The evidence for clonal spreading of quinolone resistance with a particular clonal complex of Campylobacter jejuni

Antimicrobial consumption and resistance in bacteria from humans and food-producing animals: Fourth joint inter-agency report on integrated analysis of antimicrobial agent consumption and occurrence of antimicrobial resistance in bacteria from humans and food-producing animals in the EU/EEA JIACRA IV - 2019-2021

The fourth joint inter-agency report on integrated analysis of antimicrobial consumption (AMC) and the occurrence of antimicrobial resistance (AMR) in bacteria from humans and food-producing animals (JIACRA) addressed data obtained by the Agencies' EU-wide surveillance networks for 2019-2021. The analysis also sought to identify whether significant trends in AMR and AMC were concomitant over 2014-2021. AMC in both human and animal sectors, expressed in mg/kg of estimated biomass, was compared at country and European level. In 2021, the total AMC was assessed at 125.0 mg/kg of biomass for humans (28 EU/EEA countries, range 44.3-160.1) and 92.6 mg/kg of biomass for food-producing animals (29 EU/EEA countries, range 2.5-296.5). Between 2014 and 2021, total AMC in food-producing animals decreased by 44%, while in humans, it remained relatively stable. Univariate and multivariate analyses were performed to study associations between AMC and AMR for selected combinations of bacteria and antimicrobials. Positive associations between consumption of certain antimicrobials and resistance to those substances in bacteria from both humans and food-producing animals were observed. For certain combinations of bacteria and antimicrobials, AMR in bacteria from humans was associated with AMR in bacteria from food-producing animals which, in turn, was related to AMC in animals. The relative strength of these associations differed markedly between antimicrobial class, microorganism and sector. For certain antimicrobials, statistically significant decreasing trends in AMC and AMR were concomitant for food-producing animals and humans in several countries over 2014-2021. Similarly, a proportion of countries that significantly reduced total AMC also registered increasing susceptibility to antimicrobials in indicator E. coli from food-producing animals and E. coli originating from human invasive infections (i.e., exhibited 'complete susceptibility' or 'zero resistance' to a harmonised set of antimicrobials). Overall, the findings suggest that measures implemented to reduce AMC in food-producing animals and in humans have been effective in many countries. Nevertheless, these measures need to be reinforced so that reductions in AMC are retained and further continued, where necessary. This also highlights the importance of measures that promote human and animal health, such as vaccination and better hygiene, thereby reducing the need for use of antimicrobials.

Prevalence of ciprofloxacin resistance and associated genetic determinants differed among Campylobacter isolated from human and poultry meat sources in Pennsylvania

Poultry is the primary source of Campylobacter infections and severe campylobacteriosis cases are treated with macrolides and fluoroquinolones. However, these drugs are less effective against antimicrobial-resistant strains. Here, we investigated the prevalence of phenotypic antimicrobial resistance and associated resistance genetic determinants in Campylobacter isolates collected from human clinical (N = 123) and meat (N = 80) sources in Pennsylvania in 2017 and 2018. Our goal was to assess potential differences in the prevalence of antimicrobial resistance in Campylobacter isolated from human and poultry meat sources in Pennsylvania and to assess the accuracy of predicting antimicrobial resistance phenotypes based on resistance genotypes. We whole genome sequenced isolates and identified genetic resistance determinants using the National Antimicrobial Resistance Monitoring System Campylobacter AMR workflow v2.0 in GalaxyTrakr. Phenotypic antimicrobial susceptibility testing was carried out using the E-Test and Sensititre CAMPYCMV methods for human clinical and poultry meat isolates, respectively, and the results were interpreted using the EUCAST epidemiological cutoff values. The 193 isolates were represented by 85 MLST sequence types and 23 clonal complexes, suggesting high genetic diversity. Resistance to erythromycin was confirmed in 6% human and 4% meat isolates. Prevalence of ciprofloxacin resistance was significantly higher in human isolates as compared to meat isolates. A good concordance was observed between phenotypic resistance and the presence of the corresponding known resistance genetic determinants.

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.

Increasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom

BACKGROUND

Campylobacter jejuni is the most common bacterial cause of human infectious intestinal disease.

METHODS

We genome sequenced 601 human C. jejuni isolates, obtained from two large prospective studies of infectious intestinal disease (IID1 [isolates from 1993-1996; n = 293] and IID2 [isolates from 2008-2009; n = 93]), the INTEGRATE project [isolates from 2016-2017; n = 52] and the ENIGMA project [isolates from 2017; n = 163].

RESULTS

There was a significant increase in the prevalence of the T86I mutation conferring resistance to fluoroquinolone between each of the three later studies (IID2, INTEGRATE and ENIGMA) and IID1. Although the distribution of major multilocus sequence types (STs) was similar between the studies, there were changes in both the abundance of minority STs associated with the T86I mutation, and the abundance of clones within single STs associated with the T86I mutation.

DISCUSSION

Four population-based studies of community diarrhoea over a 25 year period revealed an increase over time in the prevalence of the T86I amongst isolates of C. jejuni associated with human gastrointestinal disease in the UK. Although associated with many STs, much of the increase is due to the expansion of clones associated with the resistance mutation.

Antimicrobial resistance patterns and molecular resistance markers of Campylobacter jejuni isolates from human diarrheal cases

The aim of this study is to characterize the antimicrobial resistance of Campylobacter jejuni recovered from diarrheal patients in Belgium, focusing on the genetic diversity of resistant strains and underlying molecular mechanisms of resistance among Campylobacter jejuni resistant strains isolated from diarrheal patients in Belgium. Susceptibility profile of 199 clinical C. jejuni isolates was determined by minimum inhibitory concentrations against six commonly-used antibiotics (ciprofloxacin, nalidixic acid, tetracycline, streptomycin, gentamicin, and erythromycin). High rates of resistance were observed against nalidixic acid (56.3%), ciprofloxacin (55.8%) and tetracycline (49.7%); these rates were similar to those obtained from different national reports in broilers intended for human consumption. Alternatively, lower resistance rates to streptomycin (4.5%) and erythromycin (2%), and absolute sensitivity to gentamicin were observed. C. jejuni isolates resistant to tetracycline or quinolones (ciprofloxacin and/or nalidixic acid) were screened for the presence of the tetO gene and the C257T mutation in the quinolone resistance determining region (QRDR) of the gyrase gene gyrA, respectively. Interestingly, some of the isolates that displayed phenotypic resistance to these antimicrobials lacked the corresponding genetic determinants. Among erythromycin-resistant isolates, a diverse array of potential molecular resistance mechanisms was investigated, including the presence of ermB and mutations in the 23S rRNA gene, the rplD and rplV ribosomal genes, and the regulatory region of the cmeABC operon. Two of the four erythromycin-resistant isolates harboured the A2075G transition mutation in the 23S rRNA gene; one of these isolates exhibited further mutations in rplD, rplV and in the cmeABC regulatory region. This study expands the current understanding of how different genetic determinants and particular clones shape the epidemiology of antimicrobial resistance in C. jejuni in Belgium. It also reveals many questions in need of further investigation, such as the role of other undetermined molecular mechanisms that may potentially contribute to the antimicrobial resistance of Campylobacter.

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.

Overlap of Antibiotic Resistant Campylobacter jejuni MLST Genotypes Isolated From Humans, Broiler Products, Dairy Cattle and Wild Birds in Lithuania

Antimicrobial resistance was determined for 341 thermophilic Campylobacter jejuni isolates obtained from human clinical cases (n = 101), broiler products (n = 98), dairy cattle (n = 41) and wild birds (n = 101) with known multilocus sequence types (MLST) in Lithuania. The minimum inhibitory concentration (MIC) values for ciprofloxacin, tetracycline, gentamicin, ceftriaxone and erythromycin were determined with the agar dilution method. MIC values were compared with MLST types to find possible associations among isolation source, sequence type and resistance to antibiotics. The proportions of resistant strains were 94.2% (human), 95% (wild birds), 100% (broiler products) and 100% (dairy cattle) for one of the tested antibiotics. Most frequently, resistance to ciprofloxacin was observed (91.5%), followed by ceftriaxone with 60.4%, and tetracycline (37.8%). However only three C. jejuni strains were resistant to erythromycin (0.9%) and all tested thermophilic Campylobacter strains were sensitive to gentamicin. Most of the examined C. jejuni isolates (80.6%) showed resistance to at least one of three profiles: CIP+AXO (28.1%), TET+CIP+AXO (26.7%) and CIP (25.8%). Statistically significant differences in resistance to tetracycline were found between C. jejuni strains obtained from cattle (85.4%) and broiler products (64.3%) (P < 0.05). The majority (87.1%) of the tested strains from wild birds were resistant to ciprofloxacin (P < 0.05). The results showed that strains of novel ST's showed significantly lower resistance to ceftriaxone (P < 0.05). The ST-21 (CC21) (78.8%) was identified with significantly higher multidrug resistance relatively to other tested ST's in this study. Our results emphasize the high antimicrobial resistance of phylogenetically diverse C. jejuni strains isolated from different sources including specific genotypes of wild bird's strains in Lithuania. The results support the opinion that not only broiler products but cattle and wild birds may be a reservoir of resistant C. jejuni and stipulate a risk of spread or resistant bacteria. There is increasing need for broad surveillance and control measures to track changes and pathways of antimicrobial resistance of C. jejuni in epidemiologically distinct populations.

Antibiotic resistance, molecular characterizations, and clinical manifestations of Campylobacteriosis at a military medical center in Hawaii from 2012-2016: a retrospective analysis

Hawaii has one of the highest incidences of Campylobacteriosis in the United States, but there remains little published data on circulating strains or antimicrobial resistance. We characterized 110 clinical Campylobacter isolates (106 C. jejuni, 4 C. coli) processed at Tripler Army Medical Center in Honolulu, HI from 2012–2016. Twenty-five percent of C. jejuni isolates exhibited fluoroquinolone (FQ) resistance, compared with 16% for tetracycline (TET), and 0% for macrolides. Two of the four C. coli isolates were resistant to FQ, TET, and macrolides. C. jejuni isolates further underwent multilocus sequence typing, pulsed-field gel electrophoresis, and molecular capsular typing. Nineteen capsule types were observed, with two capsule types (HS2 and HS9) being associated with FQ resistance (p < 0.001 and p = 0.006, respectively). HS2 FQ-resistant isolates associated with clonal complex 21, possibly indicating clonal spread in FQ resistance. Macrolides should be considered for treatment of suspect cases due to lack of observed resistance.

Genetic Basis and Clonal Population Structure of Antibiotic Resistance in Campylobacter jejuni Isolated From Broiler Carcasses in Belgium

Human campylobacteriosis is the leading food-borne zoonosis in industrialized countries. This study characterized the clonal population structure, antimicrobial resistance profiles and occurrence of antimicrobial resistance determinants of a set of Campylobacter jejuni strains isolated from broiler carcasses in Belgium. Minimum inhibitory concentrations (MICs) against five commonly-used antibiotics (ciprofloxacin, nalidixic acid, tetracycline, gentamicin, and erythromycin) were determined for 204 C. jejuni isolates. More than half of the isolates were resistant to ciprofloxacin or nalidixic acid. In contrast, a lower percentage of screened isolates were resistant to gentamicin or erythromycin. C. jejuni isolates resistant to ciprofloxacin and/or nalidixic acid were screened for the substitution T86I in the quinolone resistance determining region (QRDR) of the gyrA gene, while C. jejuni isolates resistant to tetracycline were screened for the presence of the tet(O) gene. These resistance determinants were observed in most but not all resistant isolates. Regarding resistance to erythromycin, different mutations occurred in diverse genetic loci, including mutations in the 23S rRNA gene, the rplD and rplV ribosomal genes, and the intergenic region between cmeR and cmeABC. Interestingly, and contrary to previous reports, the A2075G transition mutation in the 23S rRNA gene was only found in one strain displaying a high level of resistance to erythromycin. Ultimately, molecular typing by multilocus sequence typing revealed that two sequence types (ST-824 and ST-2274) were associated to quinolones resistance by the presence of mutations in the gene gyrA (p = 0.01). In addition, ST-2274 was linked to the CIP-NAL-TET-AMR multidrug resistant phenotype. In contrast, clonal complex CC-45 was linked to increased susceptibility to the tested antibiotics. The results obtained in this study provide better understanding of the phenotypic and the molecular basis of antibiotic resistance in C. jejuni, unraveling some the mechanisms which confer antimicrobial resistance and particular clones associated to the carriage and spread of resistance genes.

Population structure and attribution of human clinical Campylobacter jejuni isolates from central Europe to livestock and environmental sources

Campylobacter jejuni is among the most prevalent causes of human bacterial gastroenteritis worldwide. Domesticated animals and, especially, chicken meat are considered to be the main sources of infections. However, the contribution of surface waters and wildlife in C. jejuni transmission to humans is not well understood. We have evaluated the source attribution potential of a six-gene multiplex PCR (mPCR) method coupled with STRUCTURE analysis on a set of 410 C. jejuni strains isolated from environment, livestock, food and humans in central Europe. Multiplex PCR fingerprints were analysed using Subclade prediction algorithm to classify them into six distinct mPCR clades. A subset of C. jejuni isolates (70%) was characterized by multilocus sequence typing (MLST) demonstrating 74% congruence between mPCR and MLST. The correspondence analysis of mPCR clades and sources of isolation indicated three distinct groups in the studied C. jejuni population-the first one associated with isolates from poultry, the second one with isolates from cattle, and the third one with isolates from the environment. The STRUCTURE analysis attributed 7.2% and 21.7% of human isolates to environmental sources based on MLST and mPCR fingerprints, respectively.

Antimicrobial Susceptibility Profiles of Human Campylobacter jejuni Isolates and Association with Phylogenetic Lineages

Campylobacter jejuni is a zoonotic pathogen and the most common bacterial cause of human gastroenteritis worldwide. With the increase of antibiotic resistance to fluoroquinolones and macrolides, the drugs of choice for treatment, C. jejuni was recently classified as a serious antimicrobial resistant threat. Here, we characterized 94 C. jejuni isolates collected from patients at four Michigan hospitals in 2011 and 2012 to determine the frequency of resistance and association with phylogenetic lineages. The prevalence of resistance to fluoroquinolones (19.1%) and macrolides (2.1%) in this subset of C. jejuni isolates from Michigan was similar to national reports. High frequencies of fluoroquinolone-resistant C. jejuni isolates, however, were recovered from patients with a history of foreign travel. A high proportion of these resistant isolates were classified as multilocus sequence type (ST)-464, a fluoroquinolone-resistant lineage that recently emerged in Europe. A significantly higher prevalence of tetracycline-resistant C. jejuni was also found in Michigan and resistant isolates were more likely to represent ST-982, which has been previously recovered from ruminants and the environment in the U.S. Notably, patients with tetracycline-resistant C. jejuni infections were more likely to have contact with cattle. These outcomes prompt the need to monitor the dissemination and diversification of imported fluoroquinolone-resistant C. jejuni strains and to investigate the molecular epidemiology of C. jejuni recovered from cattle and farm environments to guide mitigation strategies.

Epidemiology of Campylobacter jejuni infections in Sweden, November 2011-October 2012: is the severity of infection associated with C. jejuni sequence type?

BACKGROUND

Campylobacter jejuni is among the most frequent causes of bacterial gastroenteritis in Europe. Over 8,000 C. jejuni multilocus sequence typing sequence types (STs) have been described; ST-21 and ST-45 have been identified as the most frequent types in all human studies so far. In contrast to other STs, ST-22 has been associated with the Guillain-Barré syndrome and ST-677 was recently linked to severe systemic infections in Finland. We investigated risk factors associated with hospitalisation in individuals with C. jejuni infections acquired in Sweden.

METHODS

A total of 1,075 individuals with domestically acquired C. jejuni infection diagnosed between November 2011 and October 2012 in Sweden were included in this retrospective cohort study. Typing data for the isolates as well as clinical data including hospitalisation dates and diagnosis codes for individuals with C. jejuni infection were obtained. Factors associated with hospitalisation and length of hospitalisation were investigated by multivariable analysis.

RESULTS

A total of 289 individuals were hospitalised due to C. jejuni infection (26.8%); those with co-morbidities were over 14 times more likely to become hospitalised than those without (odds ratio [OR]: 14.39, 95% confidence interval [CI]: 6.84-30.26). Those with underlying co-morbidities were also hospitalised longer than those without (4.22 days vs. 2.86 days), although this was not statistically significant. C. jejuni ST-257 (OR: 2.38; CI: 1.08-5.23), but not ST-22 or ST-677, was significantly associated with hospitalisation.

CONCLUSION

ST-677 was not associated with increased hospitalisation or a longer hospital stay in our study whilst ST-257 was. However, individuals with C. jejuni infections were generally more frequently hospitalised than previously demonstrated; this requires further consideration including possible targeted interventions.

High genetic similarity of ciprofloxacin-resistant Campylobacter jejuni in central Europe

Campylobacteriosis is the leading zoonosis in the European Union with the majority of cases attributed to Campylobacter jejuni. Although the disease is usually self-limiting, some severe cases need to be treated with antibiotics, primarily macrolides and quinolones. However, the resistance to the latter is reaching alarming levels in most of the EU countries. To shed light on the expansion of antibiotic resistance in central Europe, we have investigated genetic similarity across 178 ciprofloxacin-resistant C. jejuni mostly isolated in Slovenia, Austria and Germany. We performed comparative genetic similarity analyses using allelic types of seven multilocus sequence typing housekeeping genes, and single nucleotide polymorphisms of a quinolone resistance determining region located within the DNA gyrase subunit A gene. This analysis revealed high genetic similarity of isolates from clonal complex ST-21 that carry gyrA allelic type 1 in all three of these central-European countries, suggesting these ciprofloxacin resistant isolates arose from a recent common ancestor and are spread clonally.

Antibiotic resistance modulation and modes of action of (-)-α-pinene in Campylobacter jejuni

The aim of the study was to investigate the mode of action of (-)-α-pinene in terms of its modulation of antibiotic resistance in Campylobacter jejuni. Broth microdilution and ethidium bromide accumulation assays were used to evaluate the (-)-α-pinene antimicrobial activity, modulation of antimicrobial resistance, and inhibition of antimicrobial efflux. The target antimicrobial efflux systems were identified using an insertion mutagenesis approach, and C. jejuni adaptation to (-)-α-pinene was evaluated using DNA microarrays. Knock-out mutants of the key up-regulated transcriptional regulators hspR and hrcA were constructed to investigate their roles in C. jejuni adaptation to several stress factors, including osmolytes, and pH, using Biolog phenotypical microarrays. Our data demonstrate that (-)-α-pinene efficiently modulates antibiotic resistance in C. jejuni by decreasing the minimum inhibitory concentrations of ciprofloxacin, erythromycin and triclosan by up to 512-fold. Furthermore, (-)-α-pinene promotes increased expression of cmeABC and another putative antimicrobial efflux gene, Cj1687. The ethidium bromide accumulation was greater in the wild-type strain than in the antimicrobial efflux mutant strains, which indicates that these antimicrobial efflux systems are a target of action of (-)-α-pinene. Additionally, (-)-α-pinene decreases membrane integrity, which suggests that enhanced microbial influx is a secondary mode of action of (-)-α-pinene. Transcriptomic analysis indicated that (-)-α-pinene disrupts multiple metabolic pathways, and particularly those involved in heat-shock responses. Thus, (-)-α-pinene has significant activity in the modulation of antibiotic resistance in C. jejuni, which appears to be mediated by multiple mechanisms that include inhibition of microbial efflux, decreased membrane integrity, and metabolic disruption. These data warrant further studies on (-)-α-pinene to develop its use in the control of antibiotic resistance in Campylobacter.