Monitoring of antimicrobial resistance in uropathogens from community residents and genetic correlation with isolated resistance determinants from Enterobacterales present in meat consumption

Urinary tract infection (UTI) is the most frequent infection in hospital and community settings, and E. coli is the main uropathogen. E. coli is also becoming highly resistant to first-line antibiotics. In parallel, the various environmental compartments, from wastewater treatment systems to agriculture, in particular poultry and swine production operations, show high rates of bacteria resistant to antimicrobials, thus contributing to the amplification and dissemination of resistance genes. This study thus aimed to monitor antimicrobial resistance in community-acquired bacteria causing UTI and to correlate it with the genetic determinants of resistance in E. coli isolates from animal sources.

A total of 34,293 microorganisms isolated from urine cultures were analyzed during the project period. Samples were collected from patients in primary and emergency care units in Londrina, Paraná, from June 2016 to May 2019. In parallel, samples of different brands of poultry and pork sold in supermarkets in Londrina were studied. Antimicrobial identification and sensitivity tests were performed with the VITEKⓇ 2 automated system. Isolates resistant to cephalosporins and/or carbapenems and fluoroquinolones were submitted to phenotypic tests for resistance characterization. Genetic similarity between isolates was evaluated with the ERIC-PCR technique and subsequently sequenced on the NextSeq platform (Illumina). We also compared E. coli isolates from intestinal microbiota of omnivores to that of vegetarians and/or vegans. The main virulence factors and production of β-lactamases of E. coli were analyzed by PCR and classified into phylogenetic groups.

Of all the samples analyzed, 90% were gram-negative microorganisms belonging to the Enterobacterales family. The microorganism identified most often in community urine cultures was E. coli (66.8%), of which 1,480 (6.9%) were ESBL producers.

22,189 isolates of urinary E. coli were used in the sensitivity tests performed with first-line drugs utilized in UTI treatment. The tests showed that 50% of the samples were sensitive to ampicillin, 49.8% to cephalothin, 70% to quinolones and fluoroquinolones, 80% to sulfamethoxazole/ trimethoprim, and 95% to nitrofurantoin. Quinolones resistance increased proportionally with age, as did ESBL-producing samples.

The most frequent genes that encode the production of ESBL were bla CTX-M-15 (29,17%), bla CTX-M-8 (16,67%), bla CTX-M-2 (12,50%), bla CTX-M-55 (12,50%), and bla CTX-M-14(10,42%). The most common sequence types (ST) in urine samples were ST131 (17.46%), ST648 (11.11%), ST38(7.94%), ST354 (6.35%), and ST10 (4.76%). The most frequent resistance mechanisms for quinolones were mutations in the region gyrA and parC (QRDR) and aac(6')-ib-cr genes. The combination of quinolone resistance genes associated with ESBL production genes reduces the antimicrobial arsenal for treating uncomplicated UTIs, especially in the community.

From the 100 samples of selected meats sold by various retailers in markets close to the health units, a total of 168 isolates were detected (102 from poultry and 67 from pork). Fifty-three strains were isolated from chicken samples, 23 of which were selected for whole genome sequencing. Among the poultry isolates, the analyses showed 32 different resistance genes, the most frequent being aadA1 (60,38%), sul2 (56.60%), sul1(47.17%), and bla TEM-1B (7.38%), and 15 virulence genes, such as iss (71.2%), iroN (51.9%), IpfA (40.4%), astA (44.4%), and cma (38.5%). The main genes encoding ESBL production were blaCTX-M-55(41.51%) and blaCTX-M-2 (33.96%). The two quinolone resistance genes in the poultry isolates were QnrB19 (13.21%) and QnrS1 (1.89%). The quinolone resistance genes found in these poultry isolates were blaTEM-1B (39.13%), sul2(43.48%), blaCTX-M-55 (43.48%), aadA1 (39.13%), and fosA (34.78%), and 29 virulence genes, mainly iss (66.70%), IpfA (62.50%), eilA (29.2%), astA (41.7%), and air (16.7%). The genes encoding ESBL production were bla CTX-M-55 (41.51%), blaCTX-M-2 (13.04%), bla CTX-M-15 (13.04%), and blaCTX-8(8.70%). The genes responsible for quinolone resistance found in pork isolates were QnrB19 (13.04%) and aac(6')Ib-cr (4.35%).

The genes encoding ESBL were blaCTX-M-2 (ST38, ST57, and ST117), blaCTX-M-8 (ST1485), bla CTX-M-14 (ST38 and ST354), blaCTX-M-15 (ST131 and ST410), blaCTX- M-24 (ST354), blaCTX-M-27 (ST38 and ST131), blaCTX-M-55 (ST38, ST117, ST131, ST131, ST354, ST1196, and ST1485), and bla KPC-2(ST354). The most frequent sequence types were ST131, 38, and 354. ST131 correlated closely with blaCTX-M-15 gene expression, found in 8 urine isolates.

A total of 118 patients were selected (60 omnivores and 58 vegetarians and/or vegans) to compare their microbiota isolates and dietary habits. Although there was no significant difference in the resistance profile between the groups, the presence of ESBL was verified in 7 samples from the vegetarian/vegan group and three from the omnivore group.

Recent studies correlated the consumption of chicken and pork with the acquisition of antimicrobial-resistant bacteria, causing community UTIs. Virulence factors and genetic determinants of resistance (plasmids, integrons, and transposons) have been found to be shared between samples of meat products and UTIs in humans, thus revealing that consumption of these products may lead to acquisition of resistant bacteria and/or antimicrobial resistance genes, hampering usual first-line treatment for UTI treatment in primary healthcare.

The findings indicate the pressing need to establish local and national monitoring systems for antimicrobial resistance in Brazil to provide data to support UTI treatment guidelines. The results for AMR rates in E. coli isolates from chicken and pork in the city of Londrina highlight the need for surveillance to monitor the use of antimicrobials in poultry and livestock.

The team intends to conduct continuing education in UTI diagnosis and treatment in the community and to expand studies for the development of an alternative product, phagotherapy, to be used in swine and poultry farms and in the treatment of UTIs caused by epidemic strains (e.g., CTX-M-15, ST 131). The team also plans to use SMART CDSS to improve diagnosis and antibiotic therapy and assist health professionals in diagnosing and treating UTIs, besides developing a rapid test to detect quinolones resistance in E. coli isolates from community UTIs.