Genome sequencing of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae isolated from pigs and abattoir workers in Cameroon

Frontiers in Microbiology

Volumn 9, Issue FEB, 2018, Pages

  Founou, Luria L ^a,b   Founou, Raspail C ^a,b   Allam, Mushal ^c   Ismail, Arshad ^c   Djoko, Cyrille F ^d,e   Essack, Sabiha Y ^a  

^a UNIVERSITY OF KWAZULU NATAL   (South Africa)

^b Centre of Expertise and Biological Diagnostic of Cameroon   (Cameroon)

^c NATIONAL HEALTH LABORATORY SERVICE   (South Africa)

^d UNIVERSITY OF YAOUNDÉ I   (Cameroon)

^e METABIOTA INC   (United States)

Author keywords

Enterobacteriaceae; ESBL; Food chain; Klebsiella pneumoniae; Whole genome sequencing

Indexed keywords

AMINOGLYCOSIDE ANTIBIOTIC AGENT; BETA LACTAM; CHLORAMPHENICOL; GENOMIC DNA; LINCOSAMIDE; MACROLIDE; QUINOLONE DERIVATIVE; RIFAMPICIN; STREPTOGRAMIN DERIVATIVE; SULFONAMIDE; TETRACYCLINE; TRIMETHOPRIM; VIRULENCE FACTOR;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ANTIBIOTIC RESISTANCE GENE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIOPHAGE; BACTERIUM ISOLATION; CAMEROON; CONTROLLED STUDY; DNA ISOLATION; DNA SEQUENCE; EXTENDED SPECTRUM BETA LACTAMASE PRODUCING KLEBSIELLA PNEUMONIAE; GENE; GENETIC ANALYSIS; GENOTYPING TECHNIQUE; HUMAN; HUMAN TISSUE; KLEBSIELLA PNEUMONIAE INFECTION; MOLECULAR EPIDEMIOLOGY; MORPHOLOGICAL TRAIT; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; ORAL BIOPSY; PHYLOGENY; PIG; PLASMID; RECTUM BIOPSY; SLAUGHTERHOUSE; SLAUGHTERHOUSE WORKER; SOUTH AFRICA; THROAT CULTURE; WHOLE GENOME SEQUENCING;

EID: 85041836649     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2018.00188     Document Type: Article

References (37)

1. Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., et al. (2008). The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75
2. Badri, A. M., Ibrahim, I. T., Mohamed, S. G., Garbi, M. I., Kabbashi, A. S., and Arbab, M. H. (2017). Prevalence of extended spectrum beta lactamase (ESBL) producing Escherichia coli, and Klebsiella pneumoniae isolated from raw milk samples in Al Jazirah state, Sudan. Mol. Biol. 7:1000201. doi: 10.4172/2168-9547.1000201
3. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. doi: 10.1089/cmb.2012.0021
4. Belbel, Z., Chettibi, H., Dekhil, M., Ladjama, A., Nedjai, S., and Rolain, J.-M. (2014). Outbreak of an armA methyltransferase-producing ST39 Klebsiella pneumoniae clone in a pediatric Algerian Hospital. Microb. Drug Resist. 20, 310-315. doi: 10.1089/mdr.2013.0193
5. Benzerara, Y., Gallah, S., Hommeril, B., Genel, N., Decré, D., Rottman, M., et al. (2017). Emergence of plasmid-mediated fosfomycin-resistance genes among Escherichia coli isolates, France. Emerg. Infect. Dis. 23, 1564-1567. doi: 10.3201/eid2309.170560
6. Breurec, S., Guessennd, N., Timinouni, M., Le, T. A., Cao, V., Ngandjio, A., et al. (2013). Klebsiella pneumoniae resistant to third-generation cephalosporins in five African and two Vietnamese major towns: multiclonal population structure with two major international clonal groups, CG15 and CG258. Clin. Microbiol. Infect. 19, 349-355. doi: 10.1111/j.1469-0691.2012.03805.x
7. Carattoli, A., Zankari, E., García-Fernández, A., Voldby, L., Lund, O., Villa, L., et al. (2014). In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895-3903. doi: 10.1128/AAC.02412-14
8. Chan, J., Lo, W. U., Chow, K. H., Lai, E. L., Law, P. Y., and Ho, P. L. (2014). Clonal diversity of Escherichia coli isolates carrying plasmid-mediated fosfomycin resistance gene fosA3 from livestock and other animals. Antimicrob. Agents Chemother. 58, 5638-5639. doi: 10.1128/AAC.02700-14
9. Clinical and Laboratory Standards Institute [CLSI] (2016). Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Six Informational Supplement. CLSI Document M100-S26. Wayne, PA: Clinical and Laboratory Standards Institute
10. Diancourt, L., Passet, V., Verhoef, J., Grimont, P. A., and Brisse, S. (2005). Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J. Clin. Microbiol. 43, 4178-4182. doi: 10.1128/jcm.43.8.4178-4182.2005
11. Founou, L. L., Founou, R. C., and Essack, S. Y. (2016). Antibiotic resistance in the food chain: a developing country-perspective. Front. Microbiol. 7:1881. doi: 10.3389/fmicb.2016.01881
12. Gangoue-Pieboji, J., Miriagou, V., Vourli, S., Tzelepi, E., Ngassam, P., and Tzouvelekis, L. S. (2005). Emergence of CTX-M-15-producing enterobacteria in cameroon and characterization of a bla(CTX-M-15)-carrying element. Antimicrob. Agents Chemother. 49, 441-443. doi: 10.1128/AAC.49.1.441-443.2005
13. Grant, J. R., Arantes, A. S., and Stothard, P. (2012). Comparing thousands of circular genomes using the CGView comparison tool. BMC Genomics 13:202. doi: 10.1186/1471-2164-13-202
14. Hou, J., Yang, X., Zeng, Z., Lv, L., Yang, T., Lin, D., et al. (2013). Detection of the plasmid-encoded fosfomycin resistance gene fosA3 in Escherichia coli of food-animal origin. J. Antimicrob. Chemother. 68, 766-770. doi: 10.1093/jac/dks465
15. Hudson, C., Bent, Z., Meagher, R., and Williams, K. (2014). Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain. PLOS ONE 9:e99209. doi: 10.1371/journal.pone.0099209
16. Ito, R., Mustapha, M. M., Tomich, A. D., Callaghan, J. D., McElheny, C. L., Mettus, R. T., et al. (2017). Widespread fosfomycin resistance in gram-negative bacteria attributable to the chromosomal fosA gene. mBio 8:e00749-17. doi: 10.1128/mBio.00749-17
17. Jacobson, R. K., Manesen, M. R., Moodley, C., Smith, M., Williams, S. G., Nicol, M. P., et al. (2015). Molecular characterisation and epidemiological investigation of an outbreak of blaOXA-181 carbapenemase-producing isolates of Klebsiella pneumoniae in South Africa. S. Afr. Med. J. 105, 1030-1035. doi: 10.7196/SAMJ.2015.v105i12.9926
18. Joensen, K. G., Scheutz, F., Lund, O., Hasman, H., Kaas, R. S., Nielsen, E. M., et al. (2014). Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J. Clin. Microbiol. 52, 1501-1510. doi: 10.1128/JCM.03617-13
19. Kim, J. O., Song, S. A., Yoon, E. J., Shin, J. H., Lee, H., Jeong, S. H., et al. (2017). Outbreak of KPC-2-producing Enterobacteriaceae caused by clonal dissemination of Klebsiella pneumoniae ST307 carrying an IncX3-type plasmid harboring a truncated Tn4401a. Diagn. Microbiol. Infect. Dis. 87, 343-348. doi: 10.1016/j.diagmicrobio.2016.12.012
20. Lyonga, E. E., Toukam, M., Nkenfou, C., Gonsu, H. K., Assoumou, M.-C. O., Mesembe, M., et al. (2015). Resistance pattern of enterobacteriaceae isolates from urinary tract infections to selected quinolones in Yaounde. Pan Afr. Med. J. 21:105. doi: 10.11604/pamj.2015.21.105.5469
21. Magoué, C. L., Melin, P., Gangoué-Piéboji, J., Assoumou, M. C. O., Boreux, R., and De Mol, P. (2013). Prevalence and spread of extended-spectrum β-lactamase-producing Enterobacteriaceae in Ngaoundere, Cameroon. Clin. Microbiol. Infect. 19, E416-E420. doi: 10.1111/1469-0691.12239
22. Moussé, W., Noumavo, P. A., Chabi, N. W., Sina, H., Tohoyessou, M. G., Ahoyo, T. A., et al. (2016). Phenotypic and genotypic characterization of extended spectrum β-Lactamase Klebsiella pneumoniae and fluorescent Pseudomonas spp. strains from market garden products and their watering water in Benin (West Africa). Food Nutr. Sci. 7, 192-204. doi: 10.4236/fns.2016.73021
23. Ndebi, G., Kamajou, J., and Ongla, J. (2009). Analyse des contraintes au développement de la production porcine au Cameroun. Tropicultura 27, 70-76
24. Nzalie, R. N.-T., Gonsu, H. K., and Koulla-Shiro, S. (2016). Bacterial etiology and antibiotic resistance profile of community-acquired urinary tract infections in a Cameroonian city. Int. J. Microbiol. 2016:3240268. doi: 10.1155/2016/3240268
25. Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., et al. (2014). The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 42, D206-D214. doi: 10.1093/nar/gkt1226
26. Page, A. J., Cummins, C. A., Hunt, M., Wong, V. K., Reuter, S., Holden, M. T., et al. (2015). Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691-3693. doi: 10.1093/bioinformatics/btv421
27. Perovic, O., Britz, E., Chetty, V., and Singh-Moodley, A. (2016). Molecular detection of carbapenemase-producing genes in referral Enterobacteriaceae in South Africa: a short report. S. Afr. Med. J. 106, 975-977. doi: 10.7196/SAMJ.2016.v106i10.11300
28. Perovic, O., Singh-Moodley, A., Duse, A., Bamford, C., Elliott, G., Swe-Han, K. S., et al. (2014). National sentinel site surveillance for antimicrobial resistance in Klebsiella pneumoniae isolates in South Africa, 2010-2012. S. Afr. Med. J. 104, 563-568. doi: 10.7196/samj.7617
29. Rafiq, Z., Sam, N., and Vaidyanathan, R. (2016). Whole genome sequence of Klebsiella pneumoniae U25, a hypermucoviscous, multidrug resistant, biofilm producing isolate from India. Mem. Inst. Oswaldo Cruz 111, 144-146. doi: 10.1590/0074-02760150423
30. The European Committee on Antimicrobial Susceptibility Testing [EUCAST]. (2016). Breakpoint Tables for Interpretation of MICs and Zone Diameters. Available at: http://www.eucast.org
31. Versalovic, J., Koeuth, T., and Lupski, J. R. (1991). Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19, 6823-6831
32. Villa, L., Feudi, C., Fortini, D., Brisse, S., Passet, V., Bonura, C., et al. (2017). Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone. Microb. Genom. 3:e000110. doi: 10.1099/mgen.0.000110
33. Wachino, J., Yamane, K., Suzuki, S., Kimura, K., and Arakawa, Y. (2010). Prevalence of fosfomycin resistance among CTX-M-producing Escherichia coli clinical isolates in Japan and identification of novel plasmid-mediated fosfomycin-modifying enzymes. Antimicrob. Agents Chemother. 54, 3061-3064. doi: 10.1128/AAC.01834-09
34. World Health Organization [WHO] (2017). (Global) Priority List of Antibiotic Resistant Bacteria to Guide Research, Discoveries and Development of New Antibiotics. Geneva: WHO
35. Xu, H., Miao, V., Kwong, W., Xia, R., and Davies, J. (2011). Identification of a novel fosfomycin resistance gene (fosA2) in Enterobacter cloacae from the Salmon River, Canada. Lett. Appl. Microbiol. 52, 427-429. doi: 10.1111/j.1472-765X.2011.03016.x
36. Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M., Rasmussen, S., Lund, O., et al. (2012). Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640-2644. doi: 10.1093/jac/dks261
37. Zhou, Y., Liang, Y., Lynch, K. H., Dennis, J. J., and Wishart, D. S. (2011). PHAST: a fast phage search tool. Nucleic Acids Res. 39(Suppl. 2), W347-W352. doi: 10.1093/nar/gkr485