health Organization, World Bank and United Nations, as one of the most relevant global health problems. Classical approaches to study this problem have focused in infected humans, mainly at hospitals. Nevertheless, antibiotic resistance can expand through different ecosystems and geographical allocations, hence constituting a One-Health, Global-Health problem, requiring specific integrative analytic tools. Antibiotic resistance evolution and transmission are multilayer, hierarchically organized processes with several elements (from genes to the whole microbiome) involved. However, their study has been traditionally gene-centric, each element independently studied. The development of robust-economically affordable whole genome sequencing approaches, as well as other -omic techniques as transcriptomics and proteomics, is changing this panorama. These technologies allow the description of a system, either a cell or a microbiome as a whole, overcoming the problems associated with gene-centric approaches. We are currently at the time of combining the information derived from -omic studies to have a more holistic view of the evolution and spread of antibiotic resistance. This synthesis process requires the accurate integration of -omic information into computational models that serve to analyse the causes and the consequences of acquiring AR, fed by curated databases capable of identifying the elements involved in the acquisition of resistance. In this review, we analyse the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.

Idiosyncratic variation in the fitness costs of tetracycline-resistance mutations in Escherichia coli

A bacterium's fitness relative to its competitors, both in the presence and absence of antibiotics, plays a key role in its ecological success and clinical impact. In this study, we examine whether tetracycline-resistant mutants are less fit in the absence of the drug than their sensitive parents, and whether the fitness cost of resistance is constant or variable across independently derived lines. Tetracycline-resistant lines suffered, on average, a reduction in fitness of almost 8%. There was substantial among-line variation in the fitness cost. This variation was not associated with the level of resistance conferred by the mutations, nor did it vary significantly across several genetic backgrounds. The two resistant lines with the most extreme fitness costs involved functionally unrelated mutations on different genetic backgrounds. However, there was also significant variation in the fitness costs for mutations affecting the same pathway and even different alleles of the same gene. Our findings demonstrate that the fitness costs of antibiotic resistance do not always correlate with the phenotypic level of resistance or the underlying genetic changes. Instead, these costs reflect the idiosyncratic effects of particular resistance mutations and the genetic backgrounds in which they occur.

Selection of Resistant Bacteria in Mallards Exposed to Subinhibitory Concentrations of Ciprofloxacin in Their Water Environment

Emergence and selection of antibiotic resistance following exposure to high antibiotic concentrations have been repeatedly shown in clinical and agricultural settings, whereas the role of the weak selective pressures exerted by antibiotic levels below the MIC (sub-MIC) in aquatic environments due to anthropogenic contamination remains unclear. Here, we studied how exposure to sub-MIC levels of ciprofloxacin enriches for Escherichia coli with reduced susceptibility to ciprofloxacin using a mallard colonization model. Mallards were inoculated with two isogenic extended-spectrum-β-lactamase (ESBL)-encoding E. coli strains, differing only by a gyrA mutation that results in increased MICs of ciprofloxacin, and exposed to different levels of ciprofloxacin in their swimming water. Changes in the ratios of mutant to parental strains excreted in feces over time and ESBL plasmid spread within the gut microbiota from individual birds were investigated. Results show that in vivo selection of gyrA mutants occurred in mallards during exposure to ciprofloxacin at concentrations previously found in aquatic environments. During colonization, resistance plasmids were readily transferred between strains in the intestines of the mallards, but conjugation frequencies were not affected by ciprofloxacin exposure. Our results highlight the potential for enrichment of resistant bacteria in wildlife and underline the importance of reducing antibiotic pollution in the environment.

Natural Competence and Horizontal Gene Transfer in Campylobacter

Thermophilic Campylobacter, in particular Campylobacter jejuni, C. coli and C. lari are the main relevant Campylobacter species for human infections. Due to their high capacity of genetic exchange by horizontal gene transfer (HGT), rapid adaptation to changing environmental and host conditions contribute to successful spreading and persistence of these foodborne pathogens. However, extensive HGT can exert dangerous side effects for the bacterium, such as the incorporation of gene fragments leading to disturbed gene functions. Here we discuss mechanisms of HGT, notably natural transformation, conjugation and bacteriophage transduction and limiting regulatory strategies of gene transfer. In particular, we summarize the current knowledge on how the DNA macromolecule is exchanged between single cells. Mechanisms to stimulate and to limit HGT obviously coevolved and maintained an optimal balance. Chromosomal rearrangements and incorporation of harmful mutations are risk factors for survival and can result in drastic loss of fitness. In Campylobacter, the restricted recognition and preferential uptake of free DNA from relatives are mediated by a short methylated DNA pattern and not by a classical DNA uptake sequence as found in other bacteria. A class two CRISPR-Cas system is present but also other DNases and restriction-modification systems appear to be important for Campylobacter genome integrity. Several lytic and integrated bacteriophages have been identified, which contribute to genome diversity. Furthermore, we focus on the impact of gene transfer on the spread of antibiotic resistance genes (resistome) and persistence factors. We discuss remaining open questions in the HGT field, supposed to be answered in the future by current technologies like whole-genome sequencing and single-cell approaches.

Antibiotics and antibiotic resistant genes (ARGs) in groundwater: A global review on dissemination, sources, interactions, environmental and human health risks

The discovery and evolution of antibiotics for humans and animals are among the most significant milestones of the 20th century. However, antibiotics play a significant role in the induction and dissemination of antibiotic resistance genes (ARGs) in groundwater that has recently become the primary environmental concern. They are administrated to humans and animals on a large scale and are persistent in the environment. Long term impacts of antibiotics in the ecological environment are not still clearly understood, and their occurrence and consequences have become an important research topic worldwide. The hotspot reservoirs of antibiotics and ARGs include medical facilities, livestock farming, aquaculture, landfills, on-site sanitation systems, sewage, and wastewater treatment plants. Our meta-analysis demonstrated that antibiotics, including ciprofloxacin, sulfamethoxazole, erythromycin, and tetracycline were found at high concentrations while sulfonamide and tetracycline ARGs were more prevalent in groundwater. Moreover, the highest reported concentrations of targeted antibiotics were used to calculate hazard quotient (HQ) and risk quotient (RQ) in global groundwater bodies to estimate environmental and human health risks, respectively. Due to limited available ecotoxicity data, RQ and HQ can only be calculated for a few antibiotics in groundwater. The risk assessment of antibiotics demonstrated that antibiotics with their current groundwater levels pose no human health risks, whereas only ciprofloxacin, erythromycin, flumequine, and sulfamethoxazole revealed moderate to low risks to aquatic species. The occurrence of ARGs and antibiotic resistant bacteria (ARBs) in groundwater is also not likely to pose human health risk but consumption of groundwater contaminated with ARGs and ARBs might contribute to the development of antibiotic resistance in humans. The present review also sheds light on the relationship between ARGs, antibiotics, microbial communities, and environmental factors in groundwater, and reported a significant correlation between them. It also addresses prospects for future outlooks into further areas of relevant research.

Research Note: Antimicrobial resistance of Campylobacter species isolated from chickens near Ulaanbaatar city, Mongolia

There has been no report on the prevalence of Campylobacter spp. in farm animals in Mongolia. To uncover the prevalence of Campylobacter spp. in chickens in Mongolia and their antimicrobial resistance, in this study, we isolated and characterized Campylobacter spp. from chickens in Mongolia. We collected 71 cloacal swabs of chickens from 5 farms including 4 layer farms and one broiler farm near Ulaanbaatar city and isolated 25 Campylobacter jejuni and 6 Campylobacter coli isolates. All isolates were resistant to tetracycline, and 3 C. coli isolates were resistant to erythromycin. The C. coli isolates possessed either the erm(B) gene or nucleotide substitution at nt 2,075 of 23S rDNA, both of which are known to be associated with erythromycin resistance. Sixteen of the 31 C. jejuni/C. coli isolates (51.6%) were resistant to nalidixic acid and fluoroquinolones. All the fluoroquinolone-resistant isolates possessed amino acid substitution from threonine to isoleucine at codon 86 (nucleotide substitution: ACA to ATA). Multilocus sequence typing and phylogenetic analyses showed a variation in C. jejuni/C. coli in chickens in Mongolia. In addition, some of the C. jejuni isolates seemed to be phylogenetically close to isolates in Asian and Oceanian countries. This is the first report on the characterization of antimicrobial resistance of Campylobacter spp. in farm animals in Mongolia and is valuable for implementation of measures for a prudent use of antimicrobials in farm animals.

Comparison of antimicrobial resistance in thermophilic Campylobacter strains isolated from conventional production and backyard poultry flocks

1. The aim of this study was to compare the resistance pattern of thermophilic Campylobacter spp. isolated from conventional production (n = 34) and backyard poultry flocks (n = 36) from Rio de Janeiro State, Brazil. The disc diffusion method and statistical tests were used for investigation and analysis of the resistance pattern of Campylobacter spp. isolated from different rearing systems.2. Antimicrobial resistance percentages to amoxycillin with clavulanic acid (AMC), ampicillin (AMP), ceftiofur (CTF), ciprofloxacin (CIP), enrofloxacin (ENO), erythromycin (ERI), gentamicin (GEN) and tetracycline (TET) were 32.4%, 44.1%, 67.6%, 97.1%, 82.4%, 26.5%, 5.9% and 38.2% in conventional production flocks respectively, while the backyard flock's resistance levels were 0.0%, 13.9%, 69.4%, 100.0%, 91.7%, 5.6%, 0.0% and 16.7%, respectively.3. Campylobacter spp. from conventional poultry production was more resistant to AMC, AMO, ERI and TET (P > 0.05) when compared to strains from backyard poultry. A higher frequency of resistance to fluoroquinolones (FLQ), CIP and ENO, was observed in strains from both systems, demonstrating the spread of resistant strains among poultry production environments.

Effect of antimicrobial use and production system on Campylobacter spp., Staphylococcus spp. and Salmonella spp. resistance in Spanish swine: A cross-sectional study

Antimicrobial resistance is a worldwide public health threat; hence, current trends tend to reduce antimicrobial use in food-producing animals and to monitor resistance in primary production. This study aimed at evaluating the impact of antimicrobial use and production system on swine farms in the antimicrobial resistance of Campylobacter, Salmonella and Staphylococcus, the main zoonotic pathogens in pig herds, in order to assess their potential value as sentinel microorganisms in antimicrobial resistance surveillance schemes. A total of 37 Spanish swine farms, 18 intensive and 19 organic/extensive farms, were included in the study. The antimicrobial resistance of 104 Campylobacter, 84 Staphylococcus and 17 Salmonella isolates was evaluated using Sensititre plates following the EUCAST guidelines. Mixed-effects logistic regression was used to evaluate the influence of production system and antimicrobial use in resistant and multidrug-resistant (MDR) phenotypes to the antimicrobials tested. The results showed that antimicrobial use was higher (p < .001) on intensive farms than on organic/extensive farms. MDR in Campylobacter and Staphylococcus was lower on organic/extensive farms (OR < .01p < .001). Antimicrobial resistance in Campylobacter and Staphylococcus isolates was, also for most of the antimicrobials studied, significantly higher in intensive than organic/extensive pig herds. Tetracycline resistance was associated with total antimicrobial consumption in both microbial species (p < .05), and some cross-associations between distinct antimicrobial substances were established, for instance resistance to erythromycin was associated with macrolide and phenicol consumption. No significant associations could be established for Salmonella isolates. The results demonstrate the link between antimicrobial consumption and resistance in zoonotic bacteria and evidence the potential value of using Campylobacter and Staphylococcus species in monitoring activities aimed at determining the impact of antimicrobials use/reduction on the occurrence and spread of antimicrobial resistance.

High prevalence and variable fitness of fluoroquinolone-resistant avian pathogenic Escherichia coli isolated from chickens in Korea

Colibacillosis caused by avian pathogenic Escherichia coli (APEC) is the most common bacterial disease in poultry, resulting in significant economic losses. Resistance to fluoroquinolones has been found to be high in APEC worldwide, which has increased concerns about risks to human health as well as poultry production. In the present study, we determined the prevalence, genetic traits, and fitness traits of fluoroquinolone-resistant APEC isolated from chickens in Korea using a total of 286 APEC isolates collected between 2014 and 2017. The APEC isolates were highly resistant to nalidixic acid (86.0%), ampicillin (71.7%), tetracycline (69.6%), and sulfisoxazole (61.2%), and 132 (46.2%) of the isolates were resistant to both enrofloxacin and ciprofloxacin. These fluoroquinolone-resistant isolates showed eight mutation combinations including single- or double-point mutations in the gyrA, parC, or parE genes. The isolates with double mutations (codons 83 and 87) in gyrA and additional mutations in parC and parE showed high-level fluoroquinolone resistance (minimum inhibitory concentrations, 16-128 µg/ml). The isolates fell into four phylogenetic groups, and groups A (47/132, 35.6%) and B1 (47/132, 36.4%) were the most predominant. Nine isolates (6.8%) belonged to group B2 and included major lineages of extraintestinal pathogenic E. coli, sequence type (ST) 95 (n = 3) and ST69 (n = 2). The isolates varied in their virulence-associated gene content, biofilm formation, and intramacrophage survival. Overall, fluoroquinolone-resistant APEC in poultry poses a potential risk to public health and represents a highly diverse group of the resistant bacteria that varied in their genetic and fitness traits.