Whole-genome sequencing in the epidemiology of Campylobacter jejuni infections
Llarenna, A., Taboadab, E., Rossia, M. “Whole-genome sequencing in the epidemiology of Campylobacter jejuni infections”. J. Clin. Microbiol. (2017):JCM.00017-17
JCM Accepted Manuscript Posted Online 1 March 2017 J. Clin. Microbiol. doi:10.1128/JCM.00017-17
This review article focuses on the use of whole-genome sequencing (WGS) in epidemiological investigations of Campylobacter jejuni infections. Campylobacteriosis cases are generally sporadic, and investigations to date have utilized either pulsed-field gel electrophoresis (PFGE) or multilocus sequence typing (MLST). However, WGS allows the the identification of identical strains, and thus provides a more powerful tool for researchers. This paper point out confounding factors that researchers who use WGS must keep in mind, such as genomic variants. When a strain is involved in a case of human campylobacteriosis it is possible for a strain to develop mutations resulting in variants from the original infecting strain. WGS has been applied to study how often these changes occur during human or animal colonization, and it has been found that changes are usually very small (singly nucleotide variants in one or two loci). However, researchers using WGS to investigate outbreak strains have found up to 15 SNVs in isolates taken from a single outbreak. These strains were still readily discernable from non-related control strains. Finally, we must remember that more than one strain can be involved in a single outbreak. While there are still hurdles to implementing WGS in public health settings, the authors of this paper highlight the ample evidence in support of the the benefits of its use.
Prevalence, genotyping and risk factors of thermophilic Campylobacter spreading in organic turkey farms in Germany.
Ahmed, Marwa Fawzy El Metwaly, et al. “Prevalence, genotyping and risk factors of thermophilic Campylobacter spreading in organic turkey farms in Germany.” Gut pathogens 8.1 (2016): 1.
This article discusses the prevalence of Campylobacter in organically produced turkeys in Germany. Many consumers consider organic products to be healthier and safer. The routes of poultry flock Campylobacter colonization are not fully understood as of yet, but organic flocks actually have more exposure to the environment and other animals and may present a greater food safety risk than conventional flocks. However, the prevalence of Campylobacter in organic and conventional flocks has been found to be very similar. In this study, samples were collected from five different organic turkey farms during the spring and summer. All of the farms were located in Germany, had a usual commercial flock size (1000 to 2000 birds), and a minimal distance of 1 km to the next livestock. Thirty cloacal swabs were taken from each flock as well as approximately 31 water samples collected from the main water tank. In addition, 31 pooled water samples were also taken from the drinkers in the poultry house. Darkling beetles were collected from 10 places within the barns and analyzed for the presence of Campylobacter. The temperature and relative humidity were measured as well as ammonia and carbon dioxide. All five organic turkey farms were positive for Campylobacter (147/150). Campylobacter was isolated from the darkling beetles of farm II and water samples of farms I and II. The prevalence of Campylobacter ranged from 90-100% in all five farms. flaA typing of the Campylobacter isolates revealed 24 different genotypes. The genotype of the Campylobacter isolated from the darkling beetles of farm II were identical to all eight of the Campylobacter isolates from the cloacal swabs at that same farm. There was not effect of the environmental measurements on Campylobacter status.
- Ohno, H., Wachino, J. I., Saito, R., Jin, W., Yamada, K., Kimura, K., and Arakawa, Y. (2016). A highly macrolide-resistant campylobacter jejuni strain with rare A2074T mutations in 23s rRNA genes. Antimicrobial Agents and Chemotherapy 60, 2580-2581.
This article characterizes and announces an isolate of C. jejuni with extremely high macrolide resistance and a rare A2074T mutation. There is not much known about the mutation itself and the letter announces the lab’s intent to study the isolate. The clinical isolate NC05-27 has the mutation in all three 23S rRNA genes but no other resistance factors, which suggests that the A2074T mutation is mainly responsible for the high level of macrolide resistance in NC05-27. A macrolide-susceptible C. jejuni NCTC11168 strain was transformed with DNA from NC05-27 and the transformant had a comparable level of macrolide resistance to NC05-27. Meaning that the A2074T mutation confers high macrolide resistance when present in all three 23S rRNA genes and with the A2074G, A2074C, and A2075G mutations. However the mutation A2074T conferred a loss of fitness to the bacteria.
- Heimesaat, M. M., Plickert, R., Fischer, a, Göbel, U. B., and Bereswill, S. (2013). Can microbiota transplantation abrogate murine colonization resistance against Campylobacter jejuni? European Journal of Microbiology and Immunology 3, 36-43. Available at: http://www.akademiai.com/openurl.asp?genre=article&id=doi:10.1556/EuJMI.3.2013.1.5.
- Bereswill, S., Fischer, A., Plickert, R., Haag, L. M., Otto, B., Kühl, A. A., Dashti, J. I., Zautner, A. E., Muñoz, M., Loddenkemper, C., et al. (2011). Novel murine infection models provide deep insights into the “Ménage à trois” of campylobacter jejuni, microbiota and host innate immunity. PLoS ONE 6.
Two excellent articles on how Campylobacter colonization of the gut affects host signaling and the microbiome. Also details how differing microbiomes can impact Campylobacter colonization in murine systems.
- Diego Florez-Cuadrado, María Ugarte-Ruiz, Alberto Quesada, Gonzalo Palomo, Lucas Domínguez and M. Concepción Porrero. (2015). Description of an erm(B)-carrying Campylobacter coli isolate in Europe. J. Antimicrob. Chemother.http://jac.oxfordjournals.org/content/early/2015/11/24/jac.dkv383.extract?ct doi: 10.1093/jac/dkv383
A letter to the editor that outlines the first identification of a methylase erm(B) gene in Campylobacter , which was found in Europe. The presence of this gene suggests the possibility of horizontal transfer occurring between the organisms intestinal microbiota.
- Danzeisen, J. L., Calvert, A. J., Noll, S. L., McComb, B., Sherwood, J. S., Logue, C. M., and Johnson, T. J. (2013). Succession of the turkey gastrointestinal bacterial microbiome related to weight gain. PeerJ 1, e237. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3883494&tool=pmcentrez&rendertype=abstract.
- Wei, S., Morrison, M., and Yu, Z. (2013). Bacterial census of poultry intestinal microbiome. Poult Sci 92, 671-683. Available at: http://ps.fass.org/content/92/3/671.abstract.
Both of the articles outline the changes that take place in the poultry gut microbiome in reference to weight gain, time and microbial diversity.
- Oakley, B. B., Buhr, R., Ritz, C. W., Kiepper, B. H., Berrang, M. E., Seal, B. S., and Cox, N. a (2014). Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives. BMC Vet Res 10, 282. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4251860&tool=pmcentrez&rendertype=abstract.
Oakley, B. B., Lillehoj, H. S., Kogut, M. H., Kim, W. K., Maurer, J. J., Pedroso, A., Lee, M. D., Collett, S. R., Johnson, T. J., and Cox, N. A. (2014). The chicken gastrointestinal microbiome. FEMS Microbiology Letters 360, 100-112.
The first is an article on changes in the cecal microbiome compared to organic acid feed additives and the changes that occur as birds age. The second is a mini-review about the chicken gastrointestinal microbiome covering the microbes that can occur within the microbiome due to a variety of factors.
- Katarina D. M. Pintar , Tanya Christidis, M. Kate Thomas, Maureen Anderson, Andrea Nesbitt, Jessica Keithlin, Barbara Marshall, Frank Pollari (2015). A Systematic Review and Meta-Analysis of the Campylobacter spp. Prevalence and Concentration in Household Pets and Petting Zoo Animals for Use in Exposure Assessments. PLOS One.http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144976
This article performs a meta-analysis on the prevalence of Campylobacter in pets and petting zoo animals. It examines current data for both of these animal groups and farm animals. Prevalence was determined to be highest in farm animals, then pets, and then petting zoo animals. They also identified large knowledge gaps in the literature.
- Zehra Nur Yuksekdag , Nur Sahin, Belma Aslim (2014). In vitro evaluation of the suitability potential probiotic of lactobacilli isolates from the gastrointestinal tract of chicken. European Food Research and Technology, Vol 239, Issue 2, pp 313-320. http://link.springer.com/article/10.1007/s00217-014-2224-x
This article discusses strains of Lactobacillus that are effective probiotics against C. jejuni in poultry. A panel of possible Lactobacillus strains were isolated from the chicken GI tract and evaluated as possible probiotics. Two strains of Lactobacillus, L. delbrueckii ssp. delbrueckii BAZ32 and L. acidophilus BAZ29, possessed characteristics that make them possible probiotics for poultry.
- Molnar, A., Hess, C., Pal, L., Wagner, L., Awad, W. A., Husveth, F., Hess, M., and Dublecz, K. (2015). Composition of diet modifies colonization dynamics of Campylobacter jejuni in broiler chickens. Journal of Applied Microbiology 118, 245-254.
This article provides some insight on how diet can affect the colonisation of C. jejuni in the poultry GI tract. C. jejuni colonized bird fed a corn-based diet faster than those fed a wheat with enzyme supplement-based diet. This could be due to the higher amount of indigestible components in the wheat diet that are fermented by microbes in the lower GI tract to produce short-chain fatty acids.
- Kaakoush, N. O., Sodhi, N., Chenu, J. W., Cox, J. M., Riordan, S. M., and Mitchell, H. M. (2014). The interplay between Campylobacter and Helicobacter species and other gastrointestinal microbiota of commercial broiler chickens. Gut pathogens 6, 6-18. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4060860&tool=pmcentrez&rendertype=abstract.
This article looks into possible indicator organisms and taxa in the chicken gut microbiome that correlate with Campylobacter spp. . abundance. Some observations such as lower abundance of Lactobacillus species and a higher abundance of Escherichia species have been associated with chickens colonized with C. jejuni . Information obtatined from the paper may be useful in developing competitive exclusion strategies for Campylobacter spp. .
- Danzeisen, J. L., Kim, H. B., Isaacson, R. E., Tu, Z. J., and Johnson, T. J. (2011). Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment. PLoS ONE 6.
- Danzeisen, J. L., Calvert, A. J., Noll, S. L., McComb, B., Sherwood, J. S., Logue, C. M., and Johnson, T. J. (2013). Succession of the turkey gastrointestinal bacterial microbiome related to weight gain. PeerJ 1, e237. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3883494&tool=pmcentrez&rendertype=abstract./
Both articles deal with the poultry microbiome. The first deals with changes in the cecal microbiome in response to anticoccidial and growth promoter treatment and the second is about the ileal microbiome changes related to weight gain. The first provides lots of information about growth promoter antibiotics and the changes they cause in the cecal microbiome and the second identified several markers of ileal microbiome sucession.
- Schokker, D., Veninga, G., Vastenhouw, S. A., Bossers, A., Bree, F. M. de, Kaal-Lansbergen, L. M. T. E., Rebel, J. M. J., and Smits, M. A. (2015). Early life microbial colonization of the gut and intestinal development differ between genetically divergent broiler lines. BMC genomics 16, 418. Available at: http://www.scopus.com/inward/record.url?eid=2-s2.0-84938997539&partnerID=tZOtx3y1.
This article discusses how host genetics play a role in the colonisation of Campylobacter .
Slide Decks on Antimicrobial Resistance, Campylobacter, and the Microbiome (via QIAGEN)
- Hetman BM, Mutschall SK, Thomas JE, Gannon VP, Clark CG, Pollari F, Taboada EN. (2017). The EpiQuant framework for computing the epidemiological concordance of microbial subtyping data. J Clin Microbiol. http://jcm.asm.org/content/early/2017/02/09/JCM.01945-16.long
This article describes how similar bacterial isolates (of Campylobacter jejuni) are based on put parameters from different sampling records. The program runs out of R and is called EpiQuant. They compared the epidemiological significance of 654 isolates of C. jejuni based on how they clustered using 2 different sub typing methods (MLST, and Comparative Genome Fingerprinting). The program compared the clustering based on metadata to the clustering based on sub typing to assess how effective the methods were. They determined that using this framework helped to bring epidemiological significance to certain groupings of isolates.