Distribution of quinolone resistance gene (qnr) in ESBL-producing Escherichia coli and Klebsiella spp. in Lomé, Togo

Prevalence of plasmid-mediated quinolone resistance genes and biofilm formation in different species of quinolone-resistant clinical Shigella isolates: a cross-sectional study

BACKGROUND

The purpose of this study was to look into the presence of plasmid-mediated quinolone resistance (PMQR) genes and biofilm formation in several species of clinical Shigella isolates that were resistant to quinolones.

METHODS

The stool samples of 150 patients (younger than 10 years) with diarrhea were collected in this cross-sectional study (November 2020 to December 2021). After cultivation of samples on Hektoen Enteric agar and xylose lysine deoxycholate agar, standard microbiology tests, VITEK 2 system, and polymerase chain reaction (PCR) were utilized to identify Shigella isolates. The broth microdilution method was used to determine antibiotic susceptibility. PMQR genes including qnrA, qnrB, qnrC, qnrD, qnrE, qnrS, qnrVC, qepA, oqxAB, aac(6')-Ib-cr, and crpP and biofilm formation were investigated in quinolone-resistant isolates by PCR and microtiter plate method, respectively. An enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) technique was used to determine the clonal relatedness of quinolone-resistant isolates.

RESULTS

A total of 95 Shigella isolates including S. sonnei (53, 55.8%), S. flexneri (39, 41.1%), and S. boydii (3, 3.2%) were identified. The highest resistance rates of the isolates were against ampicillin (92.6%, n = 88/95). Overall, 42 of 95 (44.2%) isolates were simultaneously resistant against two or more quinolones including 26 (61.9%) S. sonnei and 16 (38.1%) S. flexneri. All isolates were multidrug-resistant (resistance to more than 3 antibiotics). The occurrence of PMQR genes was as follows: qnrS (52.4%), qnrA and aac(6')-Ib-cr (33.3%), and qnrB (19.0%). The prevalence in species was as follows: 61.5% and 37.5% (qnrS), 19.2% and 56.3% (qnrA), 38.5% and 25.0 (aac(6')-Ib-cr), and 19.2% and 18.8% (qnrB) for S. sonnei and S. flexneri, respectively. The other PMQR genes were not detected. In total, 52.8% (28/53) of quinolone-susceptible and 64.3% (27/42) of quinolone-resistant isolates were biofilm producers. Biofilm formation was not significantly different between quinolone-resistant and quinolone-susceptible isolates (P-value = 0.299). Quinolone-resistant isolates showed a high genetic diversity according to the ERIC-PCR.

CONCLUSION

It seems that qnrS, qnrA, and aac(6')-Ib-cr play a significant role in the quinolone resistance among Shigella isolates in our region. Also the quinolone-resistant S. flexneri and S. sonnei isolates had a high genetic diversity. Hence, antibiotic therapy needs to be routinely revised based on the surveillance findings.

Prevalence and characterization of quinolone resistance and integrons in clinical Gram-negative isolates from Gaza strip, Palestine

BACKGROUND

Gram-negative bacteria with quinolone resistance and extended-spectrum beta-lactamases (ESBLs) present significant treatment challenges. This study evaluated the prevalence and characteristics of quinolone resistance in Gram-negative strains, investigating the relationship between plasmid-mediated quinolone resistance (PMQR), ESBLs, and integrons.

METHODS AND RESULTS

We collected 146 Gram-negative isolates from patients in three Palestinian hospitals. For quinolone resistance isolates, the presence and characterization of PMQR, β-lactamase genes and integrons were studied by PCR and sequencing. Out of 146 clinical isolates, 64 (43.8%) were resistant to quinolones, with 62 (97%) being multidrug-resistant (MDR) and 33 (51.5%) ESBL-producers. PMQR-encoding genes were present in 45 (70.3%) isolates, including aac(6')-Ib-cr (26.6%), qnrA (18.8%), qnrS1 (20.8%), and qnrB (6.4%). BlaCTX-M genes were detected in 50% (32/64) of isolates, with blaCTX-M-15 being the most common. BlaTEM-1, blaSHV-1 and blaVIM genes were found in 13, 6, and 4 isolates, respectively. Class I integrons were found in 31/64 (48%) of isolates, with 14 containing gene cassettes conferring resistance to trimethoprim (dhfr17, dfrA12, dfrA1) and aminoglycosides resistance genes (aadA1, aadA2, aadA5, and aadA6).

CONCLUSIONS

This study found a high rate of quinolone resistance, ESBL and integrons in clinical Gram-negative isolates from our hospitals. Urgent measures are crucial, including implementing an antimicrobial resistance surveillance system, to control and continuously monitor the development of antimicrobial resistance.

Investigation of gyrA and parC mutations and the prevalence of plasmid-mediated quinolone resistance genes in Klebsiella pneumoniae clinical isolates

BACKGROUND

The emergence of fluoroquinolone resistance in clinical isolates of Klebsiella pneumoniae is a growing concern. To investigate the mechanisms behind this resistance, we studied a total of 215 K. pneumoniae isolates from hospitals in Bushehr province, Iran, collected between 2017 and 2019. Antimicrobial susceptibility test for fluoroquinolones was determined. The presence of plasmid mediated quinolone resistance (PMQR) and mutations in quinolone resistance-determining region (QRDR) of gyrA and parC genes in ciprofloxacin-resistant K. pneumoniae isolates were identified by PCR and sequencing.

RESULTS

Out of 215 K. pneumoniae isolates, 40 were resistant to ciprofloxacin as determined by E-test method. PCR analysis revealed that among these ciprofloxacin-resistant isolates, 13 (32.5%), 7 (17.5%), 40 (100%), and 25 (62.5%) isolates harbored qnrB, qnrS, oqxA and aac(6')-Ib-cr genes, respectively. Mutation analysis of gyrA and parC genes showed that 35 (87.5%) and 34 (85%) of the ciprofloxacin-resistant isolates had mutations in these genes, respectively. The most frequent mutations were observed in codon 83 of gyrA and codon 80 of parC gene. Single gyrA substitution, Ser83→ Ile and Asp87→Gly, and double substitutions, Ser83→Phe plus Asp87→Ala, Ser83→Tyr plus Asp87→Ala, Ser83→Ile plus Asp87→Tyr, Ser83→Phe plus Asp87→Asn and Ser83→Ile plus Asp87→Gly were detected. In addition, Ser80→Ile and Glu84→Lys single substitution were found in parC gene.

CONCLUSIONS

Our results indicated that 90% of isolates have at least one mutation in QRDR of gyrA orparC genes, thus the frequency of mutations was very significant and alarming in our region.

Phenotypic and genotypic characterization of extended-spectrum beta-lactamase-producing Enterobacteriaceae in a Moroccan hospital

Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) is a major public health problem in hospitals and in the community. The objective of this work was to describe the epidemiology of ESBL-E, to study their resistance profile and to determine the genes encoding the ESBL phenotype. This is a retrospective study conducted in the bacteriology laboratory of the Mohamed V Military Training Hospital in Rabat, and covering all isolates of Enterobacteriaceae from 1 January 2018 to 31 December 2020. The molecular study of ESBL genes involved a representative sample of all ESBL isolates. The overall prevalence of ESBLs in isolated Enterobacteriaceae (1402/10268) is 13.65 %. The urinary tract was the main site of isolation of ESBL (61 %). The bacterial species most concerned are Escherichia coli (41.9 %), Klebsiella pneumoniae (42.2 %) and Enterobacter cloacae (11.9 %). The study of antibiotic susceptibility showed a resistant profile marked mainly by 100 % resistance to first generation cephalosporins (1GC) and third generation cephalosporins (3GC), 55 % to piperacillin-tazobactam, 16 % to imipenem, and 87 % to fluoroquinolones. Molecular typing of ESBL strains showed a prevalence of CTX-M (95 %), SHV (50 %) and TEM (56 %). The CTX-M-1 and the CTX-M-9 groups were the most common (96.19 % and 7.62 % respectively), and CTX-M15 was found in 78.10 % of CTX-M-1 ESBL positive isolates. Most strains had more than two coexisting resistance genes. The prevalence rate of ESBL-E is critical, and preventive action at different levels (prescriber, biologist, hospital, patient, etc.) are necessary in order to limit their spread and to manage a better therapeutic strategy.

High Carriage of tetA, sul1, sul2 and bla TEM Resistance Genes among the Multidrug-resistant Uropathogenic Escherichia coli (UPEC) Strains from Malaysian Patients

The rapid emergence of multidrug-resistant (MDR) uropathogenic Escherichia coli (UPEC) strains pose a critical challenge in urinary tract infection (UTI) treatments. However, little work elucidated the resistance mechanisms of the MDR UPEC clinical strains in Malaysia. Therefore, this study aimed to determine the antimicrobial susceptibility profiles and the prevalence of antimicrobial resistance genes among the UPEC strains. Polymerase chain reactions were conducted to detect the presence of 6 antimicrobial resistance genes among 60 UPEC strains. Meanwhile, the antimicrobial resistance profiles against 9 antimicrobials were examined through the Kirby-Bauer disk diffusion method. In this study, the MDR isolates accounted for 40.0% (24/60), with the highest prevalence of resistance towards ampicillin (43/60; 71.7%), followed by tetracycline (31/60; 51.7%), nalidixic acid (30/60; 50.0%), co-trimoxazole (20/60, 33.3%), ciprofloxacin (19/60, 31.7%), levofloxacin (16/60, 21.6%) and chloramphenicol (10/60, 16.7%). In contrast, low resistance rates were observed among minocycline (1/60; 1.7%) and imipenem (0/60; 0.0%). bla TEM was the most prevalent gene (36/60; 60.0%), followed by tetA (27/60; 45.0%), sul2 (25/60; 41.7%), sul1 (13/60; 21.7%) and tetB (8/60; 13.3%). Surprisingly, bla SHV was not detected among the UPEC isolates. The MDR, ampicillin and tetracycline-resistant isolates were significantly associated with a higher prevalence of tetA, sul1, sul2 and bla TEM. In contrast, tetB displayed no significant relationship with any of the antimicrobials tested. The patient's age and gender were not the risk factors for the carriage of the resistance genes. Our findings identified the common resistance genes carried by the antimicrobial resistant UPEC isolates and provide valuable insights into developing the best antibiotic prescription regime to treat UTIs in our local scene.

Distribution and genetic characterization of fluoroquinolone resistance gene qnr among Salmonella strains from chicken in China

The prevalence and dissemination of the plasmid-mediated fluoroquinolone (FQ) resistance gene qnr in Salmonella are considered serious public health concerns worldwide. So far, no comprehensive large-scale studies have focused on the prevalence and genetic characteristics of the qnr gene in Salmonella isolated from chickens. Herein, this study aimed to investigate the prevalence, antimicrobial resistance (AMR) patterns, and molecular characteristics of chicken-originated qnr-positive Salmonella strains from chicken farms, slaughterhouses, and markets in 12 provinces of China in 2020-2021. The overall prevalence of the qnr gene was 21.13% (56/265), with the highest prevalence in markets (36.11%, 26/72), followed in farms (17.95%, 21/117), and slaughterhouses (10.53%, 9/76). Only the qnrS and qnrB genes were detected, and the prevalence rate of the qnrS gene (19.25%, 51/265) was higher than that of the qnrB gene (1.89%, 5/265). Whole genome sequencing identified 37 distinct AMR genes and 15 plasmid replicons, and the most frequent mutation in quinolone resistance determining regions was parC (T57S; 91.49%, 43/47). Meanwhile, four different qnrS and two qnrB genetic environments were discovered among 47 qnr-positive Salmonella strains. In total, 21.28% (10/47) of the strains were capable of conjugative transfer, and all were qnrS1-positive strains, with the majority of transferable plasmids being IncHI2 types (n = 4). Overall, the prevalence of qnr-positive Salmonella strains from chickens in China and their carriage of multiple resistance and virulence genes and transferable plasmids is a major concern, which calls for continuous surveillance of qnr-positive Salmonella and the development of measures to control its prevalence and transmission.IMPORTANCESalmonella is a common foodborne pathogen responsible for 155,000 deaths annually worldwide. Fluoroquinolones (FQs) are used as first-line drugs for the treatment of Salmonella infections in several countries and regions. However, the emergence and increasing prevalence of the FQ-resistant gene qnr in Salmonella isolated from chickens have been widely reported. Gaining insight into the genetic mechanisms of AMR genes in chicken could lead to the development of preventive measures to control and reduce the risk of drug resistance. In this study, we identified qnr-positive Salmonellae isolated from chickens in different regions of China and their AMR patterns and genome-wide characteristics, providing a theoretical basis for further control of their prevalence and transmission.

High carriage of plasmid-mediated quinolone resistance (PMQR) genes by ESBL-producing and fluoroquinolone-resistant Escherichia coli recovered from animal waste dumps

BACKGROUND

There has been a rise in the consumption of fluoroquinolones in human and veterinary medicine recently. This has contributed to the rising incidence of quinolone resistance in bacteria. This study aimed at the determination of the antibiotic resistance profile of ESBL-producing and fluoroquinolone-resistant E. coli (FQEC) isolated from animal waste obtained from the waste dumps of an agricultural farm and their carriage of genes encoding PMQR.

METHODS AND RESULTS

Isolation of ESBL-producing E. coli from animal waste samples was done on CHROMagar ESBL, while presumptive isolates were purified, and identified via the detection of uidA gene. Susceptibility to a panel of ten antibiotics was done using the disc diffusion method, and detection of PMQR genes (qnrA, qnrB, qnrS, aac(6')-lb-cr, qepA and oqxAB) was done using monoplex and duplex PCR. Twenty-five ESBL-producing and FQEC were obtained from the cattle (6), piggery (7) and poultry (12) waste dumps of the farm. There was 100% resistance to cefpodoxime, cefotaxime, enrofloxacin, trimethoprim-sulfamethoxazole and penicillin by the isolates. The resistance to the other antibiotics was streptomycin (48%), ceftazidime (24%), while no isolate resisted amoxicillin-clavulanate and imipenem. The frequencies of PMQR genes detected were; qnrA (96%), oqxAB (96%), qnrB (92%), while  qnrS was detected in 88% (22) of the isolates. Aminoglycoside acetyltransferase (aac(6')-lb-cr) and quinolone efflux pump (qepA) were each detected in 20 (80%) of the isolates.

CONCLUSIONS

This study showed that animal wastes disposed indiscriminately into dumps could be a budding 'hotspot' for multidrug resistant, ESBL-producing and fluoroquinolone-resistant E. coli carrying multiple genes encoding resistance to fluoroquinolone antibiotics.

A longitudinal epidemiology study of fluoroquinolone-nonsusceptible Klebsiella pneumoniae reveals an increasing prevalence of qnrB and qnrS in Taiwan

BACKGROUND

Our objective was to investigate the prevalence of plasmid-mediated quinolone resistance (PMQR) genes in fluoroquinolone-nonsusceptible Klebsiella pneumoniae (FQNSKP) in Taiwan, 1999-2022.

METHODS

A total of 938 FQNSKP isolates were identified from 1966 isolates. The presence of PMQR and virulence genes, antimicrobial susceptibility, capsular types, and PMQR-plasmid transferability were determined.

RESULTS

An increasing number of PMQR-containing FQNSKP isolates were observed over the study period. Our results showed that 69.0% (647 isolates) of FQNSKP isolates contained at least one PMQR gene, and 40.6%, 37.0%, and 33.9% of FQNSKP carried aac(6')-Ib-cr, qnrB, and qnrS, respectively. None of FQNSKP carried qepA and qnrC. The most common combination of PMQR genes was aac(6')-Ib-cr and qnrB (12.3%). The presence of PMQR genes is strongly related to resistance to aminoglycoside, cephalosporin, tetracycline, and sulfamethoxazole/trimethoprim in FQNSKP. The capsular serotype K64 is the most common serotype we tested in both the non-PMQR and PMQR FQNSKP isolates, while K20 showed a higher prevalence in PMQR isolates. The magA and peg-344 genes showed a significantly higher prevalence rate in non-PMQR isolates than in PMQR isolates. Eleven isolates that carried the PMQR and carbapenemase genes were identified; however, three successful transconjugants showed that the PMQR and carbapenemase genes were not located on the same plasmid.

CONCLUSIONS

Our results indicated an increasing prevalence of PMQR genes, especially qnrB and qnrS, in FQNSKP in Taiwan. Moreover, the distribution of PMQR genes was associated with capsular serotypes and antimicrobial resistance gene and virulence gene distribution in FQNSKP.

Contribution of genetic factors towards cefotaxime and ciprofloxacin resistance development among Extended spectrum beta-lactamase producing-Quinolone resistant pathogenic Enterobacteriaceae

β-lactams and quinolones are widely utilised to treat pathogenic Enterobacterial isolates worldwide. Due to improper use of these antibiotics, both ESBL producing and quinolone resistant (ESBL-QR) pathogenic bacteria have emerged. Nature of contribution of beta-lactamase (bla)/quinolone resistant (QR) genes, efflux pumps (AcrAB-TolC) over-expression and outer membrane proteins (OMPs) /porin loss/reduction and their combinations towards development of this phenotype were explored in this study. Kirby-Bauer disc diffusion method was used for phenotypic characterization of these bacteria and minimum inhibitory concentration of cefotaxime and ciprofloxacin was determined by broth micro dilution assay. Presence of bla, QR, gyrA/B genes was examined by PCR; acrB upregulation by real-time quantitative PCR and porin loss/reduction by SDS-PAGE. Based on antibiogram, phenotypic categorization of 715 non-duplicate clinical isolates was: ESBL+QR+ (n = 265), ESBL+QR- (n = 6), ESBL-QR+ (n = 346) and ESBL-QR-(n = 11). Increased OmpF/K35 and OmpC/K36 reduction, acrB up-regulation, prevalence of bla, QR genes and gyrA/B mutation was observed among the groups in following order: ESBL+QR+> ESBL-QR+> ESBL+QR-> ESBL-QR-. Presence of bla gene alone or combined porin loss and efflux pump upregulation or their combination contributed most for development of a highest level of cefotaxime resistance of ESBL+QR+ isolates. Similarly, combined presence of QR genes, porin loss/reduction, efflux pump upregulation and gyrA/B mutation contributed towards highest ciprofloxacin resistance development of these isolates.

Molecular characterization of extended-spectrum β-lactamase-producing Escherichia coli isolated from lower respiratory tract samples between 2002 and 2019 in the Central Slovenia region

BACKGROUND

Antibiotic resistance is one of the most serious global health problems and threatens the effective treatment of bacterial infections. Of greatest concern are infections caused by extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC). The aim of our study was to evaluate the prevalence and molecular characteristics of ESBL-EC isolated over an 18-year pre-COVID period from lower respiratory tract (LRT) samples collected from selected Slovenian hospitals.

OBJECTIVES AND METHODS

All isolates were identified by MALDI-TOF and phenotypically confirmed as ESBLs by a disk diffusion assay. Using a PCR approach, 487 non-repetitive isolates were assigned to phylogroups, sequence type groups, and clonal groups. Isolates were also screened for virulence-associated genes (VAGs) and antimicrobial resistance genes.

RESULTS

The prevalence of ESBL-EC isolates from LRT in a large university hospital was low (1.4%) in 2005 and increased to 10.8% by 2019. The resistance profile of 487 non-repetitive isolates included in the study showed a high frequency of group 1 blaCTX-M (77.4%; n = 377), blaTEM (54.4%; n = 265) and aac(6')-Ib-cr (52%; n = 253) genes and a low proportion of blaSHV and qnr genes. Isolates were predominantly assigned to phylogroup B2 (73.1%; n = 356), which was significantly associated with clonal group ST131. The ST131 group accounted for 67.6% (n = 329) of all isolates and had a higher number of virulence factor genes than the non-ST131 group. The virulence gene profile of ST131 was consistent with that of other extraintestinal pathogenic E. coli (ExPEC) strains and was significantly associated with ten of sixteen virulence factor genes tested. Using ERIC-PCR fingerprinting, isolates with the same ERIC-profile in samples from different patients, and at different locations and sampling dates were confirmed, indicating the presence of "hospital-adapted" strains.

CONCLUSION

Our results suggest that the ESBL-EC isolates from LRT do not represent a specific pathotype, but rather resemble other ExPEC isolates, and may be adapted to the hospital environment. To our knowledge, this is the first study of ESBL-EC isolated from LRT samples collected over a long period of time.

Genomic investigation unveils high-risk ESBL producing Enterobacteriaceae within a rural environmental water body

Antimicrobial resistance is regarded as a global threat to public health, animals, and the environment, emerging in response to extensive utilization of antimicrobials. The determinants of antimicrobial resistance are transported to susceptible bacterial populations through genetic recombination or through gene transfer, mediated by bacteriophages, plasmids, transposons, and insertion sequences. To determine the penetration of antimicrobial resistance into the bacterial population of the Thiruvandarkoil Lake, a water body located in the rural settings of Puducherry, India, culture-based microbiological and genomic approaches were used. Resistant bacterial isolates obtained from microbiological screening were subjected to whole genome sequencing and the genetic determinants of antimicrobial resistance were identified using in silico genomic tools. Cephalosporin-resistant isolates were found to produce extended spectrum beta lactamases, encoded by blaVEB-6 (in Proteus mirabilis PS01), blaSHV-12 and ompK36 mutation (in Klebsiella quasipneumoniae PS02) and blaSHV-12, blaACT-16, blaCTX-M and blaNDM-1 in (Enterobacter hormaechei PS03). Genes encoding heavy metal resistance, virulence and resistance to detergents were also detected in these resistant isolates. Among ESBL-producing organisms, one mcr-9-positive Enterobacter hormaechei was also identified in this study. To our knowledge, this is the first report of mcr-9 carrying bacterium in the environment in India. This study seeks the immediate attention of policy makers, researchers, government officials and environmental activists in India, to develop surveillance programs to monitor the dissemination of antimicrobial resistance in the environment.

Characterization of Beta-Lactamase and Fluoroquinolone Resistance Determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa Isolates from a Tertiary Hospital in Yola, Nigeria

Infections due to antimicrobial resistant gram-negative bacteria cause significant morbidity and mortality in sub-Saharan Africa. To elucidate the molecular epidemiology of antimicrobial resistance in gram-negative bacteria, we characterized beta-lactam and fluoroquinolone resistance determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa isolates collected from November 2017 to February 2018 (Period 1) and October 2021 to January 2022 (Period 2) in a tertiary medical center in north-eastern Nigeria. Whole genome sequencing (WGS) was used to identify sequence types and resistance determinants in 52 non-duplicate, phenotypically resistant isolates. Antimicrobial susceptibility was determined using broth microdilution and modified Kirby-Bauer disk diffusion methods. Twenty sequence types (STs) were identified among isolates from both periods using WGS, with increased strain diversity observed in Period 2. Common ESBL genes identified included blaCTX-M, blaSHV, and blaTEM in both E. coli and K. pneumoniae. Notably, 50% of the E. coli in Period 2 harbored either blaCTX-M-15 or blaCTX-M-1 4 and phenotypically produced ESBLs. The blaNDM-7 and blaVIM-5 metallo-beta-lactamase genes were dominant in E. coli and P. aeruginosa in Period 1, but in Period 2, only K. pneumoniae contained blaNDM-7, while blaNDM-1 was predominant in P. aeruginosa. The overall rate of fluoroquinolone resistance was 77% in Period 1 but decreased to 47.8% in Period 2. Various plasmid-mediated quinolone resistance (PMQR) genes were identified in both periods, including aac(6')-Ib-cr, oqxA/oqxB, qnrA1, qnrB1, qnrB6, qnrB18, qnrVC1, as well as mutations in the chromosomal gyrA, parC and parE genes. One E. coli isolate in Period 2, which was phenotypically multidrug resistant, had ESBL blaCTX-M-15, the serine carbapenemase, blaOXA-181 and mutations in the gyrA gene. The co-existence of beta-lactam and fluoroquinolone resistance markers observed in this study is consistent with widespread use of these antimicrobial agents in Nigeria. The presence of multidrug resistant isolates is concerning and highlights the importance of continued surveillance to support antimicrobial stewardship programs and curb the spread of antimicrobial resistance.

Daily fosfomycin versus levofloxacin for complicated urinary tract infections

IMPORTANCE

Concerns over resistance and safety have been identified in the current treatment regimen for complicated urinary tract infections. Fosfomycin is a drug that is routinely used for the treatment of uncomplicated cystitis. This study shows that fosfomycin could be an oral alternative as step-down therapy for the treatment of complicated urinary tract infections, with a clinical cure rate comparable to levofloxacin but a lower microbiological success rate 3 weeks from start of antibiotics.

Extended-spectrum β-lactamase- producing gram-negative bacterial infections in severely ill COVID-19 patients admitted in a national referral hospital, Kenya

BACKGROUND

Bacterial infections in COVID-19 patients, especially those caused by multidrug-resistant gram-negative strains, are associated with increased morbidity, hospital stay and mortality. However, there is limited data on the epidemiology of extended-spectrum β-lactamase (ESBL)-producing bacteria in COVID-19 patients. Here, we assessed the prevalence and the factors associated with ESBL-producing gram-negative bacterial (GNB) infections among severely ill COVID-19 patients admitted in Kenyatta National Hospital (KNH), Kenya.

METHODS

We adopted a descriptive cross-sectional study design for patients admitted between October 2021 and February 2022, purposively recruiting 120 SARS-CoV- 2 infected participants based on clinical presentation. Demographics and clinical characteristics data were collected using structured questionnaires and case report forms. Clinical samples were collected and analyzed by standard microbiological methods in the KNH Microbiology laboratory and the Centre for Microbiology Research, Kenya Medical Research Institute.

RESULTS

GNB infections prevalence was 40.8%, majorly caused by ESBL-producers (67.3%) predominated by Klebsiella pneumoniae (45.5%). Generally, 73% of the ESBL producers harboured our target ESBL genes, mainly CTX-M-type (59%, 17/29) in K. pneumoniae (76.9%, 20/26). GNB harbouring TEM-type (83%, 10/12) and SHV-type (100%, 7/7) genes showed ESBLs phenotypes and inhibitor resistance, mainly involving clavulanate, but most of them remained susceptible to tazobactam (60%, 6/10). SHV-type genes carrying ESBL producers showed resistance to both cefotaxime (CTX) and ceftazidime (CAZ) (K. pneumoniae), CAZ (E. coli) or CTX (E. cloacae complex and K. pneumoniae). About 87% (20/23) of isolates encoding CTX-M-type β-lactamases displayed CTX/ceftriaxone (CRO) resistance phenotype. About 42% of isolates with CTX-M-type β-lactamases only hydrolyzed ceftazidime (CAZ). Isolates with OXA-type β-lactamases were resistant to CTX, CAZ, CRO, cefepime and aztreonam. Patients with comorbidities were 10 times more likely to have an ESBL-producing GNB infection (aOR = 9.86, 95%CI 1.30 - 74.63, p = 0.003).

CONCLUSION

We report a high prevalence of ESBL-GNB infections in severely ill COVID-19 patients, predominantly due to Klebsiella pneumoniae harbouring CTX-M type ESBL genes. The patient's underlying comorbidities increased the risk of ESBL-producing GNB infection. In COVID-19 pandemic, enhanced systematic and continuous surveillance of ESBL-producing GNB, strict adherence to infection control measures and antimicrobial stewardship policies are warranted in the current study setting.

Beta-lactam Resistance Profile among Klebsiella pneumoniae Clinical Isolates from Alexandria, Egypt

Klebsiella pneumoniae is a major drug-resistant human pathogen accountable for a wide range of infections. In this cross-sectional study, we aimed to determine the phenotypic and genotypic features of β-lactamase-producing K. pneumoniae clinical isolates from Alexandria, Egypt. A total of 50 nonduplicated clinical isolates of K. pneumoniae were obtained from various specimens. They were identified biochemically and by biotyping using mass spectrometry. For molecular characterization, plasmid profile analysis was performed. Screening for extended spectrum β-lactamases (ESBLs), carbapenemases and AmpC production was carried out phenotypically and genotypically. Correlation analysis was performed to assess the relationship between phenotype, genotype and resistance patterns among the studied isolates. The dendrogram demonstrated 38 distinct plasmid profiles among 62% of our isolates. According to antimicrobial susceptibility testing, 90% of isolates were multi/extensive-drug resistant. Nineteen out of 50 (38%) were resistant to cefoxitin, while only 10 (20%) were resistant to imipenem. All isolates were susceptible to colistin. Phenotypically, ESBL producers (78%) were the most common, followed by carbapenemase producers (24%). Genotypically, the most common ESBL gene was blaSHV (90%), followed by blaCTX-Mu (74%), while the most common carbapenemase genes were blaNDM (56%) and blaOXA-48 (54%). No blaKPC or blaIMP were detected. Plasmid-mediated AmpC resistance was confirmed in only two out of 19 cefoxitin-resistant isolates. Both the blaNDM and blaOXA.48 genes were significantly positive correlated (rho = 0.56, p = 0.004). Absence of blaKPC among carbapenem resistant K. pneumoniae isolates in Alexandria, Egypt. AmpC production is not the main factor behind the resistance to cefoxitin among our isolates.

Regulation Transcriptional of Antibiotic Resistance Genes (ARGs) in Bacteria Isolated from WWTP

The incidence of antibiotics and transcriptional regulation of ARGs in isolated bacteria from wastewater needs to be explored. By HPLC, in samples of untreated wastewater, ampicillin (49.74 ± 5.70 µg/mL), chloramphenicol (0.60 ± 0.03 µg/mL), tylosin (72.95 ± 2.03 µg/mL), and oxytetracycline (0.22 ± 0.01 µg/mL) was determined. Through metagenomic analysis identified 58 bacterial species belonging to 9 phyla and at least 14 species have shown resistance to a variety of antibiotics. Twenty-two bacterial isolates were proved to be resistant to fifteen antibiotics of new generation and used in medical research to combat infectious diseases. Fourteen strains were shown to harbor plasmids in size ranges of 2-5 Kb, 6-10 Kb and plasmids with size greater than 10 Kb. By quantitative PCR it was possible to identify genes sul, qnr, cat1, aadA1, and sat-1 gene were shown to be present in gDNA samples from treated and untreated samples of wastewater and by relative expression analysis, differential expression of cat1, ermB, act, and tetA genes was demonstrated in strains that showed identity with Escherichia coli, Bacteroides fragilis, and Salmonella thyphi, and that were stressed with different concentrations of antibiotics. The presence of ARGs in untreated water samples, as well as in bacterial isolates, was indicative that in these habitats there are microorganisms that can resist β-lactams, aminoglycosides, tetracyclines, sulfonamides, and quinolones.

Uropathogenic Escherichia coli (UPEC)-Associated Urinary Tract Infections: The Molecular Basis for Challenges to Effective Treatment

Urinary tract infections (UTIs) are among the most common bacterial infections, especially among women and older adults, leading to a significant global healthcare cost burden. Uropathogenic Escherichia coli (UPEC) are the most common cause and accounts for the majority of community-acquired UTIs. Infection by UPEC can cause discomfort, polyuria, and fever. More serious clinical consequences can result in urosepsis, kidney damage, and death. UPEC is a highly adaptive pathogen which presents significant treatment challenges rooted in a complex interplay of molecular factors that allow UPEC to evade host defences, persist within the urinary tract, and resist antibiotic therapy. This review discusses these factors, which include the key genes responsible for adhesion, toxin production, and iron acquisition. Additionally, it addresses antibiotic resistance mechanisms, including chromosomal gene mutations, antibiotic deactivating enzymes, drug efflux, and the role of mobile genetic elements in their dissemination. Furthermore, we provide a forward-looking analysis of emerging alternative therapies, such as phage therapy, nano-formulations, and interventions based on nanomaterials, as well as vaccines and strategies for immunomodulation. This review underscores the continued need for research into the molecular basis of pathogenesis and antimicrobial resistance in the treatment of UPEC, as well as the need for clinically guided treatment of UTIs, particularly in light of the rapid spread of multidrug resistance.

Updates on the Virulence Factors Produced by Multidrug-Resistant Enterobacterales and Strategies to Control Their Infections

The Enterobacterales order is a massive group of Gram-negative bacteria comprised of pathogenic and nonpathogenic members, including beneficial commensal gut microbiota. The pathogenic members produce several pathogenic or virulence factors that enhance their pathogenic properties and increase the severity of the infection. The members of Enterobacterales can also develop resistance against the common antimicrobial agents, a phenomenon called antimicrobial resistance (AMR). Many pathogenic Enterobacterales members are known to possess antimicrobial resistance. This review discusses the virulence factors, pathogenicity, and infections caused by multidrug-resistant Enterobacterales, especially E. coli and some other bacterial species sharing similarities with the Enterobacterales members. We also discuss both conventional and modern approaches used to combat the infections caused by them. Understanding the virulence factors produced by the pathogenic bacteria will help develop novel strategies and methods to treat infections caused by them.

Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Food-Producing Animals in Tamaulipas, Mexico

Extended-spectrum β-lactamase (ESBL)-producing E. coli has become an important global problem for the public health sector. This study aims to investigate the E. coli antimicrobial resistance profile among living food-producing animals in Tamaulipas, Mexico. A total of 200 fecal samples were collected from bovines, pigs, chickens and sheep. A total of 5.0% of the strains were phenotypically confirmed as ESBL producers. A high percentage of phenotypic antimicrobial resistance was observed against gentamicin (93.3%), tetracycline (86.6%) and streptomycin (83.3%). The gentamicin-resistant strains showed MDR, distributed among 27 resistance patterns to different antimicrobials. The antimicrobial resistance gene tet(A) was detected in 73.3% of isolates, aadA1 in 60.0% and sul2 in 43.3% of strains. The bla_CTX-M gene was found in 23.3% of strains. The virulence gene hlyA was detected in 43.3% of isolates; stx1 and stx2 were not detected in any strain. The phylotyping indicated that the isolates belonged to groups A (33.3%), B1 (16.6%), B2 (40.0%) and D (10.0%). These results show that food-producing animals might be a reservoir of ESBL-producing bacteria and may play a role in their spread.

Emergence of New Delhi Metallo-β-Lactamase (NDM) Genes Detected from Clinical Strains of Escherichia coli Isolated in Ouagadougou, Burkina Faso

The emergence and spread of carbapenem resistance in Gram-negative bacilli such as Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa through the production of carbapenemases is a global phenomenon. It threatens patient care and leads to therapeutic impasses. This study aims to genotypically determine the prevalence of the most frequent carbapenemase genes among multidrug-resistant E. coli strains isolated from patients at a biomedical analysis laboratory. A total of fifty-three unduplicated E. coli strains isolated from patient samples with a multidrug-resistant (MDR) profile were subjected to polymerase chain reaction (PCR) testing for carbapenem resistance genes. This study allowed us to identify fifteen strains carrying resistance genes among the fifty-three E. coli strains. All fifteen strains produced the metallo-β-lactamase enzymes; this represents a rate of 28.30% of study strains. Among these strains, ten carried the NDM resistance gene, NDM and VIM genes were detected in three strains and VIM was identified in two strains of E. coli. However, carbapenemases A (KPC and IMI), D (OXA-48), and IMP were not detected in the strains studied. Thus, NDM and VIM are the main carbapenemases detected in the strains in our study.

Plasmid-mediated quinolone resistance genes detected in Ciprofloxacin non-susceptible Escherichia coli and Klebsiella isolated from children under five years at hospital discharge, Kenya

BACKGROUND

The increasing spread of fluoroquinolone resistant enteric bacteria is a global public health concern. Children recently discharged from the hospital are at high risk of carriage of antimicrobial resistance (AMR) due to frequent exposure to antimicrobials during inpatient stays. This study aimed to determine the prevalence, correlates of ciprofloxacin (CIP) non-susceptibility, and distribution of plasmid-mediated quinolone resistance (PMQR) genes in Escherichia coli (E. coli) and Klebsiella spp isolated from children under five years being discharged from two Kenyan Hospitals.

METHODS

E. coli and Klebsiella spp were isolated from fecal samples from children discharged from hospital and subjected to antimicrobial susceptibility testing (AST) by disc diffusion and E-test. CIP non-susceptible isolates were screened for seven PMQR genes using multiplex polymerase chain reaction (PCR). Poisson regression was used to determine the association between the carriage of CIP non-susceptible isolates and patient characteristics.

RESULTS

Of the 280 CIP non-susceptible isolates: 188 E. coli and 92 Klebsiella spp isolates identified among 266 discharged children, 195 (68%) were CIP-non-susceptible with minimum inhibitory concentrations (MICs) of ≥ 1 µg/mL. Among these 195 isolates, 130 (67%) had high-level CIP MIC =  ≥ 32 µg/mL). Over 80% of the isolates had at least one PMQR gene identified: aac(6')lb-cr (60%), qnrB (24%), oqxAB (22%), qnrS (16%), and qepA (6%), however, qnrA was not identified in any isolates tested. Co-carriage of qnrB with acc(6')-lb-cr was the most predominant accounting for 20% of all the isolates. Ceftriaxone use during hospital admission and the presence of extended spectrum beta-lactamase (ESBL) production were significantly associated with the carriage of CIP non-susceptible E. coli and Klebsiella spp.

CONCLUSION

CIP non-susceptibility is common among E. coli and Klebsiella spp isolated from hospital discharged children in Kenya. Carriage and co-carriage of PMQR, including the newly identified qepA gene, were frequently observed. These findings suggest that children leaving the hospital may serve as an important reservoir for transmission of resistant E. coli and Klebsiella spp to the community. Enhanced surveillance for AMR determinants is critical to inform interventions to control antimicrobial-resistant bacteria.

Fluoroquinolone resistance among fecal extended spectrum βeta lactamases positive Enterobacterales isolates from children in Dar es Salaam, Tanzania

BACKGROUND

Fluoroquinolones have been, and continue to be, routinely used for treatment of many bacterial infections. In recent years, most parts of the world have reported an increasing trend of fluoroquinolone resistant (FQR) Gram-negative bacteria.

METHODS

A cross-sectional study was conducted between March 2017 and July 2018 among children admitted due to fever to referral hospitals in Dar es Salaam, Tanzania. Rectal swabs were used to screen for carriage of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE). ESBL-PE isolates were tested for quinolone resistance by disk diffusion method. Randomly selected fluroquinolone resistant isolates were characterized by using whole genome sequencing.

RESULTS

A total of 142 ESBL-PE archived isolates were tested for fluoroquinolone resistance. Overall phenotypic resistance to ciprofloxacin, levofloxacin and moxifloxacin was found in 68% (97/142). The highest resistance rate was seen among Citrobacter spp. (100%, 5/5), followed by Klebsiella. pneumoniae (76.1%; 35/46), Escherichia coli (65.6%; 42/64) and Enterobacter spp. (31.9%; 15/47). Whole genome sequencing (WGS) was performed on 42 fluoroquinolone resistant-ESBL producing isolates and revealed that 38/42; or 90.5%, of the isolates carried one or more plasmid mediated quinolone resistance (PMQR) genes. The most frequent PMQR genes were aac(6')-lb-cr (74%; 31/42), followed by qnrB1 (40%; 17/42), oqx, qnrB6 and qnS1. Chromosomal mutations in gyrA, parC and parE were detected among 19/42 isolates, and all were in E. coli. Most of the E. coli isolates (17/20) had high MIC values of > 32 µg/ml for fluoroquinolones. In these strains, multiple chromosomal mutations were detected, and all except three strains had additional PMQR genes. Sequence types, ST131 and ST617 predominated among E. coli isolates, while ST607 was more common out of 12 sequence types detected among the K. pneumoniae. Fluoroquinolone resistance genes were mostly associated with the IncF plasmids.

CONCLUSION

The ESBL-PE isolates showed high rates of phenotypic resistance towards fluoroquinolones likely mediated by both chromosomal mutations and PMQR genes. Chromosomal mutations with or without the presence of PMQR were associated with high MIC values in these bacteria strains. We also found a diversity of PMQR genes, sequence types, virulence genes, and plasmid located antimicrobial resistance (AMR) genes towards other antimicrobial agents.

Antimicrobial resistance and molecular characterization of Klebsiella species causing bovine mastitis in Nghe An province, Vietnam

Objectives

This study aimed to determine the antibiotic-resistant profile and to identify molecular characterization of some virulence genes of Klebsiella spp. isolated from mastitis samples in Vietnam.

Materials and Method

A total of 468 samples from clinical mastitis cases were collected and submitted to the Laboratory. All samples were cultured, and Klebsiella spp. was identified through biochemical reactions and confirmed by Polymerase chain reaction (PCR). Antimicrobial resistance was tested by disk diffusion method, and virulence and resistance genes were tested by PCR.

Results

An antibiogram study showed that a high proportion of isolates are multidrug-resistant (94%). All isolates were resistant to lincomycin and sulfamethoxazole, followed by ampicillin (94%), sulphonamide (66%), amoxicillin (56%), streptomycin (52%), polymyxin B (28%), colistin sulfate (12%), tetracycline (6%), ciprofloxacin (4%), florfenicol (4%), enrofloxacin (4%), piperacillin (2%), trimethoprim (2%), nalidixic acid (2%), imipenem (2%), and sulfamethoxazole/trimethoprim (2%). In contrast, all isolates showed sensitivity to gentamicin and ceftiofur. The appearance of an efflux pump system, extended-spectrum beta-lactamase (ESBL), tetracycline, and sulphonamides-resistant genes was reconfirmed using different specific primers. Capsular serotype K1 and virulence genes magA, fimH, and entB, responsible for hypermucoviscosity production, adherence, and enterobactin production, were confirmed in isolates. Multidrug resistance and virulence potential in Klebsiella spp. are changing this mastitis pathogen into a superbug and making its management harder.

Conclusions

Klebsiella spp. associated with bovine mastitis in Nghe An province were mostly multidrug-resistant and carried virulence genes including fimH, entB, and antimicrobials resistant genes (bla _SHV, acrA_Kp, tetA, etc.), but these isolates were not ESBL producers.

Quinolone-resistant Escherichia coli at the interface between humans, poultry and their shared environment- a potential public health risk

BACKGROUND

Commensal Escherichia coli residing in the guts of humans and animals are reservoirs of multidrug resistance (MDR) genes, including quinolone resistance genes, in humans and poultry. This study aimed to characterize quinolones resistance in E. coli recovered from poultry workers, chickens, and poultry farm/market environments in Abuja, Nigeria.

METHODS

This was a cross-sectional study conducted between December 2018 and April 2019 comprising poultry workers, chickens and their poultry farm/market environments. This study characterized E. coli isolates from stool, faecal and environmental samples using antimicrobial susceptibility testing and whole-genome sequencing methods. Core-genome multilocus sequences-based phylogeny was used to determine the relatedness between quinolone-resistant E. coli isolates. Data were analyzed using descriptive statistics.

RESULTS

Of 110 E. coli isolates, quinolone-resistant phenotypes were observed in 68.2% (n = 75) isolates. Whole-genome sequencing detected plasmid-mediated quinolone resistance (PMQR) genes in 63.6% (n = 70) isolates. The most prevalent PMQR gene detected in 56 of these 70 E. coli isolates was qnrS1, followed by qnrB19 in 14 isolates and aac(6')-lb-cr in two isolates. Fifteen ciprofloxacin and 19 nalidixic acid-resistant isolates respectively showed double mutations in the quinolone-resistance determining regions (QRDRs) of gyrA, with single or double mutations in parC, and a single mutation in parE. The most prevalent amino-acid substitutions observed were S83L + D87N in gyrA (46.5%, n = 20), S80I in parC (51.2%, n = 22) and S458A in parE (14%, n = 6). About 2.9% (2/70) of PMQR isolates were extended-spectrum beta-lactamase (ESBL) producers while 2.9% (2/70) had plasmid-mediated colistin resistance (PMCR) genes.

CONCLUSIONS

PMQR genes were prevalent in E. coli isolates recovered from healthy humans, chickens and poultry farm/market environments. PMCR genes (mcr-1.1) occurred in PMQR-positive isolates recovered from manure and drinking water originating from poultry farm/market environments. It was found that the gene encoding ESBL coexisted with qnrS-positive isolates of human and avian origin. Horizontal transfer of PMQR genes among E. coli isolates in the human-poultry-environment interface has public health implications for the spread of antimicrobial resistance. Relevant government agencies should enforce regulations to restrict the use of critically important antimicrobials in poultry production.

Faecal carriage of ESBL producing and colistin resistant Escherichia coli in avian species over a 2-year period (2017-2019) in Zimbabwe

Introduction

Extended spectrum beta-lactamase (ESBL) producing Escherichia coli have become widespread among food producing animals. These strains serve as a reservoir of antibiotic resistance genes (ARGs) and act as a possible source of infection to humans as transmission can occur by direct or indirect contact.

Methods

This study investigated the faecal carriage of ESBL producing and colistin resistant E. coli in poultry over a 2-year period (2017-2019) from Zimbabwe. A total of 21 ESBL positive isolates from poultry cloacal specimens were selected for whole genome sequencing from animal E. coli isolates bio-banked at the National Microbiology Reference laboratory using phenotypic susceptibility testing results from the National Escherichia coli Surveillance Program to provide representation of different geographical regions and year of isolation. Cloacal swabs were collected from 3000 broiler live birds from farm 1 and from farm 2, 40 backyard chickens and 10 ducks were sampled. Antimicrobial susceptibility and ESBL testing were performed as per Clinical Laboratory Standards Institute guidelines. Whole genome sequencing of ESBL producing isolates was used to determine sequence types (STs), ARGs, and phylogroups.

Results

Twenty-one of the included E. coli isolates were confirmed as ESBL producers. Three defined sequence type clonal complexes (CCs) were identified (ST10CC, ST155CC and ST23CC), with ST10CC associated with the most antibiotic resistant profile. The ESBL phenotype was linked to the presence of either cefotaximase-Munich-14 (CTX-M-14) or CTX-M-79. Plasmid mediated quinolone resistant determinants identified were qnrB19 and qnrS1 and one ST10CC isolate from farm 1 broiler chickens harbored a mobile colistin resistance gene (mcr-1). Phylogenetic groups most identified were B1, A and unknown.

Discussions

The avian ESBL producing E. coli belonged to a diverse group of strains. The detection of several ARGs highlights the importance of implementing enhanced control measures to limit the spread in animals, environment, and humans. This is the first report of mcr-1 in Zimbabwe, which further underscores the importance of the One Health approach to control the spread and development of AMR.

Bacterial infections epidemiology and factors associated with multidrug resistance in the northern region of Ghana

Bacterial infections caused by multidrug resistant organisms are a major global threat. There is still a knowledge gap on this situation in the Northern Region of Ghana. This study determined the prevalence and resistance profile of bacterial infections. It also identified factors associated with multidrug resistance in the study area. This was a retrospective cross-sectional design and it analyzed data from the samples received at the Tamale Zonal Public Health Reference Laboratory from June 2018 to May 2022. The data were analyzed using the R software version 4.2.0. Univariate and multivariable binary logistic regression analyses were used to determine the factors associated with multidrug resistance. The samples included all specimen types possible. The specimens were collected for the purpose of clinical bacteriology diagnostics. Overall a total of 1222 isolates were obtained. The three (3) main bacteria responsible for infections were: Klebsiella spp. (27%), Moraxella spp. (22%), Escherichia spp. (16%). High resistance levels were found against the tested antibiotics and about 41.60% of the bacterial strains isolated were multidrug resistant. Hospitalization was associated with multidrug resistance in univariate (COR 1.96; 95% CI 1.43-2.71; P-value < 0.001) and multivariable analyses (AOR 1.78; 95% CI 1.28-2.49; P-value < 0.001). There is the need for further research on the molecular epidemiology of antibiotic resistance genes in the study area to effectively control the spread of multidrug resistant pathogens. In addition, efforts to build the capacity of health professionals on infection prevention and control as well as diagnostic and antimicrobial stewardship needs urgent attention.

A review of some medicinal plants with the potential to defeat antimicrobial resistance: Cases of Benin, Togo, Ghana, Burkina Faso, and Cape Verde

Antimicrobial resistance (AMR) is a global public health problem. In the alternatives being explored for developing new antimicrobials, medicinal plants occupy an important place, particularly in Africa, where they are widely used. This review aims to analyze the potential of medicinal plants from Benin, Togo, Ghana, Burkina-Faso, and Cape Verde in the fight against AMR. A bibliographic search was conducted to explore scientific databases such as PubMed and Google Scholar. During this search, particular attention was given to epidemiological data related to AMR in these countries, medicinal plants traditionally used to treat microbial infections and medicinal plants that have been shown to be active on multidrug-resistant microbial strains. In total, 94 manuscripts were investigated. Epidemiological data showed that the problem of AMR is worsening in each target country. In addition, several medicinal plants have been demonstrated to be effective against microbial strains resistant to conventional antibiotics. A total of 532 medicinal plants were identified according to their ethnomedical uses for the treatment of microbial infections. Scientific evidence was collected on the antimicrobial potential of 91 plants. This study showed the potential of medicinal plants in the fight against AMR. Their documented traditional use, coupled with the evidence of efficacy provided, make them interesting sources for developing new antimicrobials.

Antimicrobial Resistant E. coli in Pork and Wild Boar Meat: A Risk to Consumers

Antimicrobial-resistant foodborne microorganisms may be transmitted from food producing animals to humans through the consumption of meat products. In this study, meat that was derived from farmed pigs and wild boars was analyzed and compared. Escherichia coli (E. coli) were isolated and tested phenotypically and genotypically for their resistance to quinolones, aminoglycosides and carbapenems. The co-presence of AMR-associated plasmid genes was also evaluated. A quinolone AMR phenotypic analysis showed 41.9% and 36.1% of resistant E. coli derived from pork and wild boars meat, respectively. A resistance to aminoglycosides was detected in the 6.6% of E. coli that was isolated from pork and in 1.8% of the wild boar meat isolates. No resistant profiles were detected for the carbapenems. The quinolone resistance genes were found in 58.3% of the phenotypically resistant pork E. coli and in 17.5% of the wild boar, thus showing low genotypic confirmation rates. The co-presence of the plasmid-related genes was observed only for the quinolones and aminoglycosides, but not for the carbapenems. Wild boar E. coli were the most capable to perform biofilm production when they were compared to pork E. coli. In conclusion, the contamination of pork and wild boar meat by AMR microorganisms could be a threat for consumers, especially if biofilm-producing strains colonize the surfaces and equipment that are used in the food industry.

Characterizing the antimicrobial resistance profile of Escherichia coli found in sport animals (fighting cocks, fighting bulls, and sport horses) and soils from their environment

Background and Aim

Antimicrobial resistance (AMR) is a significant threat to global health and development. Inappropriate antimicrobial drug use in animals cause AMR, and most studies focus on livestock because of the widespread use of antimicrobial medicines. There is a lack of studies on sports animals and AMR issues. This study aimed to characterize the AMR profile of E. coli found in sports animals (fighting cocks, fighting bulls, and sport horses) and soils from their environment.

Materials and Methods

Bacterial isolation and identification were conducted to identify E. coli isolates recovered from fresh feces that were obtained from fighting cocks (n = 32), fighting bulls (n = 57), sport horses (n = 33), and soils from those farms (n = 32) at Nakhon Si Thammarat. Antimicrobial resistance was determined using 15 tested antimicrobial agents - ampicillin (AM), amoxicillin-clavulanic acid, cephalexin (CN), cefalotin (CF), cefoperazone, ceftiofur, cefquinome, gentamicin, neomycin, flumequine (UB), enrofloxacin, marbofloaxacin, polymyxin B, tetracycline (TE), and sulfamethoxazole/trimethoprim (SXT). The virulence genes, AMR genes, and phylogenetic groups were also examined. Five virulence genes, iroN, ompT, hlyF, iss, and iutA, are genes determining the phylogenetic groups, chuA, cjaA, and tspE4C2, were identified. The AMR genes selected for detection were blaTEM and blaSHV for the beta-lactamase group; cml-A for phenicol; dhfrV for trimethoprim; sul1 and sul2 for sulfonamides; tetA, tetB, and tetC for TEs; and qnrA, qnrB, and qnrS for quinolones.

Results

The E. coli derived from sports animals were resistant at different levels to AM, CF, CN, UB, SXT, and TE. The AMR rate was overall higher in fighting cocks than in other animals, with significantly higher resistance to AM, CF, and TE. The highest AMR was found in fighting cocks, where 62.5% of their isolates were AM resistant. In addition, multidrug resistance was highest in fighting cocks (12.5%). One extended-spectrum beta-lactamase E. coli isolate was found in the soils, but none from animal feces. The phylogenetic analysis showed that most E. coli isolates were in Group B1. The E. coli isolates from fighting cocks had more virulence and AMR genes than other sources. The AMR genes found in 20% or more of the isolates were blaTEM (71.9%), qnrB (25%), qnrS (46.9%), and tetA (56.25%), whereas in the E. coli isolates collected from soils, the only resistance genes found in 20% or more of the isolates were blaTEM (30.8%), and tetA (23.1%).

Conclusion

Escherichia coli from fighting cock feces had significantly higher resistance to AM, CF, and TE than isolates from other sporting animals. Hence, fighting cocks may be a reservoir of resistant E. coli that can transfer to the environment and other animals and humans in direct contact with the birds or the birds' habitat. Programs for antimicrobial monitoring should also target sports animals and their environment.

Extended-Spectrum Beta-Lactamases Producing Enterobacteriaceae in the USA Dairy Cattle Farms and Implications for Public Health

Antimicrobial resistance (AMR) is one of the top global health threats of the 21th century. Recent studies are increasingly reporting the rise in extended-spectrum beta-lactamases producing Enterobacteriaceae (ESBLs-Ent) in dairy cattle and humans in the USA. The causes of the increased prevalence of ESBLs-Ent infections in humans and commensal ESBLs-Ent in dairy cattle farms are mostly unknown. However, the extensive use of beta-lactam antibiotics, especially third-generation cephalosporins (3GCs) in dairy farms and human health, can be implicated as a major driver for the rise in ESBLs-Ent. The rise in ESBLs-Ent, particularly ESBLs-Escherichia coli and ESBLs-Klebsiella species in the USA dairy cattle is not only an animal health issue but also a serious public health concern. The ESBLs-E. coli and -Klebsiella spp. can be transmitted to humans through direct contact with carrier animals or indirectly through the food chain or via the environment. The USA Centers for Disease Control and Prevention reports also showed continuous increase in community-associated human infections caused by ESBLs-Ent. Some studies attributed the elevated prevalence of ESBLs-Ent infections in humans to the frequent use of 3GCs in dairy farms. However, the status of ESBLs-Ent in dairy cattle and their contribution to human infections caused by ESBLs-producing enteric bacteria in the USA is the subject of further study. The aims of this review are to give in-depth insights into the status of ESBL-Ent in the USA dairy farms and its implication for public health and to highlight some critical research gaps that need to be addressed.

Short- and long-read metagenomics insight into the genetic contexts and hosts of mobile antibiotic resistome in Chinese swine farms

Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Intensive swine farms are recognized as hotspots for antibiotic resistance genes (ARGs). However, antibiotic resistome and their genetic contexts, hosts, and transferability in Chinese swine farms remain largely unexplored. Here, we used Illumina and Oxford Nanopore metagenomics sequencing to investigate the antibiotic resistome context of 14 distantly located large-scale (10,000 animals per year) commercial swine farms in China. We identified high abundant and diverse ARGs (609,966.8 with 1433 types, belonging to 38 different antibiotic classes) in all samples, including those encoding resistance to clinically critical important antibiotics (such as mcr, tetX, optrA, poxtA, qnr and bla_CTX-M). About 75% of the ARGs detected were carried by mobile genetic elements (mainly plasmids), suggesting their high transmission potential into receiving environments. Host-tracking analysis identified Clostridiales, Faecalibacterium prausnitzii and Escherichia coli as the predominant bacterial hosts of mobile ARGs. Notably, genome binning generated 246 high-completeness draft genomes. Genetic context analysis of the multiple resistant (MDR) genes in binned genomes showed the involvement of insertion sequences (ISs), integron and SGI2 genomic island, implying their importance role in promoting the development of MDR bacteria. Overall, these findings substantially expand our current knowledge of mobile antibiotic resistome in Chinese swine farms, and suggest reasonable management of animal wastes in swine farms to reduce the dissemination of antibiotic resistance to the environment.

The Molecular Characterization and Risk Factors of ST131 and Non-ST131 Escherichia coli in Healthy Fecal Carriers in Tehran, Iran

Background: Commensal extended-spectrum β-lactamase (ESBL) producing Escherichia coli isolates in the gut can be the reservoir of virulence factors and resistance genes. Objectives: We investigated the molecular feature, risk factors, and quinolone/fluoroquinolone (Q/FQ) resistance in sequence type 131 (ST131) and non-ST131: ESBL-producing E. coli (EPE) isolates in healthy fecal carriers. Methods: A total of 540 fecal samples and its demographic data were collected from healthy adults in Tehran in 2018. ST131 isolates were identified by MLST analysis, and the characteristics of the virulence factor, phylogenic assay, and Q/FQ resistance genes in ST131 and non-ST131 were determined by polymerase chain reaction (PCR). Results: The EPE isolates mainly belonged to the commensal phylogenetic groups A (54.9%) and D (18.1%). The type 1 fimbriae (fimH; 89.6%) gene was the predominant virulence factor, and there was a significant correlation between ferric yersiniabactin uptake (fyuA; 52.9%), aerobactin receptor (iutA; 17.6%), and group II capsule synthesis (kpsMII; 35.3%) with ST131. In Q/FQ-resistant isolates, qnrS (19%) was the predominant gene, and mutations mostly occurred at codon S83 in GyrA The number of mutations in gyrA and parC genes was significantly higher in ST131 isolates than in non-ST131 isolates. There was a significant positive correlation between diabetes, male gender, and living in the south of the city with EPE carriage (P < 0.05). Conclusions: Accumulation of multiple virulence factors and high- level resistance to Q/FQ in some phylogroups (B2 and D), particularly ST131 isolates, require to be considered in detecting resistant isolates in healthy carriers. According to the risk factor for spreading of EPE isolates (diabetes, living in low-income parts of the city, and male gender), the necessary strategies are required to be developed to control the dissemination of antimicrobial-resistant isolates in the community.

Prevalence and Molecular Characterisation of Extended-Spectrum Beta-Lactamase-Producing Shiga Toxin-Producing Escherichia coli, from Cattle Farm to Aquatic Environments

Extended-spectrum beta-lactamase (ESBL)-producing bacteria are a major problem for public health worldwide because of limited treatment options. Currently, only limited information is available on ESBL-producing Shiga toxin-producing Escherichia coli (STEC) in cattle farms and the surrounding aquatic environment. This study sought to track and characterise ESBL-producing STEC disseminating from a cattle farm into the water environment. Animal husbandry soil (HS), animal manure (AM), animal drinking water (ADW), and nearby river water (NRW) samples were collected from the cattle farm. Presumptive ESBL-producing STEC were isolated and identified using chromogenic media and mass spectrophotometry methods (MALDI-TOF-MS), respectively. The isolates were subjected to molecular analysis, and all confirmed ESBL-producing STEC isolates were serotyped for their O serogroups and assessed for antibiotic resistance genes (ARGs) and for the presence of selected virulence factors (VFs). A phylogenetic tree based on the multilocus sequences was constructed to determine the relatedness among isolates of ESBL-producing STEC. The highest prevalence of ESBL-producing STEC of 83.33% was observed in HS, followed by ADW with 75%, NRW with 68.75%, and the lowest was observed in AM with 64.58%. Out of 40 randomly selected isolates, 88% (n = 35) belonged to the serogroup O45 and 13% (n = 5) to the serogroup O145. The multilocus sequence typing (MLST) analysis revealed four different sequence types (STs), namely ST10, ST23, ST165, and ST117, and the predominant ST was found to be ST10. All 40 isolates carried sul1 (100%), while bla_OXA, bla_CTX-M, sul2, bla_TEM, and qnrS genes were found in 98%, 93%, 90%, 83%, and 23% of the 40 isolates, respectively. For VFs, only stx2 was detected in ESBL-producing STEC isolates. The results of the present study indicated that a cattle environment is a potential reservoir of ESBL-producing STEC, which may disseminate into the aquatic environment through agricultural runoff, thus polluting water sources. Therefore, continual surveillance of ESBL-producing STEC non-O157 would be beneficial for controlling and preventing STEC-related illnesses originating from livestock environments.

Plasmid-mediated quinolone resistance determinants in fluoroquinolone-nonsusceptible Escherichia coli isolated from patients with urinary tract infections in a university hospital, 2009-2010 and 2020: PMQR in UTI E. coli

OBJECTIVES

This study aimed to characterize the plasmid-mediated quinolone resistance (PMQR) in fluoroquinolone non-susceptible E. coli (FQNSEC) isolated from patients with urinary tract infections (UTIs) in 2019-2010 and 2020.

METHODS

A total of 844 E. coli isolates were collected from UTI patients at National Cheng Kung University Hospital (NCKUH). The antimicrobial susceptibility of E. coli isolates to 21 antibiotics was determined by disk diffusion tests. The distribution of phylogenetic groups, virulence factor, and PMQR genes, was determined by PCR. Conjugation assays were performed to investigate the transferrability of qnr genes from FQNSEC isolates to E. coli C600.

RESULTS

We found 211 (41.9%) and 152 (44.7%) E. coli isolates were FQNSEC in 2009-2010 and 2020, respectively. Phylogenetic group B2 was dominant in FQNSEC isolates (52.34%), followed by group F (10.47%), group B1 (9.64%), and group D (9.64%). FQNSEC isolates were more resistant to 17 of 19 tested antimicrobial agents, compared to the FQ susceptible E. coli. PMQR screening results showed that 34, 22, and 10 FQNSEC isolates containing aac(6')-Ib-cr, qnr genes, and efflux pump genes (qepA or oqxAB), respectively. PMQR E. coli isolates were more non-susceptible to gentamicin, amoxicillin, ampicillin/sulbactam, imipenem, cefazolin, cefuroxime, cefmetazole, ceftriaxone, ceftazidime, and cefepime, compared to non-PMQR FQNSEC. Moreover, 16 of 22 qnr-carrying plasmids were transferrable to the recipient C600.

CONCLUSION

Here, we reported the high prevalence of MDR- and XDR-E. coli in FQNSEC isolates. Moreover, qnr-carrying plasmids were highly transferable and lead to the resistance to other classes of antibiotics in the transconjugants.

Isolation, identification, and antibiogram studies of Escherichia coli from ready-to-eat foods in Mymensingh, Bangladesh

Background and Aim

Ready-to-eat (RTE) foods are widely used at home, restaurants, and during festivals in Bangladesh. So it is very important to investigate possible microbial contamination in RTE foods. Therefore, this study aimed to determine the total coliform count (TCC), isolate, identify, and characterize the Escherichia coli in RTE foods. The antimicrobial sensitivity of E. coli obtained from RTE foods was also performed using 12 commonly used antibiotics.

Materials and Methods

A total of 100 RTE food samples were collected aseptically and comprised of ten samples each: Burger, pizza, sandwich, chicken roll, chicken meat loaf, chicken fry, salad vegetable, ice-cream, yogurt, and milkshake sold in Mymensingh City. Samples were inoculated onto Eosin methylene blue agar and incubated at 37°C for 24 h. Isolation and identification of bacteria were performed based on cultural, staining, and biochemical properties, followed by a polymerase chain reaction.

Results

The TCC in Chicken meat loaf, burger, pizza, sandwich, salad vegetable ice-cream, and yogurt samples were 3.57 ± 0.96, 3.69 ± 0.08, 3.50 ± 0.60, 2.60 ± 0.20, 4.09 ± 0.29, 4.44 ± 0.25, and 3.14 ± 0.30 mean log colony-forming units ± standard deviation/mL, respectively. The study found a higher prevalence of E. coli in RTE salad vegetable products than in RTE meat and milk products. Forty percent of the mixed vegetable salad samples showed positive results for E. coli. Whereas E. coli prevalence in RTE meat and milk products was 20% and 16.7%, respectively. All the 21 isolates were subjected to antibiotic susceptibility test against 12 different antibiotics. It was observed that 46.1% were susceptible, 16.6% were intermediate, 46.1% were resistant, and 47.6% were multidrug-resistant (MDR) among seven different antibiotic classes. E. coli isolates were resistant to cephalexin, ceftazidime, oxytetracycline, and ampicillin and sensitive to gentamycin, followed by kanamycin, ceftriaxone, colistin, and enrofloxacin.

Conclusion

The study revealed that RTE foods are a serious issue from a public health point of view. To achieve a safer level of E. coli in RTE foods sold for human consumption, public food outlets must improve hygienic and good production procedures. Moreover, MDR E. coli in these foods pose serious public health threats.

Study of Plasmid-Mediated Quinolone Resistance in Klebsiella pneumoniae: Relation to Extended-Spectrum Beta-Lactamases

Klebsiella pneumoniae (K. pneumoniae) is an important pathogen associated with various infections. The emergence of antibiotic resistances, such as quinolone resistance and those due to extended-spectrum beta-lactamases (ESBL), reduces the available choices for treatment. The objectives of the current study include the evaluation of the prevalence of the plasmid-mediated quinolone resistance genes qepA, acrA, acrB, and aac(6’)-Ib-cr by polymerase chain reaction (PCR) in K. pneumoniae and the determination of the mechanism relating these genes to the ESBL phenotype and resistance to other groups of antibiotics. In total, 300 clinical isolates of K. pneumoniae were included in the study. Isolates were subjected to antibiotic sensitivity tests using the disc diffusion method. Quinolone resistance by the minimum inhibitory concentration method and detection of ESBL resistance by the double disc diffusion method were also determined. PCR analyses revealed the prevalence of acrA, aac(6’)-Ib-cr, acrB, and qepA in 74.3%, 73.7%, 71%, and 6.7% of the isolates, respectively. Quinolone-resistant isolates positive for plasmid-encoded genes represented 82.7% of K. pneumoniae isolates positive for ESBL activity. The results also showed that the isolates of K. pneumoniae carrying plasmid-encoded quinolone resistance genes had significantly increased resistance to amikacin, amoxicillin/clavulanate, gentamicin, and cefoxitin than those isolates without quinolone resistance genes. Therefore, there was a high prevalence of acrA, acrB, and aac(6’)-Ib-cr among K. pneumoniae and the prevalence of quinolone resistance was significantly associated with the ESBL resistance phenotype. Moreover, the presence of quinolone resistance genes was associated with resistance to aminoglycosides, namely amikacin and gentamicin.

Characterization of qnrB-carrying plasmids from ESBL- and non-ESBL-producing Escherichia coli

BACKGROUND

Escherichia coli carrying clinically important antimicrobial resistances [i.e., against extended-spectrum-beta-lactamases (ESBL)] are of high concern for human health and are increasingly detected worldwide. Worryingly, they are often identified as multidrug-resistant (MDR) isolates, frequently including resistances against quinolones/fluoroquinolones.

RESULTS

Here, the occurrence and genetic basis of the fluoroquinolone resistance enhancing determinant qnrB in ESBL-/non-ESBL-producing E. coli was investigated. Overall, 33 qnrB-carrying isolates out of the annual German antimicrobial resistance (AMR) monitoring on commensal E. coli (incl. ESBL-/AmpC-producing E. coli) recovered from food and livestock between 2013 and 2018 were analysed in detail. Whole-genome sequencing, bioinformatics analyses and transferability evaluation was conducted to characterise the prevailing qnrB-associated plasmids. Furthermore, predominant qnrB-carrying plasmid-types were subjected to in silico genome reconstruction analysis. In general, the qnrB-carrying E. coli were found to be highly heterogenic in their multilocus sequence types (STs) and their phenotypic resistance profiles. Most of them appeared to be MDR and exhibited resistances against up to ten antimicrobials of different classes. With respect to qnrB-carrying plasmids, we found qnrB19 located on small Col440I plasmids to be most widespread among ESBL-producing E. coli from German livestock and food. This Col440I plasmid-type was found to be highly conserved by exhibiting qnrB19, a pspF operon and different genes of unassigned function. Furthermore, we detected plasmids of the incompatibility groups IncN and IncH as carriers of qnrB. All qnrB-carrying plasmids also exhibited virulence factors and various insertion sequences (IS). The majority of the qnrB-carrying plasmids were determined to be self-transmissible, indicating their possible contribution to the spread of resistances against (fluoro)quinolones and other antimicrobials.

CONCLUSION

In this study, a diversity of different plasmid types carrying qnrB alone or in combination with other resistance determinants (i.e., beta-lactamase genes) were found. The spread of these plasmids, especially those carrying antimicrobial resistance genes against highest priority critically important antimicrobial agents, is highly unfavourable and can pose a threat for public health. Therefore, the dissemination pathways and evolution of these plasmids need to be further monitored.

A rich mosaic of resistance in extended-spectrum β-lactamase-producing Escherichia coli isolated from red foxes (Vulpes vulpes) in Poland as a potential effect of increasing synanthropization

In our research, we analyzed the resistance of cephalosporin-resistant E. coli strains to antimicrobial agents. The strains were collected during five years from wild animal species commonly inhabiting Poland. We have identified the type of β-lactamases produced and the multidrug-resistance profile. Most strains (73.8%) had genes encoding ESBL enzymes, mainly CTX-M-1 and TEM. Almost all AmpC-β-lactamase-producing isolates had the bla_CMY-2 gene. Almost 70% of the strains tested showed a multi-drug resistance profile. The dominant phenotype was resistance to tetracycline (69.05%), and/or sulfamethoxazole (57.1%). We also found high resistance to quinolones: ciprofloxacin 35.7% and nalidixic acid 52.4%. The phenotypic resistance of the strains was in most cases confirmed by the presence of corresponding genes. Among strains, 26.2% were carriers of plasmid-mediated quinolone resistance genes (PMQR). MLST analysis revealed a large clonal variation of the strains, which was reflected in 28 different sequence types. More than half of the strains (54.7%) were classified into the following sequence complexes: 10, 23, 69, 101, 155, 156, 168, 354, 398, 446, and 648. Only one strain in the studied group was assigned to the ExPEC pathotype and represented sequence type 117. The results of our research have confirmed that isolates obtained from wild animals possess many resistance determinants and sequence types, which are also found in food-producing animals and humans. This reflects the doctrine of "One health", which clearly indicates that human health is inextricably linked with animal health as well as degree of environmental contamination. We conclude that the resistance and virulence profiles of strains isolated from wildlife animals may be a resultant of various sources encountered by animals, creating a rich and varied mosaic of genes, which is very often unpredictable and not reflected in the correlation between the sequence type and the gene profile of resistance or virulence observed in epidemic clones.

The prevalence of plasmid-mediated quinolone resistance genes among Escherichia coli strains isolated from urinary tract infections in southwest Iran

BACKGROUND

The extensive and inappropriate use of quinolones, which are frequently used as an effective treatment for urinary tract infection (UTI) patients, has led to resistance to these antibiotics. This study was designed to determine the prevalence of quinolones resistance and the presence of plasmid-mediated quinolone resistance (PMQR) genes among extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates.

METHODS

One hundred and fourteen E. coli isolates were collected from patients' urine samples. The susceptibility of isolates to selected antibiotics was tested by the Kirby-Bauer disk diffusion method. ESBL-producing isolates were identified phenotypically using a combination disk test. Using specific primers, the frequency of aac (6')-Ib, qnrA, qnrB, qnrC, qnrD, qnrS, and qepA genes was investigated by polymerase chain reaction (PCR).

RESULTS

Among 26 ESBL-producing isolates, the highest resistance rate was observed toward nalidixic acid (80.8%) and ciprofloxacin (61.5%), respectively. Ninety-seven (85%) of all isolates harbored at least one PMQR gene, the most frequent one being aac(6')-Ib-cr variant (47.4%). Coexistence of aac(6')-Ib-cr variant and qnrB were the most broadly distributed genotype among quinolone resistance isolates. Notably, none of the isolates contained the qnrC, qnrD, and qepA genes.

CONCLUSIONS

Our results highlight the significant prevalence of PMQR genes in ESBL-producing E. coli isolates in this region. Also, the aac (6')-Ib-cr variant was the most frequent gene, particularly in ESBL positive isolates. A regular periodic monitoring program is needed to control and hinder the more spread of antibiotic resistance phenomenon and contributed genes among UTI-causing E. coli isolates.

Investigation of plasmid-mediated quinolone resistance genes among clinical isolates of Klebsiella pneumoniae in southwest Iran

Background

Extensive and inappropriate use of quinolones has led to growing resistance rates to these broad‐spectrum antibiotics. The present study purposed to investigate the prevalence of plasmid‐mediated quinolone resistance (PMQR) genes in Klebsiella pneumoniae clinical isolates.

Method

Ninety‐two non‐repetitive K. pneumoniae clinical isolates were confirmed by standard microbiological methods. Antibacterial susceptibility of isolates toward seven agents from the quinolone family was evaluated by the disc diffusion method. Ciprofloxacin minimum inhibitory concentrations (MICs) were determined using the standard agar dilution method. PCR amplification was used to detect the existence of PMQR genes in the studied isolates.

Results

In the present study, significant quinolones' resistance (40%) was observed in K. pneumoniae isolates, and most of the strains were resistant to nalidixic acid (94.6%) and ofloxacin (45.6%). MIC analysis showed 15 strains were resistant to 6–128 μg/ml of ciprofloxacin, and five were intermediately‐resistant. PMQR genes were detected in 88% of all isolates. Acc(6’)‐Ib‐cr was constituted half of the total PMQR genes detected among ciprofloxacin non‐susceptible isolates. Of 20 ciprofloxacin non‐susceptible isolates, 65% (n = 13) harbored multiple PMQR determinants, and 15 strains were determined as integron carriage.

Conclusion

The findings of this study indicated considerable resistance against quinolones, which could be correlated with the extensive and inappropriate use of this class of antibiotics as empirical treatment.

Prevalence and Molecular Characterization of Extended Spectrum β-Lactamase and Carbapenemase-Producing Enterobacteriaceae Isolates from Bloodstream Infection Suspected Patients in Addis Ababa, Ethiopia

Background

Production of Extended spectrum beta-lactamase (ESBL) and Carbapenemase is the most common strategy for drug resistance in clinical isolates of Enterobacteriaceae. This study was conducted to determine the magnitude of ESBL and Carbapenemase production (CPE) among clinical isolates of Enterobacteriaceae causing bloodstream infections (BSI) in Ethiopia.

Methods

A cross-sectional study was performed from September 2018 to January 2019 in Ethiopia. A total of 2397 BSI suspected patients were enrolled and blood culture was performed using a BacT/Alert instrument in combination with conventional methods for identification. After antimicrobial susceptibility test, phenotypic confirmation of ESBLs was done by combined disc-diffusion. Meanwhile carbapenemase production was done by modified carbapenem inactivation method. Multiplex PCR was conducted to detect the presence of bla_CTX-M,bla_SHV,bla_TEM, bla_KPC and bla_NDM genes.

Results

A total of 104 (4.3%) Enterobacteriaceae were isolated from 2397 BSI suspected patients. Klebsiella pneumoniae (55/104, 52%) was the predominant isolate followed by E. coli, (19.2%, 20/104) and K.oxytoca (17.3%, 18/104). ESBL and carbapenemase production were observed from 70 (67.3%, 57.4 −76.2% at 95% CI) and 8 (7.7%, 3.4–14.6% at 95% CI) isolates respectively. The highest frequency of ESBL and carbapenemase production was observed in K. pneumoniae 78.2% (43/55) and 9.1% (5/55), respectively. All the 70 isolates confirmed as ESBL producers harbored at least one of the ESBL genes and the majority of them carried multiple beta-lactamase genes (84.3%), where bla_CTX-M, type was the most predominant (67.3%). Similarly, the entire eight isolates positive for carbapenemase carried bla_NDM but none of them carried bla_KPC.

Conclusion

In our study, the rate of ESBL production among BSI-causing Enterobacteriaceae was alarming and most of the isolates carried multiple types of ESBL genes. A significant magnitude of CPE isolates causing BSI was recorded.

Genomic characteristics and comparative genomics of Salmonella enterica subsp. enterica serovar Schwarzengrund strain S16 isolated from chicken feces

Background

Salmonella enterica subsp. enterica serovar Schwarzengrund (S. Schwarzengrund) is most frequently isolated from commensals humans or poultry. Here we report S. Schwarzengrund strain S16, the first sequenced genome in the Republic of Korea. Additionally, genome sequencing for strain S16 was performed and compared with other S. Schwarzengrund genomes obtained from public database.

Results

Strain S16 was isolated from chicken feces. The complete genome consists of one chromosome and one plasmid. The genome size is 4,822,755 bp with 4852 coding sequences. Strain S16 was determined as serovar Schwarzengrund by in silico serotyping and typed as sequence type (ST) 96. Forty-six S. Schwarzengrund genomes yielded a pangenome of 7112 genes, core-genome of 3374 genes, accessory-genome of 2906 genes, and unique-genome of 835 genes. Eighty-one genes were unique to strain S16, including hypothetical proteins and transcriptional regulators. Genotypic analysis of antibiotic resistance of strain S16 confirmed resistance to amikacin, ciprofloxacin, sulfamethoxazole, streptomycin, and tetracycline. Unlike other S. Schwarzengrund genomes, strain S16 had a mutation of gyrB. Moreover, similar to other S. Schwarzengrund genomes reported in other countries, strain S16 was harbored for 153 virulence genes including Saf operon and cdtB gene. All the antibiotic resistance genes and virulence genes were present in the core- or accessory-genomes.

Conclusions

Complete genome of strain S16 was sequenced. Comparative genomic analysis revealed several genes responsible for antibiotic resistance and specific genomic features of strain S16 and identified virulence factors that might contribute to the human and animal pathogenicity of other S. Schwarzengrund genomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13099-021-00476-8.

Neonatal multidrug-resistant gram-negative infection: epidemiology, mechanisms of resistance, and management

Infants admitted to the neonatal intensive care unit, particularly those born preterm, are at high risk for infection due to the combination of an immature immune system, prolonged hospitalization, and frequent use of invasive devices. Emerging evidence suggests that multidrug-resistant gram-negative (MDR-GN) infections are increasing in neonatal settings, which directly threatens recent and ongoing advances in contemporary neonatal care. A rising prevalence of antibiotic resistance among common neonatal pathogens compounds the challenge of optimal management of suspected and confirmed neonatal infection. We review the epidemiology of MDR-GN infections in neonates in the United States and internationally, with a focus on extended-spectrum β-lactamase (ESBL)-producing Enterobacterales and carbapenem-resistant Enterobacterales (CRE). We include published single-center studies, neonatal collaborative reports, and national surveillance data. Risk factors for and mechanisms of resistance are discussed. In addition, we discuss current recommendations for empiric antibiotic therapy for suspected infections, as well as definitive treatment options for key MDR organisms. Finally, we review best practices for prevention and identify current knowledge gaps and areas for future research. IMPACT: Surveillance and prevention of MDR-GN infections is a pediatric research priority. A rising prevalence of MDR-GN neonatal infections, specifically ESBL-producing Enterobacterales and CRE, compounds the challenge of optimal management of suspected and confirmed neonatal infection. Future studies are needed to understand the impacts of MDR-GN infection on neonatal morbidity and mortality, and studies of current and novel antibiotic therapies should include a focus on the pharmacokinetics of such agents among neonates.

In vitro assessment of the antibacterial effects of the combinations of fosfomycin, colistin, trimethoprim and nitrofurantoin against multi-drug-resistant Escherichia coli

MDR UPEC has become a global health challenge. Our study investigates the pairwise interactions among FOS, COL, NIT and TRI against 29 UPEC strains using the checkerboard method. The synergistic combinations are further evaluated for their bactericidal effects against the most resistant strain (MRS) using the time-kill method. The results showed that 100% of these strains were resistant to TRI and NIT, whereas 75·86% of them were susceptible to FOS and COL. Among all tested strains, only seven strains were highly resistant to all used antibiotics. Remarkably, FOS/COL, COL/NIT and COL/TRI combinations represent the most effective synergistic (fractional inhibitory concentration index <1) combinations against the seven strains at MICs lower than the susceptible breakpoint ranges, followed by FOS/NIT and FOS/TRI, which achieved synergistic interactions against 1/7 and 2/7 of these strains. Importantly, the bactericidal effects (reduction ≥3·0 log₁₀  CFU per ml) were only observed with FOS/COL, COL/NIT and COL/TRI combinations against MRS after 24 h of post-treatment. Our data suggested that FOS/COL, COL/NIT and COL/TRI combinations could be a promising option against MDR UPEC infections. Additionally, FOS/NIT and FOS/TRI probably represent a good option for MDR UPEC with lower MICs.

The surveillance of colistin resistance and mobilized colistin resistance genes in multidrug-resistant Enterobacteriaceae isolated in Japan

BACKGROUND

The plasmid-mediated bacterial colistin-resistant gene, mcr, is of global concern in clinical healthcare. However, there are few reports of surveillance for mcr in Japan. The aim of this study was to assess the prevalence of colistin resistance by identifying nine mcr genes in extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae and carbapenem-resistant Enterobacteriaceae (CRE) isolates in Japan.

METHODS

A total of 273 ESBL and CRE clinical isolates were collected from patients in five tertiary hospitals from August 2016 to March 2017. Minimum inhibitory concentration (MIC) of colistin was measured using the microdilution method. Polymerase chain reaction (PCR) was performed to detect mcr-1 to mcr-9 genes in all strains. Whole-genome sequencing (WGS) analysis was conducted for any mcr-genes identified that had not been previously reported in patients from Japan.

RESULTS

The rate of colistin resistance was 7.7% in all strains, with a higher rate in the CRE strains than in the ESBL-producing strains (20.4% versus 1.1%). The mcr-5 and mcr-9 gene were detected in one ESBL-producing Escherichia coli strain (1/273, 0.37%) and three CRE strains (3/273, 1.1%), respectively. As the ESBL-producing E. coli strain was the first clinical strain with mcr-5 in Japan, WGS analysis was performed for the strain. The sequence type of the mcr-5-positive strain was ST1642 and it carried two distinct plasmids, ESBL gene-carrying pN-ES-6-1, and mcr-5.1-carrying pN-ES-6-2.

CONCLUSIONS

The results of this study showed that the frequency of colistin resistance and mcr-positive strains is not high in Japan. As the MIC for colistin was low in the mcr-5.1 and mcr-9 gene-positive strain, continuous monitoring of mcr genes is necessary.

Quinolone-resistant uropathogenic E. coli: is there a relation between qnr genes, gyrA gene target site mutation and biofilm formation?

Introduction. The resistance to quinolone reported in uropathogenic Escherichia coli (UPEC) is commonly caused by mutations in the target site encoding genes such as the gyrA gene. Bacterial plasmids carrying resistance genes such as qnr genes can also transfer resistance. Biofilms produced by UPEC can further aid the development of resistant urinary tract infections (UTIs).Hypothesis. Biofilm production is associated with higher prevalence of quinolones resistance genetic determinants.Aim. To detect the prevalence of qnr genes and gyrA gene mutation among quinolone-resistant UPEC and to investigate the relation between these genetic resistance determinants and biofilm production.Methodology. Catheterized urine samples were collected from 420 patients with evidence of UTIs and processed using standard techniques. Isolated UPEC were screened for quinolone resistance using an antimicrobial susceptibility test. Biofilm production among quinolone-resistant isolates was detected using the tissue culture plate method. All quinolone-resistant isolates were screened for qnr genes (qnrA, qnrB and qnrS) by multiplex PCR and for gyrA gene mutation by PCR-RFLP.Results. Two hundred and sixty-four UPEC isolates were detected from 420 processed urine samples. Out of the identified 264 UPEC, 123 (46.6 %) isolates were found to be quinolone-resistant, showing resistance to 1 or more of the tested quinolones. Of the 123 quinolone-resistant UPEC detected, 71(57.7 %) were biofilm producers. The qnr genes were detected among 62.6 % of the quinolone-resistant UPEC, with an estimated prevalence of 22.8, 32.5 and 37.4 % for qnrA, qnrB and qnrS genes, respectively. Additionally, the gyrA gene mutation was identified among 53.7 % of the quinolone-resistant isolates. We reported a significant association between biofilm production and the presence of qnrA, qnrB and qnrS genes. Furthermore, the gyrA gene mutation was significantly associated with biofilm-producing isolates. The coexistence of qnr genes, gyrA gene mutation and biofilm production was demonstrated in almost 40 % of the quinolone-resistant isolates.Conclusions. A significantly higher prevalence of qnr genes (qnrA, qnrB and qnrS) as well as the gyrA gene mutation was found among biofilm-forming UPEC. The reported coexistence of these different resistance mechanisms could aggravate quinolone resistance. Therefore, monitoring of resistance mechanisms and a proper stewardship programme are necessary.

Antimicrobial resistance among Enterobacteriaceae, Staphylococcus aureus, and Pseudomonas spp. isolates from clinical specimens from a hospital in Nairobi, Kenya

Background

Antimicrobial resistance among pathogens of public health importance is an emerging problem in sub-Saharan Africa. Unfortunately, published information on the burden and patterns of antimicrobial resistance (AMR) in this region is sparse. There is evidence that the burden and patterns of AMR vary by geography and facility. Knowledge of local epidemiology of AMR is thus important for guiding clinical decisions and mitigation strategies. Therefore, the objective of this study was to determine the burden and predictors of AMR and multidrug resistance (MDR) among bacterial pathogens isolated from specimens submitted to the diagnostic laboratory of a hospital in Nairobi, Kenya.

Methods

This retrospective study used laboratory records of 1,217 clinical specimens submitted for bacterial culture and sensitivity testing at the diagnostic laboratory of The Karen Hospital in Nairobi, Kenya between 2012 and 2016. Records from specimens positive for Enterobacteriaceae, Staphylococcus aureus, or Pseudomonas spp. isolates were included for analysis. Firth logistic models, which minimize small sample bias, were used to investigate determinants of AMR and MDR of the isolates.

Results

A total of 222 specimens had bacterial growth. Most Enterobacteriaceae isolates were resistant to commonly used drugs such as penicillin/β-lactamase inhibitor combinations (91.2%) and folate pathway inhibitors (83.7%). Resistance to extended-spectrum cephalosporins was also high (52.9%). Levels of AMR and MDR for Enterobacteriaceae were 88.5% and 51%, respectively. Among S. aureus isolates, 57.1% were AMR, while 16.7% were MDR. As many as 42.1% of the Pseudomonas spp. isolates were aminoglycoside-resistant and 15% were fluoroquinolone-resistant, but none exhibited resistance to antipseudomonal carbapenems. Half of Pseudomonas spp. isolates were AMR but none were MDR. Significant predictors of MDR among Enterobacteriaceae were organism species (p = 0.002) and patient gender (p = 0.024).

Conclusions

The high levels of extended-spectrum cephalosporin resistance and MDR among Enterobacteriaceae isolates are concerning. However, the relatively low levels of MDR S. aureus, and an absence of carbapenem resistance among Pseudomonas isolates, suggests that last-line drugs are still effective against S. aureus and Pseudomonas infections. These findings are relevant for guiding evidence-based treatment decisions as well as surveillance efforts and directions for future research, and contribute to the sparse literature on AMR in sub-Saharan Africa.

Characterization of Antimicrobial Resistance Patterns of Klebsiella pneumoniae Isolates Obtained from Wound Infections

CDATA[Background: Multidrug resistance among ESBL producing isolates has limited the administration of proper antibiotics. It is, therefore, important to monitor the resistance patterns of Klebsiella pneumoniae isolates and provide infection control strategies to prevent nosocomial outbreaks. This study was aimed to determine antimicrobial resistance patterns of K. pneumoniae isolates obtained from wound infections of patients in Tehran, Iran.

METHODS

A total of 102 K. pneumoniae isolates were obtained from wound infections of patients in Tehran, Iran. The production of phenotypic ESBL and carbapenemase was assessed using the double-disc synergy test (DDST) and modified Hodge test (MHT), respectively. PCR was performed for the detection of ESBL, carbapenemase, quinolone and aminoglycoside resistance genes.

RESULTS

Forty-six (45.1%) and 23 (22.5%) isolates, out of the 102 isolates, were phenotypically detected as ESBL and carbapenemase producers, respectively. The PCR results showed that 80/102 (78.4%) and 51/102 (50%) isolates possessed at least one of the assessed ESBL and carbapenemase genes, respectively. Quinolone resistance determinants (QRDs) and aac(6')-Ib genes were found amongst 50 (49%) and 67 (65.7%) isolates, respectively. Four isolates carried bla_TEM, bla_SHV, bla_CTX-M, qnrB, qnrS and aac(6')-Ib genes, simultaneously.

CONCLUSION

Due to the presence of multiple resistance genes among some K. pneumoniae strains, antibiotic agents should be used with caution to preserve their efficacy in case of life-threatening infections.

The Prevalence and Characterization of Fecal Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolated from Pigs on Farms of Different Sizes in Latvia

The aim of this study was to determine the prevalence of fecal ESBL-producing Escherichia coli (E. coli) in pigs on large and small farms in Latvia, to characterize beta-lactamase genes and establish an antimicrobial resistance profile. Fecal samples (n = 615) were collected from 4-week, 5-week, 6-week, 8-week, 12-week and 20-week-old piglets, pigs and sows on four large farms (L1, L2, L3, L4) and three small farms (S1, S2, S3) in Latvia. ChromArt ESBL agar and combination disc tests were used for the screening and confirmation of ESBL-producing E. coli. The antimicrobial resistance was determined by the disc diffusion method and ESBL genes were determined by polymerase chain reaction (PCR). Subsequently, ESBL-producing E. coli was confirmed on three large farms, L1 (64.3%), L2 (29.9%), L3 (10.7%) and one small farm, S1 (47.5%); n = 144 (23.4%). The prevalence of ESBL-producing E. coli differed considerably between the large and small farm groups (26.9% vs. 12.7%). Of ESBL E. coli isolates, 96% were multidrug-resistant (MDR), demonstrating there were more extensive MDR phenotypes on large farms. The distribution of ESBL genes was bla_TEM (94%),&nbsp;bla_CTX-M (86%) and bla_SHV (48%). On the small farm, bla_SHV dominated, thus demonstrating a positive association with resistance to amoxicillin-clavulanic acid, ceftazidime and cefixime, while on the large farms, bla_CTX-M with a positive association to cephalexin and several non-beta lactam antibiotics dominated. The results indicated the prevalence of a broad variety of ESBL-producing E. coli among the small and large farms, putting the larger farms at a higher risk. Individual monitoring of ESBL and their antimicrobial resistance could be an important step in revealing hazardous MDR ESBL-producing E. coli strains and reviewing the management of antibiotic use.

Whole Genome Sequencing of Pediatric Klebsiella pneumoniae Strains Reveals Important Insights Into Their Virulence-Associated Traits

Klebsiella pneumoniae is recognized as a common cause of nosocomial infections and outbreaks causing pneumonia, septicemia, and urinary tract infections. This opportunistic bacterium shows an increasing acquisition of antibiotic-resistance genes, which complicates treatment of infections. Hence, fast reliable strain typing methods are paramount for the study of this opportunistic pathogen’s multi-drug resistance genetic profiles. In this study, thirty-eight strains of K. pneumoniae isolated from the blood of pediatric patients were characterized by whole-genome sequencing and genomic clustering methods. Genes encoding β-lactamase were found in all the bacterial isolates, among which the bla_SHV variant was the most prevalent (53%). Moreover, genes encoding virulence factors such as fimbriae, capsule, outer membrane proteins, T4SS and siderophores were investigated. Additionally, a multi-locus sequence typing (MLST) analysis revealed 24 distinct sequence types identified within the isolates, among which the most frequently represented were ST76 (16%) and ST70 (11%). Based on LPS structure, serotypes O1 and O3 were the most prevalent, accounting for approximately 63% of all infections. The virulence capsular types K10, K136, and K2 were present in 16, 13, and 8% of the isolates, respectively. Phylogenomic analysis based on virtual genome fingerprints correlated with the MLST data. The phylogenomic reconstruction also denoted association between strains with a higher abundance of virulence genes and virulent serotypes compared to strains that do not possess these traits. This study highlights the value of whole-genomic sequencing in the surveillance of virulence attributes among clinical K. pneumoniae strains.