Parallel sequencing of porA reveals a complex pattern of Campylobacter genotypes that differs between broiler and broiler breeder chickens

Campycins are novel broad-spectrum antibacterials killing Campylobacter jejuni

Pyocins are high molecular weight bacteriocins produced by Pseudomonas aeruginosa that can be retargeted to new bacterial species by exchanging the pyocin tail fibers with bacteriophage receptor binding proteins (RBPs). Here, we develop retargeted pyocins called campycins as new antibacterials to precisely and effectively kill the major foodborne pathogen Campylobacter jejuni. We used two diverse RBPs (H-fibers) encoded by CJIE1 prophages found in the genomes of C. jejuni strains CAMSA2147 and RM1221 to construct campycin 1 and campycin 2, respectively. Campycins 1 and 2 could target all C. jejuni strains tested due to complementary antibacterial spectra. In addition, both campycins led to more than 3 log reductions in C. jejuni counts under microaerobic conditions at 42 °C, whereas the killing efficiency was less efficient under anaerobic conditions at 5 °C. Furthermore, we discovered that both H-fibers used to construct the campycins bind to the essential major outer membrane protein (MOMP) present in all C. jejuni in a strain-specific manner. Protein sequence alignment and structural modeling suggest that the highly variable extracellular loops of MOMP form the binding sites of the diverse H-fibers. Further in silico analyses of 5000 MOMP sequences indicated that the protein falls into three major clades predicted to be targeted by either campycin 1 or campycin 2. Thus, campycins are promising antibacterials against C. jejuni and are expected to broadly target numerous strains of this human pathogen in nature and agriculture. KEY POINTS: • Campycins are engineered R-type pyocins containing H-fibers from C. jejuni prophages • Campycins reduce C. jejuni counts by >3 logs at conditions promoting growth • Campycins bind to the essential outer membrane protein MOMP in a strain-dependent way.

A Longitudinal Study on Campylobacter in Conventionally Reared Commercial Broiler Flocks in the United States: Prevalence and Genetic Diversity

Poultry meat contaminated with Campylobacter, a major bacterial cause of foodborne gastroenteritis worldwide, is considered the primary source of human campylobacteriosis. Thus, reduction or elimination of Campylobacter in poultry production will have a significant impact on food safety and public health. Despite the significant progress made over the last decades, many puzzles remain about the epidemiology of Campylobacter on poultry farms, hampering the development of an effective control strategy. This longitudinal study was conducted to determine the prevalence and genetic diversity of Campylobacter in a U.S. commercial broiler production farm system. Cecal contents (15 samples/flock) and boot swabs (3 samples/flock) were collected from approximately 6-wk-old birds from 406 conventional broiler flocks reared in 53 houses on 15 farms (located within a relatively close geographic proximity and managed by the same poultry integrator) for up to eight consecutive production cycles and cultured for Campylobacter. Pulsed-field gel electrophoresis was used to investigate the genetic diversity of the Campylobacter jejuni isolates recovered from the cecal contents. The prevalence of Campylobacter at the farm, house, and flock levels were found to be 93% (14/15), 79% (42/53), and 47% (192/406), respectively. Campylobacter prevalence varied remarkably among different farms and flocks, with some farms or houses testing consistently negative while others being positive all the time over the entire study period. Campylobacter isolation rate changed significantly by sample type (higher by cecal contents vs. boot swabs) and season/production cycle (higher in spring vs. other seasons). The majority (88%; 2364/2675) of the isolates were identified as C. jejuni, and almost all the rest (11%; 303/2675) were Campylobacter coli. Genotyping showed limited diversity within a flock and suggested persistence of some C. jejuni clones over multiple production cycles on the same farm. In conclusion, this study indicated that although Campylobacter prevalence was overall high, there were marked differences in the prevalence among the broiler flocks or farms tested. Future studies aimed at identification of potential risk factors associated with differential Campylobacter status are warranted in order to develop effective on-farm interventions.

Narrative review of application of metagenomic approaches to study the link between oropharyngeal microbiome and infectious diseases

Context

Viral and bacterial infections are major causes of morbidity and mortality worldwide. The oropharyngeal microbiome could play an important role in preventing invasion of viral and bacterial pathogens by modulating its content and the host's innate immune response. Next Generation Sequencing (NGS) technologies now enable in-depth study of the genomes of microbial communities. The objective of this review is to highlight how metagenomics has contributed to establish links between changes in the oropharyngeal microbiome and emergence of bacterial and viral diseases.

Method

Two search engines, PubMed and Google scholar were used with filters to focus searches on peer-reviewed original articles published between January 2010 and September 2022. Different keywords were used and only articles with metagenomic approaches were included.

Results

This review shows that there were few articles studying the link between oropharyngeal microbiome and infectious diseases. Studies on viruses using metagenomic techniques have been growing exponentially in recent years due to the Covid-19 pandemic. This review shows that most studies still focus on the basic identification of microorganisms in different disease states and multiple microorganisms (Alloprevotella, Prevotella, Bacteroides, Haemophilus, Streptococcus, Klebsiella sp., Acinetobacter sp…), have been associated with development of infections such as childhood wheezing, influenza, Covid-19, pneumonia, meningitis, and tuberculosis.

Conclusion

The oropharyngeal microbiome, despite its importance, remains poorly studied. A limited number of articles were identified but this number has increased exponentially since 2020 due to research conducted on Covid-19. These studies have shown that metagenomic has contributed to the unbiased identification of bacteria that could be used as biomarkers of various diseases and that further research is now needed to capitalize on those findings for human health benefit.

Comparative genomics of Campylobacter jejuni from clinical campylobacteriosis stool specimens

BACKGROUND

Campylobacter jejuni is a pervasive pathogen of major public health concern with a complex ecology requiring accurate and informative approaches to define pathogen diversity during outbreak investigations. Source attribution analysis may be confounded if the genetic diversity of a C. jejuni population is not adequately captured in a single specimen. The aim of this study was to determine the genomic diversity of C. jejuni within individual stool specimens from four campylobacteriosis patients. Direct plating and pre-culture filtration of one stool specimen per patient was used to culture multiple isolates per stool specimen. Whole genome sequencing and pangenome level analysis were used to investigate genomic diversity of C. jejuni within a patient.

RESULTS

A total 92 C. jejuni isolates were recovered from four patients presenting with gastroenteritis. The number of isolates ranged from 13 to 30 per patient stool. Three patients yielded a single C. jejuni multilocus sequence type: ST-21 (n = 26, patient 4), ST-61 (n = 30, patient 1) and ST-2066 (n = 23, patient 2). Patient 3 was infected with two different sequence types [ST-51 (n = 12) and ST-354 (n = 1)]. Isolates belonging to the same sequence type from the same patient specimen shared 12-43 core non-recombinant SNPs and 0-20 frameshifts with each other, and the pangenomes of each sequence type consisted of 1406-1491 core genes and 231-264 accessory genes. However, neither the mutation nor the accessory genes were connected to a specific functional gene category.

CONCLUSIONS

Our findings show that the C. jejuni population recovered from an individual patient's stool are genetically diverse even within the same ST and may have shared common ancestors before specimens were obtained. The population is unlikely to have evolved from a single isolate at the time point of initial patient infection, leading us to conclude that patients were likely infected with a heterogeneous C. jejuni population. The diversity of the C. jejuni population found within individual stool specimens can inform future methodological approaches to attribution and outbreak investigations.

Molecular markers associated with antimicrobial resistance and genotypes of Campylobacter jejuni and Campylobacter coli isolated from broiler and swine flocks in southeast Brazil

This study aimed to identify molecular markers associated with antimicrobial resistance and genotype isolates of Campylobacter spp. from broiler and swine flocks due to its importance to one-health. C. jejuni (n=27) and C. coli (n = 35) strains were screened for the antimicrobial genetic markers C257T in gyrA, A2074C and A2075G in 23S rRNA, CmeABC, ermB, tetO and blaOXA61 by PCR. Fifteen strains had SVR-flaA and porA genes sequenced to evaluate their genetic diversity. Among C. jejuni strains 62.96% had C257T mutation and only one strain had A2075G mutation. CmeA, cmeB, cmeC, tetO and blaOXA61 were detected respectively in 92.59%, 100%, 100%, 85.19%, 85.19% of the strains. All C. coli had C257T mutation; 48.75% had A2075G and cmeA, cmeB, cmeC, tetO, blaOXA61 were detected in 8.57%, 94.29%, 91.43%, 91.43%, 80%, respectively. Twelve porA and SVR-flaA alleles were detected, with a Simpson index of diversity value of 0.962.

High resolution parallel sequencing reveals multi-strain Campylobacter in broiler chicken flocks testing ‘negative’ by conventional culture methods: implications for control of Campylobacter infection

Contaminated chicken meat is a major source of human Campylobacteriosis and rates of infection remain high, despite efforts to limit the colonisation of broiler (meat) chicken flocks on farms. Using conventional testing methods of culture or qPCR, Campylobacter is typically detected amongst broiler flocks from 3 wk of age, leading to the assumption that infection is introduced horizontally into chicken rearing houses at this time. In this study, we use parallel sequencing of a fragment of the Campylobacter outer membrane protein, encoded by the porA gene, to test for presence of Campylobacter DNA amongst fresh fecal samples collected from broiler flocks aged 23 to 28 d. Campylobacter DNA was detected in all of the 290 samples tested using the porA target, and in 48% of samples using 16S bacterial profiling, irrespective of whether or not Campylobacter could be detected using conventional qPCR thresholds. A single porAf2 variant was predominant among flocks that would be determined to be Campylobacter ‘positive’ by conventional means, but a diverse pattern was seen among flocks that were Campylobacter ‘negative’. The ability to routinely detect low levels of Campylobacter amongst broiler flocks at a much earlier age than would conventionally be identified requires a re-examination of how and when biosecurity measures are best applied for live birds. In addition, it may be useful to investigate why single Campylobacter variants proliferate in some broiler flocks and not others.

Mechanisms of biodiversity between Campylobacter sequence types in a flock of broiler-breeder chickens

Commercial poultry flocks frequently harbor the dangerous bacterial pathogen Campylobacter. As exclusion efforts frequently fail, there is interest in potential ecologically informed solutions. A long-term study of Campylobacter sequence types was used to investigate the competitive framework of the Campylobacter metacommunity and understand how multiple sequence types simultaneously co-occur in a flock of chickens. A combination of matrix and patch-occupancy models was used to estimate parameters describing the competition, transmission, and mortality of each sequence type. It was found that Campylobacter sequence types form a strong hierarchical framework within a flock of chickens and occupied a broad spectrum of transmission-mortality trade-offs. Upon further investigation of how biodiversity is thus maintained within the flock, it was found that the demographic capabilities of Campylobacter, such as mortality and transmission, could not explain the broad biodiversity of sequence types seen, suggesting that external factors such as host-bird health and seasonality are important elements in maintaining biodiversity of Campylobacter sequence types.

Parallel Sequencing Reveals Campylobacter spp. in Commercial Meat Chickens Less than 8 Days Old

Campylobacter from contaminated poultry meat is a major source of human gastroenteritis worldwide. To date, attempts to control this zoonotic infection with on-farm biosecurity measures have been inconsistent in outcome. A cornerstone of these efforts has been the detection of chicken infection with microbiological culture, where Campylobacter is generally not detectable until birds are at least 21 days old. Using parallel sequence-based bacterial 16S profiling analysis and targeted sequencing of the porA gene, Campylobacter was identified at very low levels in all commercial flocks at less than 8 days old that were tested from the United Kingdom, Switzerland, and France. These young chicks exhibited a much greater diversity of porA types than older birds testing positive for Campylobacter by culture or quantitative PCR (qPCR). This suggests that as the bacteria multiply sufficiently to be detected by culture methods, one or two variants, as indicated by porA type, dominate the infection. The findings that (i) most young chicks carry some Campylobacter and (ii) not all flocks become Campylobacter positive by culture suggest that efforts to control infection, and therefore avoid contamination of poultry meat, should concentrate on how to limit Campylobacter to low levels by the prevention of the overgrowth of single strains. IMPORTANCE Our results demonstrate the presence of Campylobacter DNA among fecal samples from a range of commercially reared meat chicks that are less than 8 days of age, consistent across 3 European countries. The recently developed, sensitive detection method indicates that infection occurs on commercial farms much earlier and more widely than previously thought, which opens up new opportunities to control Campylobacter contamination at the start of the food chain and reduce the unacceptably high levels of human disease.

Investigation of Campylobacter colonization in three Australian commercial free-range broiler farms

Campylobacter spp. contaminated poultry products are strongly associated with foodborne illnesses worldwide. Development of effective management strategies to reduce contamination by Campylobacter spp. requires an improved understanding of the numerous factors that drive these contamination processes. Currently, chicken farms are using more free-range chicken meat production systems in response to consumer preferences. However, Campylobacter spp. colonization has rarely been investigated on free-range broiler farms. The present study investigated the temporal and environmental factors influencing Campylobacter spp. colonization of free-range broilers as well as potential sources and genetic diversity of Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli) in commercial free-range broiler farms. Genetic linkages among the isolates were analyzed using flaA amplicon analysis. Campylobacter coli was first detected in fecal samples of a commercial free-range broiler flock on day 10 of rearing. Multiple genotypes of C. jejuni and C. coli were identified in this study. The farm environment was identified as a potential source of C. jejuni and C. coli colonization of free-range broilers. The dominant Campylobacter genotype varied between free-range broiler farms over time, with C. jejuni being the most frequently isolated species. These findings enhance the understanding of C. jejuni and C. coli colonization in free-range broiler farms and could inform the development of more effective intervention strategies to help control this important foodborne pathogen.

Update and review of control options for Campylobacter in broilers at primary production

The 2011 EFSA opinion on Campylobacter was updated using more recent scientific data. The relative risk reduction in EU human campylobacteriosis attributable to broiler meat was estimated for on-farm control options using Population Attributable Fractions (PAF) for interventions that reduce Campylobacter flock prevalence, updating the modelling approach for interventions that reduce caecal concentrations and reviewing scientific literature. According to the PAF analyses calculated for six control options, the mean relative risk reductions that could be achieved by adoption of each of these six control options individually are estimated to be substantial but the width of the confidence intervals of all control options indicates a high degree of uncertainty in the specific risk reduction potentials. The updated model resulted in lower estimates of impact than the model used in the previous opinion. A 3-log10 reduction in broiler caecal concentrations was estimated to reduce the relative EU risk of human campylobacteriosis attributable to broiler meat by 58% compared to an estimate larger than 90% in the previous opinion. Expert Knowledge Elicitation was used to rank control options, for weighting and integrating different evidence streams and assess uncertainties. Medians of the relative risk reductions of selected control options had largely overlapping probability intervals, so the rank order was uncertain: vaccination 27% (90% probability interval (PI) 4-74%); feed and water additives 24% (90% PI 4-60%); discontinued thinning 18% (90% PI 5-65%); employing few and well-trained staff 16% (90% PI 5-45%); avoiding drinkers that allow standing water 15% (90% PI 4-53%); addition of disinfectants to drinking water 14% (90% PI 3-36%); hygienic anterooms 12% (90% PI 3-50%); designated tools per broiler house 7% (90% PI 1-18%). It is not possible to quantify the effects of combined control activities because the evidence-derived estimates are inter-dependent and there is a high level of uncertainty associated with each.

A Mathematical Model of Campylobacter Dynamics Within a Broiler Flock

Globally, the bacterial genus Campylobacter is one of the leading causes of human gastroenteritis, with its primary route of infection being through poultry meat. The application of biosecurity measures is currently limited by a lack of understanding of the transmission dynamics within a flock. Our work is the first to undertake a mathematical modeling approach to Campylobacter population dynamics within a flock of broilers (chickens bred specifically for meat). A system of stochastic differential equations is used to model the routes of infection between co-housed birds. The presented model displays the strong correlation between housing density and Campylobacter prevalence, and shows how stochastic variation is the driving factor determining which strains of Campylobacter will emerge first within a flock. The model also shows how the system will rapidly select for phenotypic advantages, to quickly eliminate demographically-weaker strains. A global sensitivity analysis is performed, highlighting that the growth and death rate of other native bacterial species likely contributes the greatest to preventing flock outbreaks, presenting a promising approach to hypothesizing new methods of combatting disease transmission.