Complete Genome Sequences of Multidrug-Resistant Campylobacter jejuni Strain 14980A (Turkey Feces) and Campylobacter coli Strain 14983A (Housefly from a Turkey Farm), Harboring a Novel Gentamicin Resistance Mobile Element

Genomic Analysis Points to Multiple Genetic Mechanisms for Non-Transformable Campylobacter jejuni ST-50

Campylobacter jejuni and Campylobacter coli are well known for their natural competence, i.e., their capacity for the uptake of naked DNA with subsequent transformation. This study identifies non-transformable C. jejuni and C. coli strains from domestic animals and employs genomic analysis to investigate the strain genotypes and their associated genetic mechanisms. The results reveal genetic associations leading to a non-transformable state, including functional DNase genes from bacteriophages and mutations within the cts-encoded DNA-uptake system, which impact the initial steps of the DNA uptake during natural transformation. Interestingly, all 38 tested C. jejuni ST-50 strains from the United States exhibit a high prevalence of non-transformability, and the strains harbor a variety of these genetic markers. This research emphasizes the role of these genetic markers in hindering the transfer of antimicrobial resistance (AMR) determinants, providing valuable insights into the genetic diversity of Campylobacter. As ST-50 is a major clone of C. jejuni globally, we additionally determined the prevalence of the genetic markers for non-transformability among C. jejuni ST-50 from different regions of the world, revealing distinct patterns of evolution and a strong selective pressure on the loss of competence in ST-50 strains, particularly in the agricultural environment in the United States. Our findings contribute to a comprehensive understanding of genetic exchange mechanisms within Campylobacter strains, and their implications for antimicrobial resistance dissemination and evolutionary pathways within specific lineages.

Campylobacter jejuni and Campylobacter coli from Houseflies in Commercial Turkey Farms Are Frequently Resistant to Multiple Antimicrobials and Exhibit Pronounced Genotypic Diversity

Campylobacter is a leading foodborne pathogen, and poultry are a major vehicle for infection. Houseflies play important roles in colonization of broiler flocks with Campylobacter but comparable information for turkey farms is limited. Here, we investigated houseflies as potential vectors for Campylobacter in 28 commercial turkey flocks. We characterized species, genotypes, and the antimicrobial resistance (AMR) profiles of Campylobacter from turkey feces and houseflies in the same turkey house. Of the 28 flocks, 25 yielded Campylobacter from turkey droppings and houseflies, with an average of 6.25 and 3.11 Campylobacter log CFU/g feces and log CFU/fly, respectively. Three flocks were negative for Campylobacter both in turkey feces and in houseflies. Both C. coli and C. jejuni were detected in turkey feces and houseflies, with C. coli more likely to be recovered from houseflies than feces. Determination of Campylobacter species, genotypes, and AMR profiles revealed up to six different strains in houseflies from a single house, including multidrug-resistant strains. For the predominant strain types, presence in houseflies was predictive of presence in feces, and vice versa. These findings suggest that houseflies may serve as vehicles for dissemination of Campylobacter, including multidrug-resistant strains, within a turkey house, and potentially between different turkey houses and farms in the same region.

Differences in the Propensity of Different Antimicrobial Resistance Determinants to Be Disseminated via Transformation in Campylobacter jejuni and Campylobacter coli

Campylobacter jejuni and Campylobacter coli are leading zoonotic foodborne pathogens, and the drugs of choice for human campylobacteriosis are macrolides (e.g., erythromycin) and fluoroquinolones. C. jejuni and C. coli are naturally competent for transformation via naked DNA uptake, but potential differences in transformation frequency (TF) for different antimicrobial resistance (AMR) markers remain poorly understood. We determined TFs for resistance to different antibiotics using as recipient a derivative of C. jejuni NCTC 11168 (strain SN:CM) with donor DNA from multidrug-resistant C. jejuni or C. coli. TF for nalidixic acid resistance ranked significantly highest (~1.4 × 10⁻³), followed by resistance to streptomycin and gentamicin. Tetracycline resistance via chromosomal tet(O) was less commonly transferred (~7.6 × 10⁻⁷), while transformation to erythromycin resistance was rare (≤4.7 × 10⁻⁸). We also determined TFs with the contemporary poultry-derived strains C. jejuni FSIS 11810577 and C. coli FSIS 1710488 as recipients. TFs to nalidixic acid and streptomycin resistance remained the highest (~7 × 10⁻⁴). However, TF for gentamicin resistance was remarkably low in certain recipient–donor combinations, while average TF for erythromycin resistance was noticeably higher (~3 × 10⁻⁶) than with SN:CM. Findings from this experimental model provide insights into factors that may impact transformation-mediated transfer of AMR leading to AMR dissemination in the agricultural ecosystem.

Search for Campylobacter spp. Reveals High Prevalence and Pronounced Genetic Diversity of Arcobacter butzleri in Floodwater Samples Associated with Hurricane Florence in North Carolina, USA

Climate change and associated extreme weather events can have massive impacts on the prevalence of microbial pathogens in floodwaters. However, limited data are available on foodborne zoonotic pathogens such as Campylobacter or Arcobacter in hurricane-associated floodwaters in rural regions with intensive animal production. With a high density of intensive animal production as well as pronounced vulnerability to hurricanes, eastern North Carolina presents unique opportunities in this regard. Our findings revealed widespread incidence of the emerging zoonotic pathogen Arcobacter butzleri in floodwaters from Hurricane Florence. We encountered high and largely unexplored diversity while also noting the potential for regionally abundant and persistent clones. We noted pronounced partitioning of the floodwater genotypes into two source-associated clades. The data will contribute to elucidating the poorly understood ecology of this emerging pathogen and highlight the importance of surveillance of floodwaters associated with hurricanes and other extreme weather events for Arcobacter and other zoonotic pathogens.

In September 2018, Hurricane Florence caused extreme flooding in eastern North Carolina, USA, a region highly dense in concentrated animal production, especially swine and poultry. In this study, floodwater samples (n = 96) were collected as promptly post-hurricane as possible and for up to approximately 30 days and selectively enriched for Campylobacter using Bolton broth enrichment and isolation on modified charcoal cefoperazone deoxycholate agar (mCCDA) microaerobically at 42°C. Only one sample yielded Campylobacter, which was found to be Campylobacter jejuni with the novel sequence type 2866 (ST-2866). However, the methods employed to isolate Campylobacter readily yielded Arcobacter from 73.5% of the floodwater samples. The Arcobacter isolates failed to grow on Mueller-Hinton agar at 25, 30, 37, or 42°C microaerobically or aerobically but could be readily subcultured on mCCDA at 42°C microaerobically. Multilocus sequence typing of 112 isolates indicated that all were Arcobacter butzleri. The majority (85.7%) of the isolates exhibited novel sequence types (STs), with 66 novel STs identified. Several STs, including certain novel ones, were detected in diverse waterbody types (channel, isolated ephemeral pools, floodplain) and from multiple watersheds, suggesting the potential for regionally dominant strains. The genotypes were clearly partitioned into two major clades, one with high representation of human and ruminant isolates and another with an abundance of swine and poultry isolates. Surveillance of environmental waters and food animal production systems in this animal agriculture-dense region is needed to assess potential regional prevalence and temporal stability of the observed A. butzleri strains as well as their potential association with specific types of food animal production.

IMPORTANCE Climate change and associated extreme weather events can have massive impacts on the prevalence of microbial pathogens in floodwaters. However, limited data are available on foodborne zoonotic pathogens such as Campylobacter or Arcobacter in hurricane-associated floodwaters in rural regions with intensive animal production. With a high density of intensive animal production as well as pronounced vulnerability to hurricanes, eastern North Carolina presents unique opportunities in this regard. Our findings revealed widespread incidence of the emerging zoonotic pathogen Arcobacter butzleri in floodwaters from Hurricane Florence. We encountered high and largely unexplored diversity while also noting the potential for regionally abundant and persistent clones. We noted pronounced partitioning of the floodwater genotypes into two source-associated clades. The data will contribute to elucidating the poorly understood ecology of this emerging pathogen and highlight the importance of surveillance of floodwaters associated with hurricanes and other extreme weather events for Arcobacter and other zoonotic pathogens.

Prediction of antimicrobial resistance in clinical Campylobacter jejuni isolates from whole-genome sequencing data

Campylobacter jejuni is recognised as the leading cause of bacterial gastroenteritis in industrialised countries. Although the majority of Campylobacter infections are self-limiting, antimicrobial treatment is necessary in severe cases. Therefore, the development of antimicrobial resistance (AMR) in Campylobacter is a growing public health challenge and surveillance of AMR is important for bacterial disease control. The aim of this study was to predict antimicrobial resistance in C. jejuni from whole-genome sequencing data. A total of 516 clinical C. jejuni isolates collected between 2014 and 2017 were subjected to WGS. Resistance phenotypes were determined by standard broth dilution, categorising isolates as either susceptible or resistant based on epidemiological cutoffs for six antimicrobials: ciprofloxacin, nalidixic acid, erythromycin, gentamicin, streptomycin, and tetracycline. Resistance genotypes were identified using an in-house database containing reference genes with known point mutations and the presence of resistance genes was determined using the ResFinder database and four bioinformatical methods (modified KMA, ABRicate, ARIBA, and ResFinder Batch Upload). We identified seven resistance genes including tet(O), tet(O/32/O), ant(6)-Ia, aph(2″)-If, blaOXA, aph(3')-III, and cat as well as mutations in three genes: gyrA, 23S rRNA, and rpsL. There was a high correlation between phenotypic resistance and the presence of known resistance genes and/or point mutations. A correlation above 98% was seen for all antimicrobials except streptomycin with a correlation of 92%. In conclusion, we found that WGS can predict antimicrobial resistance with a high degree of accuracy and have the potential to be a powerful tool for AMR surveillance.

Molecular characterization of megaplasmids encoding the type VI secretion system in Campylobacter jejuni isolated from chicken livers and gizzards

Megaplasmids in Campylobacter spp. likely play important roles in antibiotic resistance, virulence, and horizontal gene transfer. In this study, megaplasmids pCJDM202 (119 kb) and pCJDM67L (116 kb) from C. jejuni strains WP2-202 and OD2-67, respectively, were sequenced and characterized. These megaplasmids contained genes for tetracycline resistance [tet(O)], the Type IV secretion system, conjugative transfer and the Type VI secretion system (T6SS). The T6SS genes in Campylobacter plasmids encoded genes and proteins that were similar to those identified in Campylobacter chromosomal DNA. When the megaplasmid pCJDM202 from C. jejuni WP2-202 was transferred via conjugation to C. jejuni NCTC11168 Nal⁺, transconconjugants acquired tetracycline resistance and enhanced cytotoxicity towards red blood cells. A T6SS mutant of strain WP2-202 was generated and designated Δhcp3; the mutant was significantly impaired in its ability to lyse red blood cells and survive in defibrinated blood. The cytotoxicity of Campylobacter strains towards the human embryonic kidney cell line HEK 293 was not impacted by the T6SS. In summary, the T6SS encoded by Campylobacter megaplasmids mediates lysis of RBCs and likely contributes to survival on retail meats where blood cells are abundant.

Complete Genome Sequencing of Four Arcobacter Species Reveals a Diverse Suite of Mobile Elements

Arcobacter species are recovered from a wide variety of sources, including animals, food, and both fresh and marine waters. Several Arcobacter species have also been recovered from human clinical samples and are thus associated tentatively with food- and water-borne human illnesses. Genome sequencing of the poultry isolate Arcobacter cibarius H743 and the Arcobacter acticola, Arcobacter pacificus, and Arcobacter porcinus type strains identified a large number and variety of insertion sequences. This study presents an analysis of these A. acticola, A. cibarius, A. pacificus, and A. porcinus IS elements. The four genomes sequenced here contain 276 complete and degenerate IS elements, representing 13 of the current 29 prokaryotic IS element families. Expansion of the analysis to include 15 other previously sequenced Arcobacter spp. added 73 complete and degenerate IS elements. Several of these IS elements were identified in two or more Arcobacter species, suggesting movement by horizontal gene transfer between the arcobacters. These IS elements are putatively associated with intragenomic deletions and inversions, and tentative movement of antimicrobial resistance genes. The A. cibarius strain H743 megaplasmid contains multiple IS elements common to the chromosome and, unusually, a complete ribosomal RNA locus, indicating that larger scale genomic rearrangements, potentially resulting from IS element-mediated megaplasmid cointegration and resolution may be occurring within A. cibarius and possibly other arcobacters. The presence of such a large and varied suite of mobile elements could have profound effects on Arcobacter biology and evolution.

Phylogenetic Relatedness Among Plasmids Harbored by Campylobacter jejuni and Campylobacter coli Isolated From Retail Meats

Campylobacter jejuni and Campylobacter coli are two of the major causes of foodborne illness. In this study, 29 plasmids isolated from 20 retail meat isolates of Campylobacter jejuni and Campylobacter coli were fully-sequenced individually or as a part of a whole genome sequencing approach. The fully-sequenced plasmids ranged in size from 3 to 119 kb. Molecular characterization of the sequenced plasmids was based on pangenomic analysis and types of genes present on these plasmids and similar ones from GenBank. The plasmids were categorized into four different groups. These groups include type-1 that consisted mainly of pTet plasmids with the tetO gene, type-2 plasmids commonly found in C. coli strains, type-3 which has pVir plasmids, and type-4 that consisted mainly of smaller plasmids. The type-2 plasmids were unique, common among C. coli strains, and carried several conjugative transfer genes. The type-2 plasmids were most similar to a plasmid from Helicobacter pullorum. Maximum parsimony analysis and NeighborNet analysis were used to assess the phylogenetic relatedness among the 29 plasmid sequences presented in this study in addition to the other 104 plasmid sequences of Campylobacter species available in GenBank to date. Results from MP analysis revealed multiple lineages among Campylobacter plasmids which was supported by NeighborNet analysis. Clustering of plasmids did not conform to species-specific clades which suggested an intra-species dissemination of plasmids among Campylobacter species. To our knowledge, this is the first extensive phylogenetic analysis of Campylobacter plasmids sequenced to date.

Lack of Evidence for erm(B) Infiltration Into Erythromycin-Resistant Campylobacter coli and Campylobacter jejuni from Commercial Turkey Production in Eastern North Carolina: A Major Turkey-Growing Region in the United States

In Campylobacter spp., resistance to erythromycin and other macrolides has typically implicated ribosomal mutations, especially substitutions in the 23S rRNA genes. However, in 2014, the macrolide resistance gene erm(B) was reported for the first time in Campylobacter and shown to be harbored by a multidrug resistance island in the chromosome of the swine-derived strain Campylobacter coli ZC113. erm(B)-positive C. coli and Campylobacter jejuni strains from the food supply have been mostly reported from China. However, erm(B)-positive C. coli isolates were also detected recently in fecal samples from turkeys in Spain. To determine whether erm(B) may be harbored by erythromycin-resistant Campylobacter from commercial turkey production in eastern North Carolina, a major turkey-growing region in the United States, we investigated a panel of 178 erythromycin-resistant isolates (174 C. coli, 4 C. jejuni) using PCR with erm(B)-specific primers. None of the isolates were PCR-positive for erm(B) and sequence analysis of a subset of these erythromycin-resistant isolates revealed that all harbored A2075G substitutions in the 23S rRNA genes. Data fail to provide evidence for infiltration of erm(B) into erythromycin-resistant Campylobacter from commercial turkey production in this region and suggest the need for continuing surveillance.

Next generation microbiological risk assessment: opportunities of whole genome sequencing (WGS) for foodborne pathogen surveillance, source tracking and risk assessment

Whole genome sequencing (WGS) of important foodborne pathogens is a technology under development, but is already employed in routine surveillance by public health agencies and is being increasingly exploited in tracing transmission routes and identifying contamination events (source tracking) that take place in the farm-to-fork continuum. Furthermore, data generated from WGS, complemented by other -omics data, have the potential to be integrated into and strengthen microbiological risk assessment. In this paper, we discuss the contribution of WGS in diverse areas important to food safety and public health. Additionally, an outlook of future WGS applications, which should contribute to our understanding of the ecology and physiology of foodborne microorganisms, is presented.

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

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

Whole genome sequencing and analysis of Campylobacter coli YH502 from retail chicken reveals a plasmid-borne type VI secretion system

Campylobacter is a major cause of foodborne illnesses worldwide. Campylobacter infections, commonly caused by ingestion of undercooked poultry and meat products, can lead to gastroenteritis and chronic reactive arthritis in humans. Whole genome sequencing (WGS) is a powerful technology that provides comprehensive genetic information about bacteria and is increasingly being applied to study foodborne pathogens: e.g., evolution, epidemiology/outbreak investigation, and detection. Herein we report the complete genome sequence of Campylobacter coli strain YH502 isolated from retail chicken in the United States. WGS, de novo assembly, and annotation of the genome revealed a chromosome of 1,718,974 bp and a mega-plasmid (pCOS502) of 125,964 bp. GC content of the genome was 31.2% with 1931 coding sequences and 53 non-coding RNAs. Multiple virulence factors including a plasmid-borne type VI secretion system and antimicrobial resistance genes (beta-lactams, fluoroquinolones, and aminoglycoside) were found. The presence of T6SS in a mobile genetic element (plasmid) suggests plausible horizontal transfer of these virulence genes to other organisms. The C. coli YH502 genome also harbors CRISPR sequences and associated proteins. Phylogenetic analysis based on average nucleotide identity and single nucleotide polymorphisms identified closely related C. coli genomes available in the NCBI database. Taken together, the analyzed genomic data of this potentially virulent strain of C. coli will facilitate further understanding of this important foodborne pathogen most likely leading to better control strategies. The chromosome and plasmid sequences of C. coli YH502 have been deposited in GenBank under the accession numbers CP018900.1 and CP018901.1, respectively.