Phylogeny, sequence-typing and virulence profile of uropathogenic Escherichia coli (UPEC) strains from Pakistan

Abstract

Background Escherichia coli lineage ST131 predominates across various spectra of extra-intestinal infections, including urinary tract infection (UTI). The distinctive resistance profile, diverse armamentarium of virulence factors and rapid global dissemination of ST131 E. coli makes it an intriguing pathogen. However, not much is known about the prevalence and genetic attributes of ST131 lineage in Pakistan. Methods We estimated prevalence and genetic attributes of E. coli ST131 isolates causing UTI among 155 randomly selected samples. Samples were analyzed for phylogenetic grouping, O-typing and fum C/ fim H typing. Isolates were further tested for the ESBL and virulence factors using PCR. Results Overall, 59% of the UPEC isolates belonged to the phylogenetic group B2, followed by D = 28%, B1 = 8% and A = 5%. Among 18 different Sequence-types, ST131 was the dominant lineage ( n = 71; 46%) out of which 72% of the isolates were assigned to the phylogenetic group B2, while 61% adhered to the serogroup O25b. Fum C/ fim H typing confirmed 49% of the ST131 as H30 sub-types. In this study, significant numbers of the identified ST131 isolates were MDR and 42% showed ESBL phenotypes, out of which 37% carried bla - CTX-M-15 . Moreover, different virulence factors were detected in following percentages: fim H,155(100%), iut A 86 (55%), feo B 76 (49%), pap C 75 (48%), papGII 70 (45%), kpsMTII 40 (26%), pap EF 37 (24%), fyu A 37 (24%), usp 22 (14%), pap A 20 (13%), sfa/foc 20 (13%), hly A 18 (12%), afa 15 (10%), cdt B 11 (7%), papGI 6 (4%), papGIII 6 (4%), kpsMTIII 4 (3%) and bma E2 (1%). Conclusion Conclusively, this study provides important insight into the genetic and virulence attributes of pandemic MDR ST131 strains involved in UTIs. It also highlights higher prevalence of ST131-O25b-H30 UPEC isolates in patients, which was previously unreported from this part of globe.

Prevalence of E. coli ST131 among Uropathogenic E. coli Isolates from Iraqi Patients in Wasit Province, Iraq

“…This may be due to the low percent (1.1%) of B2 isolation in his study. This prevalence of E. coli ST131 (15.1% and 44.7% of total and B2 E. coli isolates, respectively) among UPEC isolates from Iraqi patients included in this study was in accordance with what is globally known by other researchers [ 2 , 3 , 17 , 19 , 25 ], where this clone is successfully disseminated worldwide, and it has become the most predominant lineage associated with a variety of infections around the globe [ 2 , 17 ]. This high dissemination may be due to several reasons, the most important one is the epidemic potential, and virulence and multidrug resistance ability, as well as its predominance in the human gut, make them rapidly disseminated worldwide, with a high capability of causing extraintestinal infections, particularly UTIs.…”

“…Thus, rapid initiation of appropriate empirical treatment requires a good knowledge of epidemiological data concerning the sensitivity of uropathogens to antibacterial agents [ 34 ]. In this investigation, the highest rate of resistance in E. coli ST131 isolates was against β -lactams, tetracycline, trimethoprim-sulfamethoxazole, nalidixic acid, and ciprofloxacin which was comparable with the results of several studies around the globe [ 3 , 17 , 19 , 27 , 32 , 35 , 36 ], and this may be due to several reasons including inexpensive antimicrobials, indiscriminate antibiotic usage without medical prescription, and use of antibiotics for a nonoptimal duration. In addition, plasmids harboring resistance determinants can be transferred between bacteria, even between species, leading to the acquisition of resistance to new antibiotics via the emergence of mutant strains [ 4 ].…”

“…In addition, the low resistance rates against aminoglycosides (gentamicin: 17.6% and amikacin: 5.8%) reported in the present study may be attributed to the rare use of these antibiotics in AL-Kut hospitals which may be due to their high costs in comparison with β -lactams [ 37 ]. Similar resistance results of E. coli ST131 clone against gentamicin and amikacin (33.3%, 2.8%; 30%, 5%; and 44.2%, 10.4%, respectively) were revealed by Namaei et al [ 3 ], Ali et al [ 17 ], and Hojabri et al [ 26 ], respectively. Nitrofurantoin resistance was also noted in 5.8% of E. coli ST131 clinical isolates, and comparable frequencies (10%, 11.4%, and 6%, respectively) were reported by many researchers [ 17 , 32 , 38 ].…”

“…This high prevalence of group B2 among UPEC isolates obtained in this study is in agreement with what it is well known worldwide, such as studies conducted by Iraqi researchers [ 1 , 15 , 16 ]. In addition, studies from different countries [ 14 , 17 – 19 ] indicated that this group was the most prevalent among UPEC isolates. This predominance of group B2 among UPEC isolates may be attributed to the fact that most virulence factors and antibiotic resistance genes existed jointly within this group and this could increase survival fitness in the urinary tract as recognized by many researchers [ 17 , 20 , 21 ].…”

Virulence Factors and Phylogenetic Characteristics of Uropathogenic <i>Eschericihia coli</i> Strains Isolated in Saratov

“…таким образом, в исследуемой выборке штаммов упэк выявлено превалирование филогенетической подгруппы B2 3 , что соответствует литературным данным по исследованию частоты встречаемости данной подгруппы среди культур E. coli, выделенных из мочи пациентов с имп [4]. у штаммов филогенетических групп B2 и D, которые наиболее часто принадлежат к упэк, выявлено наличие определенного набора факторов вирулентности, способствующих выживанию, колонизации и персистенции возбудителя в мочевыводящих путях [4,10,11]. в данной работе гены, кодирующие основные факторы вирулентности штаммов упэк, являющихся возбудителями имп, распределены среди четырех групп, как описано ниже, на основании общепринятых литературных данных [12][13][14][15].…”