Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania

Genomic Surveillance of Foodborne Pathogens: Advances and Obstacles

CONTEXT

The genomic surveillance of foodborne pathogens in the United States has grown exponentially in the past decade, grounded in a powerful combination of novel sequencing technologies, bioinformatic approaches, data-sharing networks, and metadata harmonization efforts. This practice report examines recent advances in genomic epidemiology as applied to food safety programs and delineates State, Tribal, Local, and Territorial infrastructure necessary for continued life-saving improvements in public health.

PROGRAM

National databases of foodborne pathogen genomes, along with data sharing and evaluation networks such as GenomeTrakr and PulseNet, have transformed how connections are made among isolates and how root causes of outbreaks are determined, allowing much more timely interventions to protect public health. Freely available bioinformatics tools such as GalaxyTrakr and the National Center for Biotechnology Information Pathogen Detection database have allowed laboratories with limited local computing resources to participate in surveillance efforts and contribute to traceback investigations.

IMPLEMENTATION

In this report, we describe advances in genomic epidemiology that have occurred over the past decade and examine obstacles to fully implementing this technology within State, Tribal, Local, and Territorial public health systems.

EVALUATION

Despite a clear return on investment from governmental expenditures on genomic surveillance of foodborne pathogens, we identify significant obstacles to further sustained progress. These obstacles include workforce gaps, ineffective data sharing, and lack of constitutive and sustained funding.

DISCUSSION

Many public health laboratories face major obstacles to widespread and routine adoption of genomic surveillance technologies. While whole genome sequencing has become an integral part of routine public health microbiology, the seamless integration of these protocols into the existing practices, laboratory workflows, and information systems remains challenging. Centralized efforts to address these issues include (1) support through the Food and Drug Administration Laboratory Flexible Funding Model, (2) training and proficiency assessments, (3) open-source, standardized protocols for collecting high-quality genomic data, and (4) open access informatics software.

Salmonella enterica serovar Braenderup shows clade-specific source associations and a high proportion of molecular epidemiological clustering

Salmonella enterica serovar Braenderup (S. enterica ser. Braenderup) is an important clinical serovar in the United States. This serovar was reported by the CDC in 2017 as the fifth most common Salmonella enterica serovar associated with outbreaks in the United States, which have been linked to both fresh produce and food animal products. The goals of this study were to compare the relatedness of human clinical isolates from southeastern USA (Tennessee (n = 106), Kentucky (n = 48), Virginia (n = 252), South Carolina (n = 109), Georgia (n = 159), Alabama (n = 8), Arkansas (n = 26), and Louisiana (n = 91)) and global clinical (n = 5,153) and nonclinical (n = 1,053) isolates obtained from the NCBI. Additionally, we also examined the population structure of S. enterica ser. Braenderup strains (n = 3,131) on EnteroBase and found that all the strains of this serovar are associated with a single cgMLST eBurst group (ceBG 185), confirming that this serovar is monophyletic. We divided the S. enterica ser. Braenderup population into two clades (Clade I and Clade II) and one clade group (Clade Group III). The composition of distinct environmental isolates in the clades differed: Clade I was significantly associated with produce (90.7%; P < 0.0001) and water, soil, and sediment (76.9%; P < 0.0001), and Clade II was significantly associated with poultry environments (62.8%; P < 0.0001). The clade-specific gene associations (e.g., Clade I-associated competence proteins and cytochrome_c_asm protein and Clade II-associated heme-exporter protein and dimethyl sulfoxide [DMSO] reductase-encoding genes) provide potential insights into possible mechanisms driving environmental adaptation and host-pathogen interaction. Phylogenetic analyses identified 218 molecular epidemiological clusters in the current study, which represented a greater proportion of potentially outbreak-related isolates than previously estimated.

IMPORTANCE

This study provides insights into the genomic diversity of S. enterica ser. Braenderup by revealing distinct clade-specific source attribution patterns and showing that a greater proportion of isolates were associated with epidemiological clusters based on the genomic relatedness than previously estimated. Specifically, we analyzed the diversity of human clinical isolates from southeastern USA and compared them with the global clinical and nonclinical isolates. Our analysis showed different clades of S. enterica ser. Braenderup linked to different environments, providing insights on the potential source of human sporadic infection and outbreaks. These findings can enhance public health surveillance and response strategies targeting S. enterica serovar Braenderup by expanding our understanding of potential transmission pathways and the genomic diversity of clinical and environmental isolates.

Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data

OBJECTIVES

Integrating pathogen genomic surveillance with bioinformatics can enhance public health responses by identifying risk and guiding interventions. This study focusses on the two predominant Campylobacter species, which are commonly found in the gut of birds and mammals and often infect humans via contaminated food. Rising incidence and antimicrobial resistance (AMR) are a global concern, and there is an urgent need to quantify the main routes to human infection.

METHODS

During routine US national surveillance (2009-2019), 8856 Campylobacter genomes from human infections and 16,703 from possible sources were sequenced. Using machine learning and probabilistic models, we target genetic variation associated with host adaptation to attribute the source of human infections and estimate the importance of different disease reservoirs.

RESULTS

Poultry was identified as the primary source of human infections, responsible for an estimated 68% of cases, followed by cattle (28%), and only a small contribution from wild birds (3%) and pork sources (1%). There was also evidence of an increase in multidrug resistance, particularly among isolates attributed to chickens.

CONCLUSIONS

National surveillance and source attribution can guide policy, and our study suggests that interventions targeting poultry will yield the greatest reductions in campylobacteriosis and spread of AMR in the US.

DATA AVAILABILITY

All sequence reads were uploaded and shared on NCBI's Sequence Read Archive (SRA) associated with BioProjects; PRJNA239251 (CDC / PulseNet surveillance), PRJNA287430 (FSIS surveillance), PRJNA292668 & PRJNA292664 (NARMS) and PRJNA258022 (FDA surveillance). Publicly available genomes, including reference genomes and isolates sampled worldwide from wild birds are associated with BioProject accessions: PRJNA176480, PRJNA177352, PRJNA342755, PRJNA345429, PRJNA312235, PRJNA415188, PRJNA524300, PRJNA528879, PRJNA529798, PRJNA575343, PRJNA524315 and PRJNA689604. Contiguous assemblies of all genome sequences compared are available at Mendeley data (assembled C. coli genomes doi: 10.17632/gxswjvxyh3.1; assembled C. jejuni genomes doi: 10.17632/6ngsz3dtbd.1) and individual project and accession numbers can be found in Supplementary tables S1 and S2, which also includes pubMLST identifiers for assembled genomes. Figshare (10.6084/m9.figshare.20279928). Interactive phylogenies are hosted on microreact separately for C. jejuni (https://microreact.org/project/pascoe-us-cjejuni) and C. coli (https://microreact.org/project/pascoe-us-ccoli).

First study in the frequency of isolation and phenotypic antimicrobial resistance profiles of pig and cattle origin Campylobacter strains in Romania

Campylobacter spp. is recognized as one of the most common pathogens involved in the development of gastrointestinal infections in humans. The current study aimed to enhance the knowledge on the occurrence and molecular characterization of Campylobacter spp. in pigs and cattle origin caecum samples (n = 56) collected in one year, from nine Romanian slaughterhouses, and to determine the antimicrobial resistance profile of the isolated strains. All Campylobacter spp. strains (n = 41) isolated from swine and cattle caecum samples were analyzed in terms of antimicrobial resistance, in accordance with the EURL protocol and with the Commission Implementing Decision No. 2020/1729. The prevalence rate for C. coli. in pig caecum samples was 92.3% (36/39), and the prevalence of C. jejuni, in cattle origin samples was 29.4% (5/17). C. coli strains isolated from pigs proved resistant to tetracycline 75% (27/36), ciprofloxacin 69.4% (25/36), erythromycin 8.3% (3/36), ertapenem 2.8% (1/36) and gentamicin 2.8% (1/36), but no resistance was observed towards chloramphenicol. C. jejuni strains originating from cattle expressed resistance to ciprofloxacin 60.0% (3/5) and tetracycline 20.0% (1/5), but they were susceptible to chloramphenicol, erythromycin, ertapenem and gentamicin. In the present study, 19.5% (7/36) C. coli strains isolated from pigs were identified as multidrug-resistant (MDR) bacteria. The obtained results demonstrated that pigs especially, but cattle to, can be considered important natural reservoirs for zoonotic multidrug-resistant Campylobacter strains, having a stimulating effect for further studies aiming at the molecular screening of the genotypic antimicrobial resistance processing of a higher number of samples.

Foodborne pathogenic bacteria in wild European hedgehogs (Erinaceus europaeus)

BACKGROUND

European hedgehogs (Erinaceus europaeus) are widely distributed across Europe. They may play an important role by spreading zoonotic bacteria in the environment and to humans and animals. The aim of our work was to study the prevalence and characteristics of the most important foodborne bacterial pathogens in wild hedgehogs.

RESULTS

Faecal samples from 148 hospitalised wild hedgehogs originating from the Helsinki region in southern Finland were studied. Foodborne pathogens were detected in 60% of the hedgehogs by PCR. Listeria (26%) and STEC (26%) were the most common foodborne pathogens. Salmonella, Yersinia, and Campylobacter were detected in 18%, 16%, and 7% of hedgehogs, respectively. Salmonella and Yersinia were highly susceptible to the tested antimicrobials. Salmonella Enteritidis and Listeria monocytogenes 2a were the most common types found in hedgehogs. All S. Enteritidis belonged to one sequence type (ST11), forming four clusters of closely related isolates. L. monocytogenes was genetically more diverse than Salmonella, belonging to 11 STs. C. jejuni ST45 and ST677, Y. pseudotuberculosis O:1 of ST9 and ST42, and Y. enterocolitica O:9 of ST139 were also found.

CONCLUSIONS

Our study shows that wild European hedgehogs should be considered an important source of foodborne pathogens, and appropriate hygiene measures after any contact with hedgehogs and strict biosecurity around farms are therefore important.

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.

Prevalence, genomic characterization and antimicrobial resistance of Campylobacter spp. isolates in pets in Shenzhen, China

The prevalence of Campylobacter spp.in pets is a potential concern for human health. However, little is known about the pet-related Campylobacter spp. in China. A total of 325 fecal samples were collected from dogs, cats, and pet foxes. Campylobacter spp. were isolated by culture, and MALDI-TOF MS was used to identify 110 Campylobacter spp. isolates in total. C. upsaliensis (30.2%, 98/325), C. helveticus (2.5%, 8/325), and C. jejuni (1.2%, 4/325) were the three found species. In dogs and cats, the prevalence of Campylobacter spp. was 35.0% and 30.1%, respectively. A panel of 11 antimicrobials was used to evaluate the antimicrobial susceptibility by the agar dilution method. Among C. upsaliensis isolates, ciprofloxacin had the highest rate of resistance (94.9%), followed by nalidixic acid (77.6%) and streptomycin (60.2%). Multidrug resistance (MDR) was found in 55.1% (54/98) of the C. upsaliensis isolates. Moreover, 100 isolates, including 88 C. upsaliensis, 8 C. helveticus, and 4 C. jejuni, had their whole genomes sequenced. By blasting the sequence against the VFDB database, virulence factors were identified. In total, 100% of C. upsaliensis isolates carried the cadF, porA, pebA, cdtA, cdtB, and cdtC genes. The flaA gene was present in only 13.6% (12/88) of the isolates, while the flaB gene was absent. By analyzing the sequence against the CARD database, we found that 89.8% (79/88) of C. upsaliensis isolates had antibiotic target alteration in the gyrA gene conferring resistance to fluoroquinolone, 36.4% (32/88) had the aminoglycoside resistance gene, and 19.3% (17/88) had the tetracycline resistance gene. The phylogenetic analysis using the K-mer tree method obtained two major clades among the C. upsaliensis isolates. All eight isolates in subclade 1 possessed the gyrA gene mutation, the aminoglycoside and tetracycline resistance genes, and were phenotypically resistant to six classes of antimicrobials. It has been established that pets are a significant source of Campylobacter spp. strains and a reservoir for them. This study is the first to have documented the presence of Campylobacter spp. in pets in Shenzhen, China. In this study, C. upsaliensis of subclade 1 required additional attention due to its broad MDR phenotype and relatively high flaA gene prevalence.

Phylogeny and Genomic Characterization of Clinical Salmonella enterica Serovar Newport Collected in Tennessee

Salmonella enterica subsp. enterica serovar Newport (S. Newport) is a clinically and epidemiologically significant serovar in the United States. It is the second most prevalent clinically isolated Salmonella serovar in the United States, and it can contaminate a wide variety of food products. In this study, we evaluated the population structure of S. Newport clinical isolates obtained by the Tennessee Department of Health during routine surveillance (n = 346), along with a diverse set of other global clinical isolates obtained from EnteroBase (n = 271). Most of these clinical isolates belonged to established lineages II and III. Additionally, we performed lineage-specific phylogenetic analyses and were able to identify 18 potential epidemiological clusters among the isolates from Tennessee, which represented a greater proportion of Tennessee isolates belonging to putative epidemiological clusters than the proportion of isolates of this serovar that are outbreak related. IMPORTANCE This study provides insight on the genomic diversity of one of the Salmonella serovars that most frequently cause human illness. Specifically, we explored the diversity of human clinical isolates from a localized region (Tennessee) and compared this level of diversity with the global context. Additionally, we showed that a greater proportion of isolates were associated with potential epidemiological clusters (based on genomic relatedness) than historical estimates. We also identified that one potential cluster was predicted to be multidrug resistant. Taken together, these findings provide insight on Salmonella enterica serovar Newport that can impact public health surveillance and responses and serve as a foundational context for the Salmonella research community.

Whole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance

Campylobacteriosis is the most common cause of acute gastrointestinal bacterial infection in Europe, with most infections linked to the consumption of contaminated food. While previous studies found an increasing rate of antimicrobial resistance (AMR) in Campylobacter spp. over the past decades, the investigation of additional clinical isolates is likely to provide novel insights into the population structure and mechanisms of virulence and drug resistance of this important human pathogen. Therefore, we combined whole-genome sequencing and antimicrobial-susceptibility testing of 340 randomly selected Campylobacter jejuni isolates from humans with gastroenteritis, collected in Switzerland over an 18 year period. In our collection, the most common multilocus sequence types (STs) were ST-257 (n=44), ST-21 (n=36) and ST-50 (n=35); the most common clonal complexes (CCs) were CC-21 (n=102), CC-257 (n=49) and CC-48 (n=33). High heterogeneity was observed among STs, with the most abundant STs recurring over the entire study period, while others were observed only sporadically. Source attribution based on ST assigned more than half of the strains to the 'generalist' category (n=188), 25  % as 'poultry specialist' (n=83), and only a few to 'ruminant specialist' (n=11) or 'wild bird' origin (n=9). The isolates displayed an increased frequency of AMR from 2003 to 2020, with the highest rates of resistance observed for ciprofloxacin and nalidixic acid (49.8 %), followed by tetracycline (36.9 %). Quinolone-resistant isolates carried chromosomal gyrA mutations T86I (99.4 %) and T86A (0.6 %), whereas tetracycline-resistant isolates carried tet(O) (79.8 %) or mosaic tetO/32/O (20.2 %) genes. A novel chromosomal cassette carrying several resistance genes, including aph(3')-III, satA and aad(6), and flanked by insertion sequence elements was detected in one isolate. Collectively, our data revealed an increasing prevalence of resistance to quinolones and tetracycline in C. jejuni isolates from Swiss patients over time, linked to clonal expansion of gyrA mutants and acquisition of the tet(O) gene. Investigation of source attribution suggests that infections are most likely related to isolates from poultry or generalist backgrounds. These findings are relevant to guide future infection prevention and control strategies.

Genomic Diversity of Campylobacter lari Group Isolates from Europe and Australia in a One Health Context

Members of the Campylobacter lari group are causative agents of human gastroenteritis and are frequently found in shellfish, marine waters, shorebirds, and marine mammals. Within a One Health context, we used comparative genomics to characterize isolates from a diverse range of sources and geographical locations within Europe and Australia and assess possible transmission of food, animal, and environmental isolates to the human host. A total of 158 C. lari isolates from Australia, Denmark, France, and Germany, which included 82 isolates from human stool and blood, 12 from food, 14 from domestic animal, 19 from waterbirds, and 31 from the environment were analyzed. Genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance (AMR) traits was carried-out. Most of the isolates belonged to C. lari subsp. lari (Cll; 98, 62.0%), while C. lari subsp. concheus and C. lari urease-positive thermotolerant Campylobacter (UPTC) were represented by 12 (7.6%) and 15 (9.5%) isolates, respectively. Furthermore, 33 (20.9%) isolates were not assigned a subspecies and were thus attributed to distant Campylobacter spp. clades. Whole-genome sequence-derived multilocus sequence typing (MLST) and core-genome MLST (cgMLST) analyses revealed a high genetic diversity with 97 sequence types (STs), including 60 novel STs and 14 cgMLST clusters (≤10 allele differences), respectively. The most prevalent STs were ST-21, ST-70, ST-24, and ST-58 (accounting for 13.3%, 4.4%, 3.8%, and 3.2% of isolates, respectively). A high prevalence of the 125 examined virulence-related loci (from 76.8 to 98.4% per isolate) was observed, especially in Cll isolates, suggesting a probable human pathogenicity of these strains. IMPORTANCE Currently, relatedness between bacterial isolates impacting human health is easily monitored by molecular typing methods. These approaches rely on discrete loci or whole-genome sequence (WGS) analyses. Campylobacter lari is an emergent human pathogen isolated from diverse ecological niches, including fecal material from humans and animals, aquatic environments, and seafood. The presence of C. lari in such diverse sources underlines the importance of adopting an integrated One Health approach in studying C. lari population structure for conducting epidemiological risk assessment. This retrospective study presents a comparative genomics analysis of C. lari isolates retrieved from two different continents (Europe and Australia) and from different sources (human, domestic animals, waterbirds, food, and environment). It was designed to improve knowledge regarding C. lari ecology and pathogenicity, important for developing effective surveillance and disease prevention strategies.