Analysis of the Distribution Characteristics and Antibiotic Resistance of Nonfermentative Bacteria Isolated from Urine Cultures

Öz

Nonfermentative bacteria are an important cause of urinary tract infection in patients with underlying disease and hospitalization. The aim of this study was to investigate the distribution and antibiotic resistance profiles of nonfermentative bacteria isolated from urine cultures. Nonfermentative bacteria (n=1,395) isolated from urine samples in the Clinical Microbiology Laboratory of Hacettepe University Faculty of Medicine Hospital between October 2017 and October 2019 were examined retrospectively. The bacteria were identified by conventional methods and MALDI-TOF MS. Antibiotic susceptibility tests were performed with BD Phoenix automated system, disc diffusion, gradient test and broth microdilution. During the study period, 6.6 % of the bacteria isolated from urine cultures were nonfermentative bacteria. Among the nonfermentative bacteria, Pseudomonas spp. (68.3 %) was the most common, followed by Acinetobacter spp. (18.8 %) and Stenotrophomonas maltophilia (9.6 %) respectively. Others were Achromobacter spp. (n=16), Burkholderia spp. (n=6), Alcaligenes faecalis (n=5), Delftia acidovorans (n=5), Chryseobacterium indologenes (n=3), Elizabethkingia meningoseptica (n=3), Myroides spp. (n=2), Comamonas kerstersii (n=1), Cupriavidus spp. (n=1), Ralstonia pickettii (n=1), Roseomonas mucosa (n=1) and Sphingomonas paucimobilis (n=1). Antibiotic resistance rates were highest in Acinetobacter baumannii/calcoaceticus complex isolates. Nonfermentative bacteria cause serious infections and high antibiotic resistance rates are detected in these bacteria. For this reason, each center should determine the distribution and antimicrobial resistance patterns of nonfermentative bacteria at certain intervals.

Anahtar Kelimeler

• antibiotic resistance
• nonfermentative bacteria
• urine culture

İdrar Kültürlerinden İzole Edilen Nonfermentatif Bakterilerin Dağılım Özelliklerinin ve Antibiyotik Direncinin Analizi

Öz

Nonfermentatif bakteriler altta yatan hastalığı olan ve hastanede yatan hastalarda önemli üriner sistem enfeksiyonu etkenleridir. Bu çalışmada idrar kültürlerinden izole edilen nonfermentatif bakterilerin dağılımının ve antibiyotik direnç profillerinin incelenmesi amaçlanmıştır. Hacettepe Üniversitesi Tıp Fakültesi Hastanesi Klinik Mikrobiyoloji Laboratuvarı’nda Ekim 2017-Ekim 2019 tarihleri arasında idrar örneklerinden izole edilen 1.395 nonfermentatif bakteri retrospektif olarak incelenmiştir. Bakterilerin tanımlanması konvansiyonel yöntemler ve MALDI-TOF MS ile yapılmıştır. Antibiyotik duyarlılık testleri BD Phoenix otomatize sistemi, disk difüzyon, gradiyent test ve sıvı mikrodilüsyon ile gerçekleştirilmiştir. Çalışma süresinde idrar kültürlerinden izole edilen bakterilerin % 6,6’sını nonfermentatif bakteriler oluşturmuşlardır. Nonfermentatif bakteriler arasında en sık Pseudomonas spp. (% 68,3) izole edilmiş, bunu sırası ile Acinetobacter spp. (% 18,8) ve Stenotrophomonas maltophilia (% 9,6) izlemiştir. Diğer izole edilen nonfermentatif bakteriler ise Achromobacter spp. (n=16), Burkholderia spp. (n=6), Alcaligenes faecalis (n=5), Delftia acidovorans (n=5), Chryseobacterium indologenes (n=3), Elizabethkingia meningoseptica (n=3), Myroides spp. (n=2), Comamonas kerstersii (n=1), Cupriavidus spp. (n=1), Ralstonia pickettii (n=1), Roseomonas mucosa (n=1) ve Sphingomonas paucimobilis’tir (n=1). Antibiyotik direnç profilleri değerlendirildiğinde en yüksek direnç oranları Acinetobacter baumannii/calcoaceticus kompleks izolatlarında saptanmıştır. Nonfermentatif bakterilerin ciddi enfeksiyonlara neden olmaları ve bu bakterilerde yüksek antibiyotik direnç oranlarının saptanması nedeniyle her merkez belirli aralıklar ile nonfermentatif bakterilerin dağılımını ve antimikrobiyal direnç paternlerini tespit etmelidir.

Anahtar Kelimeler

• antibiyotik direnci
• idrar kültürü
• nonfermentatif bakteriler

Kaynakça

1. Adegoke AA, Stenström TA, Okoh AI. Stenotrophomonas maltophilia as an emerging ubiquitous pathogen: looking beyond contemporary antibiotic therapy. Frontiers in Microbiology. 2017;8:2276-93. https://doi.org/10.3389/fmicb.2017.02276
2. Almuzara M, Cittadini R, Estraviz ML, Ellis A, Vay C. First report of Comamonas kerstersii causing urinary tract infection. New Microbes New Infect. 2018;24:4-7. https://doi.org/10.1016/j.nmni.2018.03.003
3. Bhuyar G, Jain S, Shah H, Mehta V. Urinary tract infection by Chryseobacterium indologenes. Indian Journal of Medical Microbiology. 2012;30(3):370-2. https://doi.org/10.4103/0255-0857.99511
4. Boinett CJ, Cain AK, Hawkey J, Do Hoang NT, Khanh NNT, Thanh DP, et al. Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. Microbial Genomics. 2019;5(2): e000246. https://doi.org/10.1099/mgen.0.000246
5. CDC. Antibiotic Resistance Threats in the United States. 2019. https://www.cdc.gov/drugresistance/pdf/threats-report/2019-ar-threats-report-508.pdf (Erişim tarihi: Ocak 2020)
6. Chin CY, Tipton KA, Farokhyfar M, Burd EM, Weiss DS, Rather PN. A high-frequency phenotypic switch links bacterial virulence and environmental survival in Acinetobacter baumannii. Nature Microbiology. 2018;3(5):563-9. https://doi.org/10.1038/s41564-018-0151-5
7. Cikman A, Parlak M, Bayram Y, Guducuoglu H, Berktas M. Antibiotics resistance of Stenotrophomonas maltophilia strains isolated from various clinical specimens. Afr Health Sci. 2016;16(1):149-52. https://doi.org/10.4314/ahs.v16i1.20
8. Crossman LC, Gould VC, Dow JM, et al. The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Genome Biol. 2008;9(4):R74. https://doi.org/10.1186/gb-2008-9-4-r74

9. Dé I, Rolston KVI, Han XY. Clinical significance of roseomonas species isolated from catheter and blood samples: Analysis of 36 cases in patients with cancer. Clin Infect Dis. 2004;38(11):1579-84. https://doi.org/10.1086/420824
10. del Mar Ojeda-Vargas M, Suarez-Alonso A, de Los Angeles Perez-Cervantes M, Suarez-Gil E, MonzonMoreno C. Urinary tract infection associated with Comamonas acidovorans. Clin Microbiol Infect. 1999;5(7):443-4. https://doi.org/10.1111/j.1469-0691.1999.tb00170.x
11. Enoch DA, Birkett CI, Ludlam HA. Non-fermentative Gram-negative bacteria. Int J Antimicrob Agents. 2007;29(5):S33-S41. https://doi.org/10.1016/S0924-8579(07)72176-3
12. EUCAST. Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0. 2019. https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables. pdf (Erişim tarihi: Ocak 2020)
13. Flores-Mireles AL, Walker JN, Caparon M, Hultgren SJ. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol. 2015;13(5):269-84. https://doi.org/10.1038/nrmicro3432
14. Gajdacs M, Burian K, Terhes G. Resistance levels and epidemiology of non-fermenting gram-negative bacteria in urinary tract infections of inpatients and outpatients (RENFUTI): A 10-Year Epidemiological Snapshot. Antibiotics (Basel). 2019;8(3):143-55. https://doi.org/10.3390/antibiotics8030143
15. Hagiya H, Ogawa H, Takahashi Y, Hasegawa K, Iwamuro M, Otsuka F. A Nephrostomy-associated urinary tract infection caused by elizabethkingia meningoseptica. Intern Med. 2015;54(24):3233-6. https://doi.org/10.2169/internalmedicine.54.4998
16. Hsueh PR, Teng LJ, Yang PC, et al. Nosocomial infections caused by Sphingomonas paucimobilis: clinical features and microbiological characteristics. Clin Infect Dis. 1998;26(3):676-81. https://doi.org/10.1086/514595
17. Hu SH, Yuan SX, Qu H, et al. Antibiotic resistance mechanisms of Myroides sp. J Zhejiang Univ Sci B. 2016;17(3):188-99. https://doi.org/10.1631/jzus.B1500068
18. Jachna-Sawicka K, Gospodarek E. [Evaluation of occurrence of Alcaligenes faecalis in clinical samples of patients of the university hospital in Bydgoszcz]. Med Dosw Mikrobiol. 2009;61(1):87-92.
19. Jefferies JMC, Cooper T, Yam T, et al. Pseudomonas aeruginosa outbreaks in the neonatal intensive care unit - a systematic review of risk factors and environmental sources. Journal of Medical Microbiology. 2012;61(8):1052-61. https://doi.org/10.1099/jmm.0.044818-0
20. Jimenez-Guerra G, Heras-Canas V, Gutierrez-Soto M,, et al. Urinary tract infection by Acinetobacter baumannii and Pseudomonas aeruginosa: evolution of antimicrobial resistance and therapeutic alternatives. J Med Microbiol. 2018;67(6):790-7. https://doi.org/10.1099/jmm.0.000742
21. Kam SK, Lee WS, Ou TY, Teng SO, Chen FL. Delftia acidovorans bacteremia associated with ascending urinary tract infections proved by molecular method. Journal of Experimental & Clinical Medicine. 2012;4(3):180-2. https://doi.org/10.1016/j.jecm.2012.04.010
22. Karlowsky JA, Lagace-Wiens PR, Simner PJ, et al. Antimicrobial resistance in urinary tract pathogens in Canada from 2007 to 2009: CANWARD surveillance study. Antimicrob Agents Chemother. 2011;55(7):3169-75. https://doi.org/10.1128/AAC.00066-11
23. Kobayashi T, Nakamura I, Fujita H, et al. First case report of infection due to Cupriavidus gilardii in a patient without immunodeficiency: a case report. BMC Infect Dis. 2016;16:493. https://doi.org/10.1186/s12879-016-1838-y
24. Lee KW, Lee ST, Cho H. Burkholderia cepacia causing nosocomial urinary tract infection in children. Child Kidney Dis. 2015;19(2):143-7. https://doi.org/10.3339/chikd.2015.19.2.143
25. Li FK, Chan KW, Chan TM, Lai KN. Burkholderia urinary tract infection after renal transplantation. Transplant Infectious Disease. 2003;5(1):59-61. https://doi.org/10.1034/j.1399-3062.2003.00006.x
26. Lu PL, Liu YC, Toh HS, et al. Epidemiology and antimicrobial susceptibility profiles of Gram-negative bacteria causing urinary tract infections in the AsiaPacific region: 2009-2010 results from the study for monitoring antimicrobial resistance erends (SMART). Int J Antimicrob Agents. 2012;40 Suppl:S37-43. https://doi.org/10.1016/S0924-8579(12)70008-0
27. Matar GM. Editorial: Pseudomonas and Acinetobacter: From drug resistance to pathogenesis. Front Cell Infect Microbiol. 2018;8:68. https://doi.org/10.3389/fcimb.2018.00068
28. Medina M, Castillo-Pino E. An introduction to the epidemiology and burden of urinary tract infections. Ther Adv Urol. 2019;11:1756287219832172. https://doi.org/10.1177/1756287219832172
29. Morrissey I, Hackel M, Badal R, Bouchillon S, Hawser S, Biedenbach D. A review of ten years of the study for monitoring antimicrobial resistance trends (SMART) from 2002 to 2011. Pharmaceuticals (Basel). 2013;6(11):1335-46. https://doi.org/10.3390/ph6111335
30. Omar A, Camara M, Fall S, et al. Chryseobacterium indologenes in a woman with acute leukemia in Senegal: a case report. Journal of Medical Case Reports. 2014;8(1):138-42. https://doi.org/10.1186/1752-1947-8-138
31. Orme J, Rivera-Bonilla T, Loli A, Blattman NN. Native valve endocarditis due to Ralstonia pickettii: A case report and literature review. Case Rep Infect Dis. 2015;2015:324675. https://doi.org/10.1155/2015/324675
32. Raghavan S, Thomas B, Shastry BA. Elizabethkingia meningoseptica: emerging multidrug resistance in a nosocomial pathogen. BMJ Case Reports. 2017;2017:bcr-2017-221076. https://doi.org/10.1136/bcr-2017-221076
33. Ryan MP, Adley CC. Sphingomonas paucimobilis: a persistent Gram-negative nosocomial infectious organism. J Hosp Infect. 2010;75(3):153-7. https://doi.org/10.1016/j.jhin.2010.03.007
34. Tandogdu Z, Wagenlehner FM. Global epidemiology of urinary tract infections. Curr Opin Infect Dis. 2016;29(1):73-9. https://doi.org/10.1097/QCO.0000000000000228
35. Tena D, Gonzalez-Praetorius A, Perez-Balsalobre M, Sancho O, Bisquert J. Urinary tract infection due to Achromobacter xylosoxidans: report of 9 cases. Scand J Infect Dis. 2008;40(2):84-7. https://doi.org/10.1080/00365540701558714
36. Weiner LM, Webb AK, Limbago B, et al. Antimicrobialresistant pathogens associated with healthcareassociated infections: summary of data reported to the national healthcare safety network at the centers for disease control and prevention, 2011-2014. Infect Control Hosp Epidemiol. 2016;37(11):1288-301. https://doi.org/10.1017/ice.2016.174
37. Wong D, Nielsen TB, Bonomo RA, Pantapalangkoor P, Luna B, Spellberg B. Clinical and pathophysiological overview of Acinetobacter infections: a century of challenges. Clinical Microbiology Reviews. 2017;30(1):409-47. https://doi.org/10.1128/CMR.00058-16