Characterization of acmeABCOperon in a Quinolone- ResistantCampylobacter coliIsolate of Irish Origin

Genomic resistant determinants of multidrug-resistant Campylobacter spp. isolates in Peru

OBJECTIVES

Antimicrobial resistant (AMR) Campylobacter is a global health threat; however, there is limited information on genomic determinants of resistance in low- and middle-income countries. We evaluated genomic determinants of AMR using a collection of whole genome sequenced Campylobacter jejuni and C. coli isolates from Iquitos, Peru.

METHODS

Campylobacter isolates from two paediatric cohort studies enriched with isolates that demonstrated resistance to ciprofloxacin and azithromycin were sequenced and mined for AMR determinants.

RESULTS

The gyrA mutation leading to the Thr86Ile amino acid change was the only gyrA mutation associated with fluoroquinolone resistance identified. The A2075G mutation in 23S rRNA was present, but three other 23S rRNA mutations previously associated with macrolide resistance were not identified. A resistant-enhancing variant of the cmeABC efflux pump genotype (RE-cmeABC) was identified in 36.1% (35/97) of C. jejuni genomes and 17.9% (12/67) of C. coli genomes. Mutations identified in the CmeR-binding site, an inverted repeat sequence in the cmeABC promoter region that increases expression of the operon, were identified in 24/97 C. jejuni and 14/67 C. coli genomes. The presence of these variants, in addition to RE-cmeABC, was noted in 18 of the 24 C. jejuni and 9 of the 14 C. coli genomes.

CONCLUSIONS

Both RE-cmeABC and mutations in the CmeR-binding site were strongly associated with the MDR phenotype in C. jejuni and C. coli. This is the first report of RE-cmeABC in Peru and suggests it is a major driver of resistance to the principal therapies used to treat human campylobacteriosis in this setting.

The characterization and correlation between the phenotypic and genotypic resistance of Campylobacter spp. isolates from commercial broilers and native chickens in the south of Thailand

RESEARCH HIGHLIGHTS

High Campylobacter prevalence in chickens; C. jejuni more prevalent than C. coli.Susceptibility to macrolides but resistance to quinolones/tetracyclines in isolates.Homogeneous resistance patterns within farms; higher in broilers than in native birds.Partial association between phenotypic and genotypic resistance among isolates.

Prevalence and antimicrobial resistance of Campylobacter jejuni and C. coli identified in a slaughterhouse in Argentina

The aim of this study was to evaluate the percentage of Campylobacter (C. jejuni and C. coli) from samples collected at the slaughterhouse to describe the prevalence of resistance to selected antimicrobials, and to characterize the genetic determinants. In total, from 333 samples analyzed, 31% were positive for Campylobacter. More positive samples were detected before the chiller (46%) than after the chiller (16%). C. coli (59%) was more prevalent than C. jejuni (41%). Antimicrobial resistance differences between C. jejuni and C. coli were found (p < 0.001). Multidrug resistance was found in 72% of C. coli isolates and 69% of C. jejuni isolates (p < 0.001). Most C. jejuni isolates (57%) had the three genes of the cmeABC efflux pump. The tet(O) gene and resistance-associated point mutations within both the gyrA and 23S rRNA genes were detected in 100% of C. coli isolates. On the other hand, C. jejuni only had more prevalence of the bla_OXA-61 gene than C. coli (p < 0.001), and most of the C. jejuni isolates (70–80%) had the tet(O) and gyrA point mutation. These results could contribute to knowledge about the status of thermotolerant Campylobacter resistant to antimicrobials isolated from food animals in Argentina and to develop an antimicrobial resistance surveillance system.

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From samples analyzed, 31% were positive for Campylobacter.

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More positive samples were detected before the chiller (46%) than after it (16%).

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Multidrug resistance was found in 72% of C. coli isolates and 69% of C. jejuni isolates.

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The tet(O) gene was detected in 100% of the tetracycline-, resistantC. coliisolates.

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C.jejuni only had more prevalence of the bla_OXA-61 gene than C. coli (p < 0.001).

Genome sequence of a multidrug-resistant Campylobacter coli strain isolated from a newborn with severe diarrhea in Lebanon

A multidrug-resistant (MDR) Campylobacter coli (C. coli) strain was isolated from a 2-month-old newborn who suffered from severe diarrhea in Lebanon. Here, whole-genome sequencing (WGS) analysis was deployed to determine the genetic basis of antimicrobial resistance and virulence in the C. coli isolate and to identify its epidemiological background (sequence type). The identity of the isolate was confirmed using API® Campy, MALDI-TOF, and 16S rRNA gene sequencing analysis. The antimicrobial susceptibility phenotype was determined using the disk diffusion assay. Our analysis showed that resistance to macrolide and quinolone was potentially associated with the presence of multiple point mutations in antibiotic targets on the chromosomal DNA. Furthermore, tetracycline and aminoglycoside resistance were encoded by genes on a pTet plasmid. The bla_OXA-61, which is associated with beta-lactam resistance, was also detected in the C. coli genome. A set of 30 genes associated with the virulence in C. coli was detected using WGS analysis. MLST analysis classified the isolate as belonging to a new sequence type (ST-9588), a member of ST-828 complex which is mainly associated with humans and chickens. Taking together, this study provides the first WGS analysis of Campylobacter isolated from Lebanon. The detection of a variety of AMR and virulence determinants strongly emphasizes the need for studying the burden of Campylobacter in Lebanon and the Middle East and North Africa (MENA) region, where information on campylobacteriosis is scant.

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.

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.

Molecular Epidemiology and Resistance Profile of Campylobacter jejuni and Campylobacter coli Strains Isolated from Different Sources in Brazil

Aims: The objectives of this study were to genotype a total of 48 Campylobacter jejuni and 39 Campylobacter coli strains isolated in Brazil from 1995 to 2016 by multilocus sequence typing (MLST) and to determine their resistance profile. The presence or points of mutation in the related resistance genes was verified. Results: By MLST, C. jejuni strains were typed into 36 STs and C. coli strains were typed into 27 STs. A total of 70.8% of C. jejuni and 35.9% of C. coli were resistant to at least one antimicrobial tested. The tet(O) gene was detected in 43.7% C. jejuni and in 12.8% C. coli. The ermB gene was not detected and one C. jejuni presented the mutation in the 23S rRNA gene. Besides, 58.3% C. jejuni presented the substitution T86I in the quinolone resistance-determining region of gyrA and 15.4% C. coli presented the substitution T38I. The cmeB gene was detected in 97.9% C. jejuni and in 97.4% C. coli. Conclusion: The presence of C. jejuni and C. coli resistant to some antimicrobial agents of clinical use is of public health concern. The presence of STs shared between Brazilian strains and isolates of different countries is of concern since it might suggest a possible spread of these shared types.

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.

Antimicrobial susceptibilities and resistance genes in Campylobacter strains isolated from poultry and pigs in Australia

AIMS

To evaluate the phenotypic and genotypic profiles of Campylobacter spp. from poultry faecal samples from free range or intensively raised meat chickens and free range egg layers. In addition, a case-comparison study of antibiotic resistance genes from different groups of poultry and some pig strains previously collected was carried out.

METHODS

Resistance to different antibiotics was assessed using the agar dilution method. In addition, all the strains were tested for ampicillin (bla(OXA-61) ), erythromycin (aph-3-1), tetracycline tet(O), streptomycin (aadE), and the energy-dependent multi-drug efflux pump (cmeB) resistance genes using multiplex polymerase chain reaction.

RESULTS

The evaluation of phenotypic resistance revealed all of the strains from poultry were sensitive to ciprofloxacin, gentamicin, erythromycin or tylosin. But, widespread resistance to lincomycin (51-100%), extensive resistance to ampicillin (33·3-60·2%) and less resistance to tetracycline (5·6-40·7%) were observed in the different groups of chickens. Antibiotic resistance genes bla(OXA-61,) cmeB and tet(O) were found in 82·6-92·7%, 80·3-89% and 22·3-30·9% Camp. coli isolates from pigs, whilst 59-65·4% and 19·2-40·7% Camp. jejuni from chickens were found to encode bla(OXA-61) and tet(O), respectively.

CONCLUSION

No significant difference between isolates from free range egg layers and meat chickens (P < 0·05) was found. However, there were significant differences between the pig strains and all the groups of poultry strains (P < 0·05) with regard to carriage of resistance genes. In addition, pulsed field gel electrophoresis of selected resistant isolates from the poultry and pig revealed closely related clonal groups.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results suggest the resistant strains are persisting environmental isolates that have been acquired by the different livestock species. Furthermore, the different treatment practices in poultry and pigs have resulted in differences in resistance profiles in Campylobacter isolates.

Characterization of erythromycin-resistant porcine isolates of Campylobacter coli

Erythromycin-resistant Campylobacter organisms were isolated from swine, and their resistance to the antibiotic was characterized. One hundred fourteen Campylobacter organisms were isolated from 572 swine intestinal samples. All isolates were identified as Campylobacter coli by sequence analysis of 16S rRNA gene and polymerase chain reactions with primers specific to hippuricase gene in Campylobacter jejuni and aspartokinase gene in C. coli. Minimal inhibitory concentrations (MICs) of erythromycin were determined by using the agar dilution method, and 80 isolates were found to be resistant to erythromycin (MIC ≥ 4 μg/ml). Of these, 31 isolates had low-level resistance (MIC =4-16 μg/ml), and 49 isolates had high-level resistance (HLR, MIC ≥ 32 μg/ml). The HLR isolates carried a point mutation at position A2075 → G in domain V of the 23S rRNA gene, whereas the low-level resistance isolates carried no mutation. These 49 HLR isolates were characterized by pulsed-field gel electrophoresis and multilocus sequence typing to study their genetic diversity. Pulsed-field gel electrophoresis identified 16 distinct types with 50% genetic similarity as the cutoff. On the other hand, 28 different sequence types (STs), including 10 new STs, were identified with multilocus sequence typing. Forty-six of 49 erythromycin HLR isolates showed crossresistance to 6 macrolide derivatives. The correlation between the inhibitory activity of carbonyl cyanide m-chlorophenylhydrazone and the existence of cmeB, which is responsible for efflux in HLR isolates, was found to be low. Erythromycin resistance was transferred from 38 of the 43 HLR isolates to susceptible C. coli by natural transformation, with a frequency of 1.217 x 10(-8)-4.618 x 10(-5) per recipient cell. All transformants were erythromycin resistant and had A2075 → G mutation in at least one of three copies of the 23S rRNA gene. Results indicate that variable genotypes of HLR C. coli coexist in swine and high-level erythromycin resistance can be transferred to other strains.

Contribution of the multidrug efflux transporter CmeABC to antibiotic resistance in different Campylobacter species

CmeABC, a multidrug efflux system in Campylobacter jejuni, plays an important role in the resistance to different antimicrobials and toxic compounds. Although this efflux system has been well characterized in C. jejuni and to a less extent in C. coli, it is unknown if CmeABC homologs are functional in other Campylobacter spp. In this study, the cmeABC homologs were identified and functionally characterized in five Campylobacter species including C. jejuni, C. coli, C. lari, C. upsaliensis, and C. fetus. Our results indicated that cmeABC is present in all five Campylobacter spp. and the genomic organization of this efflux operon is similar among the Campylobacter spp. Insertional mutagenesis of cmeB increased the susceptibilities of all the five Campylobacter spp. to structurally diverse antimicrobials. Together, these results indicated that the CmeABC efflux system is conserved at both the genomic and functional levels in all five Campylobacter spp. examined in this study, further highlighting the significant role of CmeABC in Campylobacter pathobiology.

Efflux-mediated drug resistance in bacteria: an update

Drug efflux pumps play a key role in drug resistance and also serve other functions in bacteria. There has been a growing list of multidrug and drug-specific efflux pumps characterized from bacteria of human, animal, plant and environmental origins. These pumps are mostly encoded on the chromosome, although they can also be plasmid-encoded. A previous article in this journal provided a comprehensive review regarding efflux-mediated drug resistance in bacteria. In the past 5 years, significant progress has been achieved in further understanding of drug resistance-related efflux transporters and this review focuses on the latest studies in this field since 2003. This has been demonstrated in multiple aspects that include but are not limited to: further molecular and biochemical characterization of the known drug efflux pumps and identification of novel drug efflux pumps; structural elucidation of the transport mechanisms of drug transporters; regulatory mechanisms of drug efflux pumps; determining the role of the drug efflux pumps in other functions such as stress responses, virulence and cell communication; and development of efflux pump inhibitors. Overall, the multifaceted implications of drug efflux transporters warrant novel strategies to combat multidrug resistance in bacteria.

Effect of putative efflux pump inhibitors and inducers on the antimicrobial susceptibility of Campylobacter jejuni and Campylobacter coli

The CmeABC efflux pump plays an important role in the antimicrobial resistance of Campylobacter jejuni and Campylobacter coli. The aim of this investigation was to study the effect of putative efflux pump inhibitors, phenyl-arginine-beta-naphthylamide (PAbetaN) and 1-(1-naphthylmethyl)-piperazine (NMP), as well as the effect of putative efflux pump inducers, sodium salicylate and sodium deoxycholate, on the MIC levels of erythromycin, ciprofloxacin, kanamycin, tetracycline and rifampicin for C. jejuni and C. coli. Our results indicated that susceptibility to erythromycin and rifampicin increased, respectively, 8- to 32- and 8- to 64-fold in the presence of PAbetaN and to a lesser extent in the presence of NMP. Salicylate produced a 2- to 4-fold increase in ciprofloxacin MIC values, whereas little effect was observed in the presence of deoxycholate.

Sequence variation in the outer membrane protein-encoding gene cmeC, conferring multidrug resistance among Campylobacter jejuni and Campylobacter coli strains isolated from different hosts

A novel PCR primer pair was used to detect the presence of cmeC in 131 Campylobacter jejuni and C. coli strains isolated from various hosts (cattle, turkeys, humans, and pigs). DNA sequence analysis revealed a high degree of genetic variation between the two species, while extremely limited genetic variation among isolates of the same species was detected.

Antibiotic-resistant Campylobacter: could efflux pump inhibitors control infection?

Campylobacter is the most common cause of bacterial gastroenteritis in the world. Poultry is the main reservoir of human infections. The widespread use of antibiotics in agriculture and veterinary medicine has resulted in the emergence of an increasing number of antibiotic-resistant Campylobacter strains that can be transmitted to humans through the food chain. Of particular concern to public health is the prevalence of resistance to macrolides and fluoroquinolones that are used in the treatment of life-threatening campylobacteriosis. The CmeABC efflux system has been shown to contribute to the intrinsic and acquired resistance to these antibiotics. In addition, by mediating resistance to bile, it is essential for colonization of the chicken gut in vivo. Inhibition of CmeABC may provide an effective means of reversing antibiotic resistance and decreasing the transmission of Campylobacter via the food chain. This would positively impact on public health by decreasing the morbidity, mortality and increased healthcare costs associated with the treatment of antibiotic-resistant Campylobacter.

Mechanisms of fluoroquinolone and macrolide resistance in Campylobacter spp

The incidence of human Campylobacter infections is increasing worldwide, as well as the proportion of isolates resistant to fluoroquinolones and/or macrolides, the drugs of choice to treat campylobacteriosis. In this review, we report recent developments in the understanding of the resistance mechanisms to fluoroquinolones and macrolides. In addition, we will discuss the recent findings on multidrug resistance in Campylobacter spp.