Phenotypic and molecular characterization of plasmid mediated AmpC β-lactamases among Escherichia coli, Klebsiella spp., and Proteus mirabilis isolated from urinary tract infections in Egyptian hospitals

Emergence of extensive drug resistance and high prevalence of multidrug resistance among clinical Proteus mirabilis isolates in Egypt

BACKGROUND

Proteus mirabilis is an opportunistic pathogen that has been held responsible for numerous nosocomial and community-acquired infections which are difficult to be controlled because of its diverse antimicrobial resistance mechanisms.

METHODS

Antimicrobial susceptibility patterns of P. mirabilis isolates collected from different clinical sources in Mansoura University Hospitals, Egypt was determined. Moreover, the underlying resistance mechanisms and genetic relatedness between isolates were investigated.

RESULTS

Antimicrobial susceptibility testing indicated elevated levels of resistance to different classes of antimicrobials among the tested P. mirabilis clinical isolates (n = 66). ERIC-PCR showed great diversity among the tested isolates. Six isolates (9.1%) were XDR while all the remaining isolates were MDR. ESBLs and AmpCs were detected in 57.6% and 21.2% of the isolates, respectively, where blaTEM, blaSHV, blaCTX-M, blaCIT-M and blaAmpC were detected. Carbapenemases and MBLs were detected in 10.6 and 9.1% of the isolates, respectively, where blaOXA-48 and blaNDM-1 genes were detected. Quinolone resistant isolates (75.8%) harbored acc(6')-Ib-cr, qnrD, qnrA, and qnrS genes. Resistance to aminoglycosides, trimethoprim-sulfamethoxazole and chloramphenicol exceeded 80%. Fosfomycin was the most active drug against the tested isolates as only 22.7% were resistant. Class I or II integrons were detected in 86.4% of the isolates. Among class I integron positive isolates, four different gene cassette arrays (dfrA17- aadA5, aadB-aadA2, aadA2-lnuF, and dfrA14-arr-3-blaOXA-10-aadA15) and two gene cassettes (dfrA7 and aadA1) were detected. While class II integron positive isolates carried four different gene cassette arrays (dfrA1-sat1-aadA1, estXVr-sat2-aadA1, lnuF- dfrA1-aadA1, and dfrA1-sat2).

CONCLUSION

P. Mirabilis ability to acquire resistance determinants via integrons may be held responsible for the elevated rates of antimicrobial resistance and emergence of XDR or even PDR strains limiting the available therapeutic options for management of infections caused by those strains.

Antibiotic resistance and virulence profiles of Proteus mirabilis isolated from broiler chickens at abattoir in South Africa

BACKGROUND

Proteus mirabilis has been identified as an important zoonotic pathogen, causing several illnesses such as diarrhoea, keratitis and urinary tract infections.

OBJECTIVE

This study assessed the prevalence of P. mirabilis in broiler chickens, its antibiotic resistance (AR) patterns, ESBL-producing P. mirabilis and the presence of virulence genes.

METHODS

A total of 26 isolates were confirmed as P. mirabilis from 480 pooled broiler chicken faecal samples by polymerase chain reaction (PCR). The disk diffusion method was used to evaluate the antibacterial susceptibility test, while nine virulence genes and 26 AR genes were also screened by PCR.

RESULTS

All 26 P. mirabilis isolates harboured the ireA (siderophore receptors), ptA, and zapA (proteases), ucaA, pmfA, atfA, and mrpA (fimbriae), hlyA and hpmA (haemolysins) virulence genes. The P. mirabilis isolates were resistant to ciprofloxacin (62%) and levofloxacin (54%), while 8 (30.7%) of the isolates were classified as multidrug resistant (MDR). PCR analysis identified the blaCTX-M gene (62%), blaTEM (58%) and blaCTX-M-2 (38%). Further screening for AMR genes identified mcr-1, cat1, cat2, qnrA, qnrD and mecA, 12%, 19%, 12%, 54%, 27% and 8%, respectively for P. mirabilis isolates. The prevalence of the integron integrase intI1 and intI2 genes was 43% and 4%, respectively.

CONCLUSIONS

The rise of ciprofloxacin and levofloxacin resistance, as well as MDR strains, is a public health threat that points to a challenge in the treatment of infections caused by these zoonotic bacteria. Furthermore, because ESBL-producing P. mirabilis has the potential to spread to humans, the presence of blaCTX -M -producing P. mirabilis in broilers should be kept under control. This is the first study undertaken to isolate P. mirabilis from chicken faecal samples and investigate its antibiotic resistance status as well as virulence profiles in South Africa.

Detection of FOX-AmpC-β-lactamase gene and antibiogram of AmpC-beta-lactamase-producing pathogens isolated from chronic suppurative otitis media patients in Nigeria

Background and Objectives

AmpC-producing Gram-negative bacterial (GNB) pathogens are distributed worldwide, especially in clinical settings. This study aimed to determine the antibiogram and the type of AmpC-β-lactamase gene harboured by GNB pathogens implicated in chronic suppurative otitis media (CSOM) cases.

Materials and Methods

Ear swab samples (300) collected from patients with active CSOM were analysed using standard microbiological techniques. Phenotypic and molecular detection of AmpC β-lactamase production was done by cefoxitin/cloxacillin double-disk synergy test and PCR respectively. Antibiogram was determined by disk diffusion technique.

Results

Among the GNB pathogens isolated from CSOM patients, P. aeruginosa was the most predominant (36.3%); followed by K. pneumoniae (22.3%), and E. coli (13.7%). Patients with active CSOM showed increased bacteria isolation rate from bilateral ear discharges than unilateral ear discharges. E. coli and P. aeruginosa were more prevalent among patients with duration of discharge >2 weeks; recording 9.0% and 20.3% respectively. AmpC β-lactamase producers accounted for 14.0%; they were highly resistant (60%-100%) to cephalosporins, trimethoprim-sulfamethoxazole, ofloxacin, amoxicillin, and tetracycline, but very susceptible (70.4%-100%) to ciprofloxacin, imipenem, and amikacin. Multiple antibiotic resistance indices of isolates ranged from 0.7-0.8. FOX-AmpC-β-lactamase gene was detected in 3.9% of the isolates.

Conclusion

The detection of AmpC β-lactamase-producing multidrug-resistant GNB pathogens harbouring FOX-AmpC-β-lactamase gene among patients with CSOM infections in our study is a serious public health problem which needs urgent intervention.

Evaluation of six commercial and in-house phenotypic tests for detection of AmpC β-lactamases: is routine detection possible?

Background

Phenotypic characterization of the prevalent AmpC β-lactamases in clinical isolates is essential for making informed empirical decisions and critical for strengthening antimicrobial stewardship programmes. This study focused on assessing six assays, two in-house and four commercial phenotypic tests for detection of AmpC, to study the feasibility of making its detection a routine diagnostic microbiology laboratory activity.

Methods

A total of 116 non-duplicate Gram-negative bacteria that were resistant to third-generation cephalosporins and amoxicillin/clavulanic acid, and resistant or susceptible to piperacillin/tazobactam and carbapenems, were screened by cefoxitin discs for AmpC. These isolates were subjected to two in-house (AmpC Tris-EDTA and disc approximation) methods and four commercial tests: D69C AmpC Detection Set; D72C ESBL, AmpC & Carbapenemase Detection Set; combination disc test: ESBL + AmpC Screen Disc Kit; and AmpC MIC Test Strip for confirmation of AmpC production. Ten whole-genome-sequenced AmpC-confirmed Gram-negative isolates were used as positive controls and one as a negative control.

Results

The prevalence of AmpC β-lactamases was 16%. Escherichia coli was a major carrier of plasmid-mediated AmpC (26.5%), followed by Klebsiella pneumoniae (23.4%). Phenotypically, 61% of AmpCs were detected by Tris-EDTA (accuracy: 73.8%), 76% by disc approximation (accuracy: 89.2%), 75% by the D69C AmpC Detection Set (accuracy: 95.4%), 74% by the D72C AmpC, ESBL & Carbapenemase Detection Set (accuracy: 95.4%), 76% by the combination disc test (accuracy: 95.4%) and 63% by AmpC MIC Test Strip (accuracy: 87.7%). The sensitivity and specificity of D69C were 97.9% and 88.2%, respectively, and 95.9% and 93.8% for the combination disc test, while for the disc approximation test and D72C they were 93.9% and 75%, and 93.9% and 100%, respectively. Screening by cefoxitin screening was less sensitive (75%) and specific (25%). Disc approximation and the combination disc test detect AmpC in Enterobacterales and also Pseudomonas aeruginosa and Acinetobacter species.

Conclusions

We recommend the in-house disc approximation test and the commercial D69C, as well as the combination disc test, as excellent tools for detection of AmpC. The cefoxitin test overcalls AmpC and cannot be considered a good stand-alone test for AmpC detection.

Antibiotic Resistance Profiles and ARG Detection from Isolated Bacteria in a Culture-Dependent Study at the Codfish Industry Level

The antibiotic resistance phenomenon horizontally involves numerous bacteria cultured from fresh or processed seafood matrix microbiomes. In this study, the identified bacteria from food-producing processes and industrial environments were screened for phenotypic and genotypic resistance determinants. A total of 684 bacterial strains [537 from processed codfish (Gadus morhua and Gadus macrocephalus) products as salted and seasoned and soaked and 147 from environmental samples] were isolated. Antibiotic susceptibility tests showed resistance against tetracycline, oxacillin, and clindamycin in the Staphylococcus genus (both from food and environmental samples) and against beta-lactams (cefotaxime, carbapenems, etc.) and nitrofurans (nitrofurantoin) from E. coli and Salmonella enterica serovar. Enteritidis isolates. One-thousand and ten genetic determinants-tetracycline tetC (25.17%), tetK (21.06%), tetL (11.70%), clindamycin ermC (17.23%), ermB (7.60%), linezolid cfr (8.22%), optrA (3.62%), poxtA (2.05%), and oxacillin mecA (17.37%)-were amplified from Gram-positive resistant and phenotypically susceptible bacteria. Concerning Gram-negative bacteria, the beta-lactam-resistant genes (bla_TEM, bla_CIT, bla_CTX-M, bla_IMP, bla_KPC, bla_OXA-48-like) represented 57.30% of the amplified ARGs. This study found high antibiotic resistance genes in circulation in the fish food industry chain from the macro- to microenvironment. The obtained data confirmed the diffusion of the "antibiotic resistance phenomenon" and its repercussions on the One-health and food-producing systems.

β-Lactamase Producing Escherichia coli Encoding blaCTX-M and blaCMY Genes in Chicken Carcasses from Egypt

Escherichia coli with multidrug resistance and β-lactamase genes may constitute a great public health hazard due to the potential for their transmission to humans through the food chain. This study determined the prevalence, antibiotic resistance profiles, phylogroups, and β-lactamase genes of E. coli isolates from chicken carcasses marketed in Mansoura, Egypt. Interestingly, E. coli was detected in 98% (98/100) of the chicken carcasses examined, which seemed among the highest contamination rates by E. coli worldwide. From the 425 genetically verified uidA gene-positive E. coli, 85 isolates were further studied for antimicrobial resistance profiles, phylogroups, and β-lactamase genes. Interestingly, 89.41% of E. coli (76/85) strains tested against 24 different antibiotics were multidrug-resistant. Of the examined 85 E. coli isolates, 22 (25.88%) isolates harbored bla_CTX-M and were resistant to ampicillin, cefazoline, and ceftriaxone, while three of them were resistant to ceftazidime besides. Nine (10.59%) E. coli strains harbored AmpC- β-lactamase bla_CMY and were resistant to ampicillin. One isolate co-carried bla_CMY and bla_CTX-M genes, though it was negative for the bla_TEM gene. Of the 35 isolates that harbored either extended-spectrum β-lactamase (ESBL) and/or AmpC β-lactamase genes, six strains (17.14%) were assigned to pathogenic phylogroup F and one to phylogroup E, whereas 28 (80%) isolates belonged to commensal phylogenetic groups.

Prevalence of extended-spectrum β-lactamases, AmpC, and carbapenemases in Proteus mirabilis clinical isolates

Background

Proteus mirabilis is an opportunistic pathogen, causing a variety of community-acquired and nosocomial illnesses. It poses a potential threat to patients via the production of β-lactamases, which decrease the efficacy of antimicrobial treatment and impair the management of its pathogenicity. Hence, this study was established to determine the prevalence of extended-spectrum β-lactamases (ESBLs), AmpC, and carbapenemases of P. mirabilis isolated from various clinical specimens.

Results

Proteus mirabilis was identified in 20.7% (58/280) of specimens. ESBL producers were present at a rate of 51.7% (30/58). All AmpC-positive isolates (n = 20) produced ESBLs as well, so 66.7% of ESBL-producing isolates coproduced AmpC enzymes. The modified Hodge test confirmed carbapenemase production in six out of seven imipenem nonsusceptible isolates. Of these, only two (5.7%) isolates were also ESBL-and AmpC-positive. Antibiotic resistance reached the highest level for cotrimoxazole (62.1%, n = 36/58 isolates) and the lowest for imipenem (12.1%, n = 7/58 isolates). The levels of multidrug-resistant (MDR) was 41.4% among the tested isolates. The bla_SHV (83.3%), bla_AmpC (80%), and bla_VIM-1 (50%) were the most detected genes in phenotypically confirmed ESBL-, AmpC-, and carbapenemase-producing isolates, respectively. Besides, more than a half of the tested P. mirabilis strains (53%) coproduced ESBLs and AmpC. Moreover, two isolates coproduced ESBLs and AmpC together with carbapenemases. Furthermore, dendrogram analysis showed great genetic divergence based on the 21 different enterobacterial repetitive intergenic consensus (ERIC) patterns (P1–P21) through the 34 β-lactamase producers. ERIC analysis distinguished clonal similarities between isolates 21 and 22 in P2 and 9 and 10 in P4, which were isolated from the same clinical source and possessed similar patterns of β-lactamase-encoding genes.

Conclusion

Hence, there is an urgent need to monitor hospitalized patients and improve healthcare in order to reduce the incidence of infection and outbreaks of infection with antibiotic-resistant Proteus.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02662-3.

Detection of β-Lactamase Resistance and Biofilm Genes in Pseudomonas Species Isolated from Chickens

Bacteria of the genus Pseudomonas are pathogens in both humans and animals. The most prevalent nosocomial pathogen is P. aeruginosa, particularly strains with elevated antibiotic resistance. In this study, a total of eighteen previously identified Pseudomonas species strains, were isolated from chicken. These strains were screened for biofilm formation and antibiotic resistance. In addition, we evaluated clove oil’s effectiveness against Pseudomonas isolates as an antibiofilm agent. The results showed that Pseudomonas species isolates were resistant to most antibiotics tested, particularly those from the β-lactamase family. A significant correlation (p < 0.05) between the development of multidrug-resistant isolates and biofilms is too informal. After amplifying the AmpC-plasmid-mediated genes (blaCMY, blaMIR, DHA, and FOX) and biofilm-related genes (psld, rhlA, and pelA) in most of our isolates, PCR confirmed this relationship. Clove oil has a potent antibiofilm effect against Pseudomonas isolates, and may provide a treatment for bacteria that form biofilms and are resistant to antimicrobials.

Ampicillinase C Beta-lactamase Producers among Isolates of Enterobacteriaceae in a Tertiary Care Centre: A Descriptive Cross-sectional Study

Introduction

Ampicillinase C beta-lactamase-producing organisms are often resistant to multiple antimicrobial agents, and therapeutic options against these pathogens are limited. Limited information is available regarding Ampicillinase C beta-lactamase producers. The aim of this study was to find out the prevalence of Ampicillinase C beta-lactamase producers among isolates of Enterobacteriaceae in a tertiary care centre.

Methods

A descriptive cross-sectional study was carried out in the Clinical Microbiology Laboratory of a tertiary care centre from May 2021 to October 2021. Ethical approval was received from the Institutional Review Committee (Reference number: 044-077/078). Isolates of Enterobacteriaceae from various clinical samples were collected by convenience sampling. Ampicillinase C screening for beta-lactamase producers among the Enterobacteriaceae isolates was done using cefoxitin (30 μg) disc. Detection of Ampicillinase C beta-lactamase producers among the screen-positive isolates was done by cefoxitin-cloxacillin double-disc synergy test. An increase in the zone size of ≥4 mm was considered as Ampicillinase C beta-lactamase producers. Point estimate and 95% Confidence Interval were calculated.

Results

Among the total 481 isolates of Enterobacteriaceae, 49 (10.19%) (7.50-12.90, 95 % Confidence Interval) were detected as Ampicillinase C beta-lactamase producers among isolates of Enterobacteriaceae.

Conclusions

The prevalence of Ampicillinase C beta-lactamase producers was lower than in other studies done in similar settings. Meropenem could be a drug of choice for the treatment of infections due to Ampicillinase C beta-lactamase-producing gram-negative bacteria.

Keywords

antibiotic; beta-lactamase; Enterobacteriaceae; gram-negative bacteria.

Genomic Characterization of International High-Risk Clone ST410 Escherichia coli Co-Harboring ESBL-Encoding Genes and blaNDM-5 on IncFIA/IncFIB/IncFII/IncQ1 Multireplicon Plasmid and Carrying a Chromosome-Borne blaCMY-2 from Egypt

The accelerated dispersion of multidrug-resistant (MDR) Escherichia coli due to the production of extended-spectrum β-lactamases (ESBLs) or AmpC enzymes has been noted in Egypt, presenting a serious treatment challenge. In this study, we investigate the prevalence of ESBLs and AmpC enzymes among 48 E. coli isolates collected from patients with urinary tract infections admitted to a teaching hospital in Alexandria. Phenotypic and genotypic methods of detection are conducted. Isolates producing both enzymes are tested for the mobilization of their genes by a broth mating experiment. Whole genome sequencing (WGS) is performed for isolate EC13655. The results indicate that 80% of the isolates are MDR, among which 52% and 13% were ESBL and AmpC producers, respectively. Conjugation experiments fail to show the mobilization of blaCMY-2 in EC13655, which was chosen for WGS. In silico analysis reveals that the isolate belongs to a ST410-H24Rx high-risk clone. It coharbors the ESBL-encoding genes blaCTX-M-15, blaTEM-1, and blaOXA-1 on an IncFIA/IncFIB/IncFII/IncQ1 multireplicon plasmid. The chromosomal location of blaCMY-2 is detected with a flanking upstream copy of ISEcp1. This chromosomal integration of blaCMY-2 establishes the stable maintenance of the gene and thus, necessitates an imperative local surveillance to reduce further spread of such strains in different clinical settings.

Systematic Review of Plasmid AmpC Type Resistances in Escherichia coli and Klebsiella pneumoniae and Preliminary Proposal of a Simplified Screening Method for ampC

Beta-lactamase (BL) production is a major public health problem. Although not the most frequent AmpC type, AmpC-BL is increasingly isolated, especially plasmid AmpC-BL (pAmpC-BL). The objective of this study was to review information published to date on pAmpC-BL in Escherichia coli and Klebsiella pneumoniae, and on the epidemiology and detection methods used by clinical microbiology laboratories, by performing a systematic review using the MEDLINE PubMed database. The predictive capacity of a screening method to detect AmpC-BL using disks with cloxacillin (CLX) was also evaluated by studying 102 Enterobacteriaceae clinical isolates grown in CHROMID ESBL medium with the addition of cefepime (FEP), cefoxitin (FOX), ertapenem (ETP), CLX, and oxacillin with CLX. The review, which included 149 publications, suggests that certain risk factors (prolonged hospitalization and previous use of cephalosporins) are associated with infections by pAmpC-BL-producing microorganisms. The worldwide prevalence has increased over the past 10 years, with a positivity rate ranging between 0.1 and 40%, although AmpC was only detected when sought in a targeted manner. CMY-2 type has been the most prevalent pAmpC-BL-producing microorganism. The most frequently used phenotypic method has been the double-disk synergy test (using CLX disks or phenyl-boronic acid and cefotaxime [CTX] and ceftazidime) and the disk method combined with these inhibitors. In regard to screening methods, a 1-µg oxacillin disk with CLX showed 88.9% sensitivity, 100% specificity, 100% positive predictive value (PPV), 98.9% negative predictive value (NPV), and 98.9% validity index (VI). This predictive capacity is reduced with the addition of extended-spectrum beta-lactamases, showing 62.5% sensitivity, 100% specificity, 100% PPV, 93.5% NPV, and 94.1% VI. In conclusion, there has been a worldwide increase in the number of isolates with pAmpC-BL, especially in Asia, with CMY-2 being the most frequently detected pAmpC-BL-producing type of microorganism. Reduction in its spread requires routine screening with a combination of phenotypic methods (with AmpC inhibitors) and genotypic methods (multiplex PCR). In conclusion, the proposed screening technique is an easy-to-apply and inexpensive test for the detection of AmpC-producing isolates in the routine screening of multidrug-resistant microorganisms.

Detection of AmpC and ESBL-producing Enterobacterales isolated from urinary tract infections in Tunisia

Urinary tract infections (UTIs) are the most frequent human infections in community and hospitals. This study aimed to determine the distribution of bacterial uropathogens among urinary tract infections diagnosed within the regional hospital Houcine Bouzaiene (Gafsa, South West Tunisia) during a survey of 54 days from the 8th of November to the 31st of December 2017. Enterobacterales strains were tested for antimicrobial resistance by disk diffusion method and extended-spectrum β-lactamase (ESBL) production was tested by double-disc synergy test. Strains were further subjected to a molecular assessment of ESBL and AmpC β-lactamase production by PCR. Overall, 173 bacterial isolates were studied, out of which 91.3% were Enterobacterales. Escherichia coli was the dominant pathogen, followed by Klebsiella pneumoniae. High to moderate resistance rates were observed, ranging from 66% to 90.7% for penicillins, from 6.7% to 18.6% for cephalosporins and from 16.2% to 25.4% for fluoroquinolones. Enterobacterales with decreased susceptibility to third-generation cephalosporins (3rd GC) carried several resistance genes: blaCTX-M group 1 and group 9, and ACC and FOX AmpC β-lactamase genes. Overall, ESBLs and AmpC β-lactamases were detected in 57% and 14% of the 3rd GC-resistant isolates, respectively. This study proved the high potential of K. pneumaniae species to develop resistance against commonly used antibiotics. Thus, rigorous monitoring of the antibiotic resistance of clinical pathogens have to be implemented in Tunisia. Our results are very relevant to evaluate efficiency of the Tunisian therapeutic strategies against UTIs and adapt them to the emerging problem of antimicrobial resistance.

The Spread of Plasmidic AmpC in a General Lebanese Hospital Over Nine Consecutive Years and the Relationship With Restricted Isolation Protocols

Background: The dreaded bacterial infection by extended-spectrum β-lactamases (ESBL)-producers has always troubled the medical field whether on the public, scientific, or clinical levels. One of the lesser known β-lactamases, which is capable of hydrolyzing broad and extended-spectrum cephalosporins—i.e., cephamycins plus oxyimino-β-lactams—are the AmpC β-lactamases. This group, which has also been termed occasionally—and incorrectly—as ESBL Class C, confers resistance to β-lactamase inhibitors. The prevalence of plasmidic AmpC (pAmpC) strains is possibly still a matter of debate considering the unevenly matched data between phenotypically-detected and molecularly-detected pAmpC.

Aim: In the absence of any study in Lebanon addressing the AmpC, our intention was to determine the numbers and percentages of AmpC Enterobacteriaceae isolates, notably plasmid-mediated ones, across different wards at the Centre Hospitalier du Nord (CHN), Lebanon, and highlight the importance of infection control protocols.

Materials and Methods: Carriage and infection with pAmpC Enterobacteriaceae were retrospectively investigated between 2011 and 2015 and prospectively between 2016 and 2019 at the Centre Hospitalier du Nord Hospital, North Lebanon. The rise or decline in the numbers of such strains, in concordance with the allegedly intensive isolation of the patients, were analyzed.

Results: Intensive care unit (ICU) data shows an initial rise in infection isolates from 2012 to 2014 and in the carriage isolates from 2012 to 2013 with later notable overall decrease in the both isolates' numbers with the application of the isolation protocols at CHN from 2014 onwards. Floors 2, 3, and 4 seemed to house the bulk of the isolates as well.

Conclusion: Preventive measures, such as on-going surveillance of the hospital wards by specialized healthcare personnel and strict implementation of infection control practices, should be a top priority in any medical center in order to isolate such strains and try to put a limit for the development and the dissemination of any possible multidrug resistant strains.

Evaluation of Two Phenotypic Methods for the Detection of Plasmid-Mediated AmpC β-Lactamases among Enterobacteriaceae Isolates

Objectives  AmpC β-lactamases are cephalosporinases that confer resistance to cephalothin, cefazolin, cefoxitin, penicillin, and β-lactamase inhibitor-β-lactam combinations. Even though the AmpC resistance is reported, but the accurate occurrence of AmpC β-lactamases in Enterobacteriaceae members is still unknown. Techniques to identify AmpC producers are still evolving but not yet optimized for the clinical laboratory. Here we aimed to compare the test performance of two different phenotypic methods, that is inhibitor-based assay using boronic acid and disk approximation test for AmpC detection in Enterobacteriaceae isolates from a tertiary hospital microbiology laboratory.

Materials and Methods  The study includes 137 nonrepeat Enterobacteriaceae strains. Bacterial isolates, that yielded a zone diameter of less than 18 mm for cefoxitin by disk diffusion method were considered potential AmpC producers and further confirmed by phenotype methods—inhibitor-based assay using boronic acid and disk approximation test. A multiplex polymerase chain reaction was used to detect the most common plasmid-mediated AmpC genes: ACC, FOX, MOX, DHA, CIT, and EBC.

Results  Of the 137 clinical isolates, 58 (42.33%) were cefoxitin resistant, while 53.4 and 18.9% of the cefoxitin-resistant isolates were positive by inhibitor-based assay and disk approximation test. Multiplex PCR detected 42 (30.6%) isolates with AmpC genes. Of the 42 isolates, the inhibitor-based assay detected 25 (59.5%) isolates, while the disk approximation test detected nine (21.4%) isolates.

Conclusion  Our findings suggest that inhibitor-based assay using boronic acid can be used for the detection of the isolates that harbor AmpC β-lactamases. This method is cost-effective, simple to perform, and easy to interpret. Thus AmpC detection as a routine in clinical laboratories can help in appropriate therapeutic intervention and improved infection control.

Evidence of potentially unrelated AmpC beta-lactamase producing Enterobacteriaceae from cattle, cattle products and hospital environments commonly harboring the blaACC resistance determinant

The occurrence and genetic relatedness of AmpC beta-lactamase producing Enterobacteriaceae isolated from clinical environments, groundwater, beef, human and cattle faeces were investigated. One hundred seventy-seven (177) samples were collected and cultured on MacConkey agar. A total of 203 non-repetitive isolates were characterised using genus/species-specific PCRs and the identified isolates were subjected to antibiotic susceptibility testing. The production of AmpC beta-lactamases was evaluated using cefoxitin disc, confirmed by the D96C detection test and their encoding genes detected by PCR. The D64C extended-spectrum beta-lactamases (ESBL) test was also performed to appraise ESBLs/AmpC co-production. The genetic fingerprints of AmpC beta-lactamase producers were determined by ERIC-PCR. A total of 116 isolates were identified as E. coli (n = 65), Shigella spp. (n = 36) and Klebsiella pneumoniae (n = 15). Ciprofloxacin resistance (44.4-55.4%) was the most frequent and resistance against the Cephem antibiotics ranged from 15-43.1% for E. coli, 25-36.1% for Shigella spp., and 20-40% for K. pneumoniae. On the other hand, these bacteria strains were most sensitive to Amikacin (0%), Meropenem (2.8%) and Piperacillin-Tazobactam (6.7%) respectively. Nineteen (16.4%) isolates comprising 16 E. coli and 3 Shigella spp. were confirmed as AmpC beta-lactamase producers. However, only E. coli isolates possessed the corresponding resistance determinants: blaACC (73.7%, n = 14), blaCIT (26%, n = 5), blaDHA (11%, n = 2) and blaFOX (16%, n = 3). Thirty-four (27.3%) Enterobacteriaceae strains were confirmed as ESBL producers and a large proportion (79.4%, n = 27) harboured the blaTEM gene, however, only two were ESBLs/AmpC co-producers. Genetic fingerprinting of the AmpC beta-lactamase-producing E. coli isolates revealed low similarity between isolates. In conclusion, the findings indicate the presence of AmpC beta-lactamase-producing Enterobacteriaceae from cattle, beef products and hospital environments that commonly harbour the associated resistance determinants especially the blaACC gene, nonetheless, there is limited possible cross-contamination between these environments.

Phenotypic and Genotypic Characteristics of Uropathogenic Escherichia coli Isolates from Kenya

Introduction: Uropathogenic Escherichia coli (UPECs) are a significant cause of urinary tract infections (UTIs). In Kenya, UTIs are typically treated with β-lactam antibiotics without antibiotic susceptibility testing, which could accelerate antibiotic resistance among UPEC strains.

Aim: This study determined the occurrence of UPEC producing extended-spectrum β-lactamases (ESBLs), the genes conferring resistance to β-lactams, and the phylogenetic groups associated with ESBLs in Kenyan UPECs.

Methodology: Ninety-five UPEC isolates from six Kenyan hospitals were tested for ESBL and plasmid-mediated AmpC β-lactamase (pAmpC) production by combined disk diffusion and disk approximation tests, respectively. Real-time and conventional polymerase chain reactions (PCRs) were used to detect three ESBL and six pAmpC genes, respectively, and phylogenetic groups were assigned by a quadruplex PCR method.

Results: Twenty-four percent UPEC isolates were ESBL producers with bla_CTX-M (95.6%), bla_TEM (95.6%), and bla_SHV (21.7%) genes detected. Sixteen isolates had bla_CTX-M/TEM, whereas five had bla_{TEM/CTX-M/SHV}. A total of 5/23 ESBLs were cefoxitin resistant, but no AmpC genes were detected. The UPECs belonged predominantly to phylogenetic groups B2 (31/95; 32.6%) and D (30/95; 31.6%), while groups B2 and A had the most ESBL producers.

Conclusions: β-Lactam antibiotics have reduced utility for treating UTIs as a quarter of UPECs were ESBL producing. Single or multiple ESBL genes were present in UPECs, belonging primarily to phylogenetic groups B2 and A.

Clonal Relationship and Resistance Profiles Among ESBL-Producing Escherichia coli

AmpC β-lactamases hydrolyze all β-lactams except cefepime and carbapenems. The study of AmpC-producing E. coli has high priority for the infection control committee. This research is aimed to investigate the resistant urinary AmpC-generating E. coli isolates and identify their genetic variety. Some 230 E. coli isolates from patients suffering urinary tract infection symptoms were studied in 2017-2018 to assess their susceptibility toward antimicrobial agents. AmpC gene was evaluated by PCR and molecular typing using the 10-loci MLVA method. MLVA images were examined by BioNumerics 6.6 software through the use of the UPGMA algorithms. Thirty-eight AmpC-generating E. coli isolates were detected. The most abundant determinant was bla_CIT and bla_EBC , bla_FOX , and bla_DHA had the next ranks, respectively. Six major clusters and a singleton were identified by MLVA. AmpC beta-lactamases in urinary isolates of E. coli in the hospital under study and high rate of additional resistance to gentamicin, cotrimoxazole and ciprofloxacin. The most frequent gene determinant of AmpC beta-lactamase was bla_CIT and vary depending on time and geographical location.

Phenotypic Identification and Genotypic Characterization of Plasmid-Mediated AmpC β-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae Isolates in Iran

One of the mechanisms of Klebsiella pneumoniae and Escherichia coli resistance to β-lactam antibiotics is the production of β-lactamase enzymes. Among these are the AmpC β-lactamases, which confer resistance to a class of antibiotics. However, little is known about the AmpC β-lactamases of K. pneumoniae and E. coli clinical isolates in Qazvin, Iran. This study was designed to assess the AmpC β‑lactamases-producing strains and also identify the prevalence of AmpC β‑lactamases genes. Antimicrobial susceptibility tests were performed on 435 K. pneumoniae and E. coli isolates using disk diffusion technique. Plasmid-mediated AmpC genes were studied using a multiplex PCR assay. The AmpC β-lactamase-producer isolates were studied by employing cefoxitin disk diffusion test, AmpC induction test, AmpC cefoxitin-EDTA test, and boronic acid disk test. Our results showed that of 46 (18.4%) cefoxitin-insensitive E. coli isolates, 10 (21.7%) were positive for AmpC β-lactamase genes, among them 4 (8.69%) isolates were positive for bla_DHA genes and 6 (13%) for bla_CIT genes. Of 57 (30.4%) cefoxitin-insensitive K. pneumoniae isolates, 10 (17.5%) were positive for AmpC gene with 4 (6.34%) and 6 (9.5%) isolates positive for bla_DHA and bla_CIT genes, respectively. However, no MOX, ACC, FOX, or EBC genes were detected in the isolates. Considering the results of different confirmatory phenotypic tests, the AmpC cefoxitin-EDTA test showed a higher discriminatory power for detecting AmpC β-lactamase-producing strains. The specificity and sensitivity of AmpC cefoxitin-EDTA were 77%, 100% for K. pneumonia and 70%, 90% for E. coli higher than the other two tests, respectively. Also, the authors demonstrated high prevalence rate for resistance to certain antibiotics, such as cefuroxime, trimethoprim-sulfamethoxazole, ampicillin, and cefotaxime. In conclusion, our study provided valuable information regarding the plasmid-mediated AmpC β-lactamase gene content, antibiotic resistance, and confirmatory phenotypic tests for AmpC β-lactamases in E. coli and K. pneumoniae isolates from clinical sources.

Prevalence and molecular characteristics of ESBL and AmpC β -lactamase producing Enterobacteriaceae strains isolated from UTIs in Egypt

BACKGROUND

Infections caused by Enterobacteriaceae are mainly treated with the β-lactam antibiotics, nevertheless, the emergence of species with plasmid-borne β-lactamases has decreased the efficacy of these antibiotics. Therefore, continuing studies on the resistance pattern of different regions is important for assessment of proper antimicrobial therapy protocols. The study aimed to characterize extended-spectrum β-lactamase (ESBL) and AmpC β -lactamase (AmpC) producing Enterobacteriaceae isolated from community-acquired UTIs in Egypt.

METHODS

Out of 705 urine samples, 440 Enterobacteriaceae isolates were investigated to detect ESBL and AmpC β -lactamases producers by phenotypic and molecular methods.

RESULTS

Out of 440 Enterobacteriaceae isolates, 311 were identified as ESBL producers by phenotypic testing. ESBL genes were detected in 308 isolates. BlaCTX-M-type was the most prevalent 254 (81.6%), out of them blaCTXM-15 was the commonest (152, 48.8%) followed by blaCTX-M-1 (140, 45%), blaCTX-M-8 (72, 23.1%) and lastly blaCTX-M-2 (4, 1.3%). blaTEM gene also was detected in a high rate (189, 60.7%). Two hundred and thirty-five (75.5%) of ESBL producers harbored blaCTX-M in combination with blaTEM and/or blaSHV genes. Multiple drug resistance in the ESBL-producers was significantly (P < 0.05) higher than in non-ESBL producers. Imipenem was the most effective drug against ESBL producers. Among 35 cefoxitin resistant isolates, 18 (51.4%) identified as carrying AmpC genes by multiplex PCR. Within AmpC β -lactamase genes, DHA gene was the predominant gene (15, 42.3%). CIT and MOX genes were also present, but in a low rate (5, 14.2% and 4, 11.4%) respectively. Co-existence of multiple AmpC genes was detected exclusively in K. pneumoniae isolates. E. coli isolates harbored DHA gene only. However, FOX gene was not detected in the study isolates. Seventeen of isolates carrying AmpC genes were also positive for ESBL genes.

CONCLUSION

The study shows that the prevalence of ESBL producing Enterobacteriaceae spread in south Egypt is alarming, however AmpC β -lactamase production is not so high.

Detection of CMY-type beta-lactamases in Escherichia coli isolates from paediatric patients in a tertiary care hospital in Mexico

Background

The aim of this study was to detect CMY-type beta-lactamases in E. coli isolates obtained from paediatric patients.

Methods

In total, 404 infection-causing E. coli isolates resistant to third and fourth generation cephalosporins (3GC, 4GC) were collected from paediatric patients over a 2 years period. The identification and susceptibility profiles were determined with an automated microbiology system. Typing of bla_CMY and other beta-lactamase genes (bla_TEM, bla_SHV, bla_CTX-M, bla_VIM, bla_IMP, bla_KPC, bla_NDM, bla_OXA and bla_GES) was realized by PCR and sequencing. Phenotypic detection of AmpC-type enzymes was performed using boronic acid (20 mg/mL) and cloxacillin (20 mg/mL) as inhibitors, and the production of extended-spectrum beta-lactamases was determined with the double-disk diffusion test with cefotaxime (CTX) and ceftazidime (CAZ) discs alone and in combination with clavulanic acid. The CarbaNP test and modified carbapenem inhibition method (mCIM) were used for isolates with decreased susceptibility to carbapenems. The clonal origin of the isolates was established by pulsed-field gel electrophoresis (PFGE), phylotyping method and multilocus sequence typing.

Results

CMY-type beta-lactamases were detected in 18 isolates (4.5%). The allelic variants found were CMY-2 (n = 14) and CMY-42 (n = 4). Of the E. coli strains with CMY, the AmpC phenotypic production test was positive in 11 isolates with cloxacillin and in 15 with boronic acid. ESBL production was detected in 13 isolates. Coexistence with other beta-lactamases was observed such as CTX-M-15 ESBL and original spectrum beta-lactamases TEM-1 and TEM-190. In one isolate, the CarbaNP test was negative, the mCIM was positive, and OXA-48 carbapenemase was detected. Phylogroup A was the most frequent (n = 9) followed by B2, E and F (n = 2, respectively), and through PFGE, no clonal relationship was observed. Eleven different sequence types (ST) were found, with ST10 high-risk clone being the most frequent (n = 4). Seventy-two percent of the isolates were from health care-associated infections; the mortality rate was 11.1%.

Conclusions

This is the first report in Mexico of E. coli producing CMY isolated from paediatric patients, demonstrating a frequency of 4.5%. In addition, this is the first finding of E. coli ST10 with CMY-2 and OXA-48.

High prevalence of blaCMY AmpC beta-lactamase in ESBL co-producing Escherichia coli and Klebsiella spp. clinical isolates in the northeast of Iran

OBJECTIVE

The production of β-lactamase enzymes such as AmpC β-lactamases and extended-spectrum β-lactamases (ESBLs) is among the main mechanisms for resistance to expanded-spectrum cephalosporins. The present study was conducted to investigate the prevalence and molecular epidemiology of plasmid-mediated AmpC beta (β)-lactamase in ESBL co-producing Escherichia coli (E. coli) and Klebsiella spp. (Klebsiella pneumoniae and Klebsiella oxytoca) clinical isolates in the northeast of Iran.

METHODS

A total of 602 E. coli and Klebsiella spp. clinical isolates were collected from three hospitals in Mashhad (northeast of Iran). A combination disk test (CDT) was performed for the phenotypic detection of ESBLs. Screening for the detection of AmpC β-lactamases was performed by a susceptibility test to a cefoxitin disc among ESBL producing isolates. A confirmatory test for AmpC β-lactamases was performed using the Mast® D68C test. Identification of plasmid-mediated AmpC cluster genes was done by multiplex polymerase chain reaction (PCR).

RESULTS

Among 336 ESBL-producing strains, 230 (68.4%) isolates were resistant to cefoxitin. Results of the Mast® D68C test showed that 30% (69/230) of cefoxitin-resistant isolates simultaneously exhibited ESBL and AmpC activity and 22% (51/230) of isolates probably showed multi-drug resistant (MDR) phenotype. Results of multiplex PCR among ESBL-positive isolates showed that, 16.7% (56/336) of isolates were positive for plasmid-borneampC cluster genes, and CMY (38%) was the most frequent genotype of plasmid mediated AmpC.

CONCLUSION

Findings of the study revealed that an increase in the prevalence of ESBL and AmpC co-producer in E. coli and Klebsiella spp. strains may become an important public health issue. Therefore, there is a vital need for surveillance of spread of these clinical isolates.

Genetics of Acquired Antibiotic Resistance Genes in Proteus spp

Proteus spp. are commensal Enterobacterales of the human digestive tract. At the same time, P. mirabilis is commonly involved in urinary tract infections (UTI). P. mirabilis is naturally resistant to several antibiotics including colistin and shows reduced susceptibility to imipenem. However higher levels of resistance to imipenem commonly occur in P. mirabilis isolates consecutively to the loss of porins, reduced expression of penicillin binding proteins (PBPs) PBP1a, PBP2, or acquisition of several antibiotic resistance genes, including carbapenemase genes. In addition, resistance to non-β-lactams is also frequently reported including molecules used for treating UTI infections (e.g., fluoroquinolones, nitrofurans). Emergence and spread of multidrug resistant P. mirabilis isolates, including those producing ESBLs, AmpC cephalosporinases and carbapenemases, are being more and more frequently reported. This review covers Proteus spp. with a focus on the different genetic mechanisms involved in the acquisition of resistance genes to multiple antibiotic classes turning P. mirabilis into a dreadful pandrug resistant bacteria and resulting in difficult to treat infections.

Phenotypic and molecular characterization of antimicrobial resistant Escherichia coli from urinary tract infections in Port-Harcourt, Nigeria

Introduction

Multidrug resistance among Escherichia coli causing Urinary Tract Infections (UTIs) is a major public health problem, threatening the effective treatment of UTIs. This study investigated the phenotypic and molecular characteristics of E. coli associated with UTIs in Port-Harcourt, Nigeria.

Methods

Twenty-five non-duplicate isolates of E. coli from UTIs patients at the University of Port-Harcourt Teaching Hospital, Nigeria were identified using Matrix-Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry. The antimicrobial susceptibility patterns were determined using Kirby-Bauer disc diffusion technique. Phenotypic expression of Extended Spectrum Beta Lactamases (ESBLs) and AmpC beta-lactamase were determined using standard laboratory methods and polymerase chain reaction (PCR) was used to detect ESBLs, AmpC, Quinolones and Aminoglycosides resistance genes.

Results

The isolates exhibited high rates of resistance to co-trimoxazole (76%), nalidixic acid (68%), ciprofloxacin (60%), gentamicin (44%) and low resistance to cefotaxime (20%) but were fully susceptible to cefoperazone/sulbactam, amikacin, nitrofurantoin, colistin and carbapenems. Phenotypic expression of ESBLs was recorded in 6(24%) isolates while genotypic detection revealed the highest prevalence of blaTEM 22(88%), followed by blaCTX-M-15 16(64%), blaSHV 7(28%) and blaOXA-1 6(24%) while AmpC (blaCMY-2) gene was detected in 8(32%) isolates. Amongst the quinolone resistant isolates, qnr variants (qnrB, qnrD and qnrS) and aac(6')-Ib genes were detected in 7(28%) and 3(12%) isolates respectively while all gentamicin resistant isolates possessed the aacC2 gene. The co-expression of blaCTX-M-15 with quinolones and aminoglycoside genes were 20% and 40% respectively. The prevalence of multiple drug resistance was 52%.

Conclusion

A high proportion of the studied E. coli isolates co-expressed ESBLs, quinolones and aminoglycosides resistance genes which call for prompt antibiotic stewardship and preventive strategies to limit the spread of these genes.

Antibiotic Resistance of Enterobacteriaceae Isolated from Fresh Fruits and Vegetables and Characterization of their AmpC β-Lactamases

Enterobacteria may gain antibiotic resistance and be potent pathogens wherever they are present, including in fresh fruits and vegetables. This study tested the antibiotic resistance of enterobacteria isolated from 13 types of local and imported fresh fruits and vegetables (n = 105), using the standard Kirby-Bauer disk diffusion method. Phenotypic and genotypic characterizations of AmpC β-lactamases were determined in cefoxitin-resistant isolates. Ten percent of the enterobacteria tested (n = 88) were pansusceptible, 74% were resistant to at least one antibiotic, and 16% were multidrug resistant. Enterobacteria isolates showed the highest antibiotic resistance against ampicillin (66%), cephalothin (57%), amoxicillin-clavulanic acid (33%), cefoxitin (31%), tetracycline (9%), nalidixic acid (7%), trimethoprim (6%), and kanamycin (5%). Three isolates showed intermediate resistance to the clinically important antibiotic imipenem. Escherichia coli isolated from lettuce exhibited multidrug resistance against five antibiotics. Fifteen isolates were confirmed to have AmpC β-lactamase, using the inhibitor-based test and the antagonism test; the latter test confirmed that the enzyme was an inducible type. Four types of ampC β-lactamase genes (CIT, EBC, FOX, and MOX) were detected in eight isolates: four Enterobacter cloacae isolates and one isolate each of Citrobacter freundii, Enterobacter asburiae, Enterobacter hormaechei, and Enterobacter ludwigii. It was concluded that fresh fruits and vegetables might play a role as a source or vehicle for transferring antibiotic-resistant bacteria that might spread to other countries through exportation. The clinically significant AmpC β-lactamase was rarely documented in the literature on bacteria isolated from fruits and vegetables, and to our knowledge, this is the first report on the detection of an inducible type in such commodities.

First Detection of Carbapenem-Resistant Escherichia fergusonii Strains Harbouring Beta-Lactamase Genes from Clinical Samples

Recently discovered extraintestinal Escherichia fergusonii obtained from non-clinical samples has exhibited the potential for acquiring multiple beta-lactamase genes, just like many extraintestinal Escherichia coli strains. Albeit, they are often omitted or classified as E. coli. This study aimed to, therefore, identify carbapenem-resistant extended-spectrum beta-lactamase (ESBL) producing E. fergusonii isolates from clinical samples, determine their evolutionary relatedness using 16S rRNA sequencing analysis and screen for beta-lactamase genes. A total of 135 septic wound samples were obtained from patients on referral at a General Hospital in Lagos, Nigeria. For the phenotypic identification of isolates from culture-positive samples, morphological, and physiological tests were carried out. Identities of the isolates harbouring beta-lactamase genes were assigned to their genus strains using the 16S rRNA sequencing. The Kirby Bauer disc diffusion technique and double-disc synergy test were used to screen isolates for multidrug resistance and ESBL production. Carbapenem-resistant ESBL producing isolates were screened for beta-lactamase genes in a polymerase chain reaction. Three E. fergusonii isolates (CR11, CR35 and CR49) were obtained during this study. E. fergusonii strains were motile, non-lactose and non-sorbitol fermenting but positive for cellobiose and adonitol fermentation. The I6S rRNA assigned the phenotypically identified isolates to E. fergusonii species. All three isolates were multidrug-resistant, carbapenem-resistant and ESBL producers. Isolates CR11 and CR35 harboured cefotaximase (CTX-M) and temoniera (TEM) beta-lactamase genes while CR49 harboured sulfhydryl variable (SHV) beta-lactamase gene. We herein report the detection of multiple beta-lactamase genes in carbapenem-resistant ESBL producing E. fergusonii from clinical samples.

Understanding the Epidemiology of Multi-Drug Resistant Gram-Negative Bacilli in the Middle East Using a One Health Approach

In the last decade, extended-spectrum cephalosporin and carbapenem resistant Gram-negative bacilli (GNB) have been extensively reported in the literature as being disseminated in humans but also in animals and the environment. These resistant organisms often cause treatment challenges due to their wide spectrum of antibiotic resistance. With the emergence of colistin resistance in animals and its subsequent detection in humans, the situation has worsened. Several studies reported the transmission of resistant organisms from animals to humans. Studies from the middle east highlight the spread of resistant organisms in hospitals and to a lesser extent in livestock and the environment. In view of the recent socio-economical conflicts that these countries are facing in addition to the constant population mobilization; we attempt in this review to highlight the gaps of the prevalence of resistance, antibiotic consumption reports, infection control measures and other risk factors contributing in particular to the spread of resistance in these countries. In hospitals, carbapenemases producers appear to be dominant. In contrast, extended spectrum beta lactamases (ESBL) and colistin resistance are becoming a serious problem in animals. This is mainly due to the continuous use of colistin in veterinary medicine even though it is now abandoned in the human sphere. In the environment, despite the small number of reports, ESBL and carbapenemases producers were both detected. This highlights the importance of the latter as a bridge between humans and animals in the transmission chain. In this review, we note that in the majority of the Middle Eastern area, little is known about the level of antibiotic consumption especially in the community and animal farms. Furthermore, some countries are currently facing issues with immigrants, poverty and poor living conditions which has been imposed by the civil war crisis. This all greatly facilitates the dissemination of resistance in all environments. In the one health concept, this work re-emphasizes the need to have global intervention measures to avoid dissemination of antibiotic resistance in humans, animals and the environment in Middle Eastern countries.

Prevalence of plasmid-mediated AmpC in Enterobacteriaceae isolated from humans and from retail meat in Zagazig, Egypt

Background

The objective of this study was to determine the prevalence of plasmid-mediated AmpC (pAmpC) among Enterobacteriaceae isolated from humans and from retail meat in Egypt.

Methods

Enterobacteriaceae were isolated from patients with suspected bloodstream infection, human fecal samples, retail chicken meat samples and retail sheep meat samples. All group I Enterobacteriaceae were analyzed for presence of pAmpC genes by PCR. Antibiotic susceptibility testing was performed in all pAmpC positive isolates, followed by phenotypic and genotypic ESBL and carbapenemase testing on indication.

Results

The prevalence of pAmpC among group I Enterobacteriaceae isolated from 225 patients with bloodstream infection was 5.6% [95%CI 2.2–13.4]. Among 100 patients with community-onset gastroenteritis the prevalence in fecal samples was 4.8% [95%CI 2.1–10.7]. The prevalence among 112 chicken carcasses and 100 sheep meat samples was 2.4% [95%CI 0.7–8.4] and 1.1% [95%CI 0.2–5.7], respectively. In half of the AmpC positive isolates we detected an ESBL gene and 2 isolates harbored a carbapenemase gene. In five isolates there was resistance to at least three important alternative antibiotic drugs.

Conclusions

We consider the prevalence of pAmpC in Egypt, as found in our study, moderately low. To follow future trends in prevalence of pAmpC worldwide, a standardized screening algorithm for the detection of pAmpC is needed.

Acquisition of plasmid-mediated cephalosporinase producing Enterobacteriaceae after a travel to the tropics

Travelers are at high risk of acquiring multi-drug resistant Enterobacteriaceae (MRE) while traveling abroad. Acquisition of extended spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) while traveling has been extensively described, but not that of plasmid-mediated cephalosporinase producing Enterobacteriaceae (pAmpC-E). Here, we characterized the pAmpC-E acquired in 574 French travelers to tropical areas enrolled in the VOYAG-R study. Among the 526 MRE isolated at return, 57 (10.8%) from 49 travelers were pAmpC-E. The acquisition rate of pAmpC-E was 8.5% (49/574) ranging from 12.8% (25/195) in Asia, 7.6% (14/184) in Latin America to 5.1% (10/195) in Africa. The highest acquisition rates were observed in Peru (21.9%), India (21.4%) and Vietnam (20%). The carriage of pAmpC-E decreased quickly after return with 92.5% of colonized travelers being negative at one month. Most enzymes were CMY types (96.5%, n = 55, only met in Escherichia coli), including 40 CMY-2 (70.2%), 12 CMY-42 (21.1%), 1 CMY-6 and two new CMY-2 variants. The remaining were two DHA observed in Klebsiella pneumoniae. CMY-2 producing strains were acquired worldwide whereas CMY-42, except for one, were all acquired in Asia. Bla_CMY-2 genes were associated with different plasmid types, including IncI1 (45. 2%), IncF (10%), IncF-IncI (7.5%), IncA/C (5%) and IncR (2.5%) whereas bla_CMY-42 were all associated with IncI1 plasmids. Even though the pAmpC-E acquisition rate was much lower than that of ESBL-E, it was significant, especially in Asia, showing that pAmpC-E, especially CMY-type producing E. coli have spread in the community settings of tropical regions.

Emergence of co-existence of blaNDM with rmtC and qnrB genes in clinical carbapenem-resistant Klebsiella pneumoniae isolates in burning center from southeast of Iran

Dissemination of carbapenemase-producing Klebsiella pneumoniae along with 16S rRNA methyltransferase (16S-RMTase) has been caused as a great concern for healthcare settings. The aim of this study was to investigate the prevalence of resistance genes among K. pneumoniae isolates. During October 2015 to February 2016, 30 non-duplicative K. pneumoniae strains were isolated from clinical specimens in a burn center in Kerman, Iran. Antibiotic susceptibility tests of isolates, carbapenemase, extended-spectrum beta-lactamases (ESBLs) and AmpC beta-lactamase-producing isolates were determined by phenotypic methods. The beta-lactamase, oqxA/B efflux pumps, qnr A, B, S, 16S-RMTase (rmt A, B, and C), and mcr-1 resistance genes were determined by PCR. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was used for molecular typing. According to our findings, tigecycline has been shown the most active agent against K. pneumoniae isolates. Antibiotic resistance genes, bla_TEM-1, bla_SHV-12, bla_CTX-M-15, bla_CTX-M-2, bla_NDM-1, bla_FOX, bla_MOX, bla_EBC, bla_ACC, bla_CIT, rmtC, qnrB, qnrS, oqxA, and oqxB, were detected in 11 (36.7%), 13 (43.3%), 11 (36.6%), 5 (16.6%), 9 (30%), 1 (3.3%), 1 (3.3%), 1 (3.3%), 1 (3.3%), 2 (6.7%), 1 (3.3%), 9 (30%), 2 (6.7%), 18 (60%), and 13 (43.3%) of isolates, respectively. The bla_NDM-1 with rmtC was simultaneously observed in one isolate. ERIC-PCR results revealed 25 distinct patterns in eight clusters (A-H) and five singletons. This study highlights the high prevalence of bla_NDM and emergence of rmtC among carbapenem-resistant K. pneumoniae. The resistance genes are often co-located on the conjugative plasmids, so it might be the reason of the rapid spread of them. The prevalence of multidrug-resistant K. pneumoniae isolates limits the available treatment options and presents tremendous challenges to public health.

First Detection of FOX-1 AmpC β-lactamase Gene Expression Among Escherichia coli Isolated from Abattoir Samples in Abakaliki, Nigeria

Objectives

Gram-negative bacteria represent the most relevant reservoir of resistance to antibiotics in the environment. The natural selection of resistant clones of bacteria in the environment by antimicrobial selective pressure is a relevant mechanism for spreading antibiotic resistance traits in both the community and hospital environment. This is in scenarios where antimicrobials are used irrationally, and even in the propagation of livestock, poultry birds, and for other veterinary purposes. This study sought to detect the prevalence of FOX-1 AmpC β-lactamase genes from abattoir samples.

Methods

The isolation of Escherichia coli, antimicrobial susceptibility testing, and β-lactamase characterization was carried out using standard microbiology techniques. The production of AmpC β-lactamase was phenotypically carried out using the cefoxitin-cloxacillin double-disk synergy test (CC-DDST), and FOX-1 AmpC genes was detected in the E. coli isolates using multiplex polymerase chain reaction.

Results

Forty-eight E. coli isolates were recovered from the anal swabs of cows and 35 (72.9%) isolates were positive for the production of β-lactamase. Notably, high percentages of resistance to cefoxitin (91.7%), ceftriaxone (83.3%), imipenem (85.4%), ceftazidime (87.5%), ofloxacin (81.3%), and gentamicin (85.4%) were found. FOX-1 genes were detected in three (6.3%) of the 48 E. coli isolates phenotypically screened for AmpC enzyme production.

Conclusions

Abattoirs could represent a major reservoir of resistance genes especially AmpC β-lactamase, and this could serve as a route for the dissemination of multidrug-resistant bacteria in the community. Thus, the molecular identification of drug-resistant genes is vital for a reliable epidemiological investigation and the forestalling of the emergence and spread of these organisms through the food chain in this region.

Occurrence of blaCMY-42 on an IncI1 plasmid in multidrug-resistant Escherichia coli from a tertiary referral hospital in India

OBJECTIVES

Plasmids of different replicon types are believed to be associated with the carriage and transmission of antimicrobial resistance genes. The present study was undertaken to examine the association of bla_CIT with particular plasmid types and to identify Escherichia coli strains involve in the maintenance of this resistance determinant in the plasmid.

METHODS

Phenotypic screening of AmpC β-lactamases was performed by the modified three-dimensional extract method, followed by antimicrobial susceptibility testing and determination of minimum inhibitory concentrations (MICs). Genotyping screening of β-lactamase genes was performed by PCR assay, followed by sequencing. Transferability of the bla_CMY gene was performed by transformation and conjugation experiments. Plasmid incompatibility typing and DNA fingerprinting by enterobacterial repetitive intergenic consensus (ERIC)-PCR were performed.

RESULTS

Among 203 E. coli obtained from different clinical specimens (pus, urine, stool and sputum), 37 were detected as harbouring the bla_CIT gene and sequencing of this gene showed nucleotide sequence similarity with the bla_CMY-42 variant. This study revealed IncI1-type plasmids as carriers of bla_CMY-42 and its propagation within E. coli ST5377, ST361 and ST672. According to the stability results, the bla_CMY-42-encoding plasmid can be maintained in E. coli strains for a longer duration without any antimicrobial pressure.

CONCLUSIONS

These finding document bla_CMY-42 on IncI1-type plasmids, which are considered to be the main vehicles for the spread of bla_CMY-42 in this hospital setting. Thus, a proper strategy should be developed to curb the expansion of IncI1-type plasmids in the hospital and community environment.

Co-Occurrence of Plasmid-Mediated AmpC β-Lactamase Activity Among Klebsiella pneumoniae and Escherichia Coli

Introduction:

Extended-spectrum β-lactamases (ESBLs), including the AmpC type, are important mechanisms of resistance among Klebsiella pneumoniae and Escherichia coli isolates.

Objective:

The aim of the study was to investigate the occurrence of AmpC-type β-lactamase producers isolated from two hospitals in Tripoli, Libya.

Methods:

All clinical isolates (76 K. pneumoniae and 75 E. coli) collected over two years (2013-2014) were evaluated for susceptibility to a panel of antimicrobials and were analyzed phenotypically for the ESBL and AmpC phenotype using E-test and ESBL and AmpC screen disc test. Both ESBL and AmpC-positive isolates were then screened for the presence of genes encoding plasmid-mediated AmpC β-lactamases by polymerase chain reaction (PCR).

Results:

Of the K. pneumoniae and E. coli tested, 75% and 16% were resistant to gentamicin, 74% and 1.3% to imipenem, 71% and 12% to cefoxitin, 80% and 12% to cefepime, 69% and 22.6% to ciprofloxacin, respectively. None of the E. coli isolates were multidrug resistant compared with K. pneumoniae (65.8%). K. pneumoniae ESBL producers were significantly higher (85.5%) compared with (17.3%) E. coli isolates (P <0.0001, OR=4.93). Plasmid-mediated AmpC genes were detected in 7.9% of K. pneumoniae, and 4% E. coli isolates. There was low agreement between phenotypic and genotypic methods, phenotypic testing underestimated detection of AmpC enzyme and did not correlate well with molecular results. The gene encoding CMY enzyme was the most prevalent (66.6%) of AmpC positive isolates followed by MOX, DHA and EBC. Only one AmpC gene was detected in 5/9 isolates, i.e, bla_CMY (n=3), bla_MOX (n=1), bla_DHA (n=1). However, co-occurrence of AmpC genes were evident in 3/9 isolates with the following distribution: bla_CMY and bla_EBC (n=1), and bla_CMY and bla_MOX (n=2). Neither bla_FOX nor bla_ACC was detected in all tested isolates. All AmpC positive strains were resistant to cefoxitin and isolated from patients admitted to intensive care units.

Conclusion:

Further studies are needed for detection of other AmpC variant enzyme production among such isolates. Continued surveillance and judicious antibiotic usage together with the implementation of efficient infection control measures are absolutely required.

Emergence of CMY-2- and DHA-1-type AmpC β-lactamases in Enterobacter cloacae isolated from several hospitals of Qazvin and Tehran, Iran

BACKGROUND AND OBJECTIVES

The emergence of plasmid-mediated AmpC (pAmpC) β-lactamases conferring resistance to third-generation cephalosporins has become a major clinical concern worldwide. The aims of this study were to determine the prevalence of pAmpC-producing E. cloacae isolates and typing of them in Qazvin and Tehran provinces, Iran.

MATERIALS AND METHODS

A total of 120 cefoxitin non-susceptible isolates of E. cloacae were obtained from educational hospitals of Qazvin and Tehran, Iran. Bacterial identification was performed by standard laboratory methods and API 20E strips. Susceptibility to cefoxitin was determined by Kirby-Bauer disk diffusion method. PCR and sequencing were employed to detect pAmpC families' genes (ACC, FOX, MOX, DHA, CIT and EBC) and the clonal relatedness of pAmpC-positive isolates was evaluated by enterobacterial repetitive intergenic consensus (ERIC)-PCR method.

RESULTS

In total, 20 (16.7%) isolates of E. cloacae were positive for presence of pAmpC genes among those bla_DHA-1 (14.2%) was the most common gene followed by bla_CMY-2 (2.5%). Results of ERIC-PCR showed that that the prevalence of DHA-1 and CMY-2-producing E. cloacae isolates was not due to clonal outbreaks.

CONCLUSION

In present study, we showed the first emergence of DHA-1 and CMY-2 types of pAmpC-producing E. cloacae isolates in Iran. The appearance of pAmpC should be considered as a warning for the implementation of appropriate infection control and therapeutic policies in order to prevent the dissemination of these resistant organisms in our hospital settings.

Detection and genotype analysis of AmpC β-lactamase in Klebsiella pneumoniae from tertiary hospitals

The aim of the present study was to investigate the phenotype and genotype of plasmid-mediated AmpC (pAmpC) β-lactamase in Klebsiella pneumoniae and its antibiotic resistance. A total of 130 non-repetitive clinical isolates of Klebsiella pneumoniae, obtained from tertiary hospitals, were phenotypically screened for pAmpC β-lactamase production with the cefoxitin disk diffusion test. β-lactamase genes in the screened isolates were detected using multiplex polymerase chain reaction (PCR); carbapenemase genes in pAmpC β-lactamase-producing isolates that were resistant to imipenem were detected using PCR. Out of the 130 isolates of Klebsiella pneumoniae, 62 strains (47.7%) were resistant to cefoxitin, including 14 strains (10.8%) positive for pAmpC β-lactamase (DHA type), among which 12 strains (85.7%) were susceptible to imipenem, and 2 strains, which were carrying Klebsiella pneumoniae carbapenemase (KPC)-2 gene, were resistant to imipenem. The pAmpC β-lactamase-producing Klebsiella pneumoniae isolates from the tertiary hospitals were mainly of DHA-1 genotype, and the majority were susceptible to carbapenems; drug-resistant strains were associated with KPC-2 expression.

Escherichia coli β-Lactamases: What Really Matters

Escherichia coli strains belonging to diverse pathotypes have increasingly been recognized as a major public health concern. The β-lactam antibiotics have been used successfully to treat infections caused by pathogenic E. coli. However, currently, the utility of β-lactams is being challenged severely by a large number of hydrolytic enzymes – the β-lactamases expressed by bacteria. The menace is further compounded by the highly flexible genome of E. coli, and propensity of resistance dissemination through horizontal gene transfer and clonal spread. Successful management of infections caused by such resistant strains requires an understanding of the diversity of β-lactamases, their unambiguous detection, and molecular mechanisms underlying their expression and spread with regard to the most relevant information about individual bacterial species. Thus, this review comprises first such effort in this direction for E. coli, a bacterial species known to be associated with production of diverse classes of β-lactamases. The review also highlights the role of commensal E. coli as a potential but under-estimated reservoir of β-lactamases-encoding genes.

Carriage of beta-lactamase-producing Enterobacteriaceae among nursing home residents in north Lebanon

BACKGROUND

Multidrug-resistant (MDR) Enterobacteriaceae can cause severe infections with high morbidity, mortality, and health care costs. Individuals can be fecal carriers of these resistant organisms. Data on the extent of MDR Enterobacteriaceae fecal carriage in the community setting in Lebanon are very scarce. The aim of this study was to investigate the fecal carriage of MDR Enterobacteriaceae among the elderly residents of two nursing homes located in north Lebanon.

METHODS

Over a period of 4 months, five fecal swab samples were collected from each of 68 elderly persons at regular intervals of 3-4 weeks. Fecal swabs were subcultured on selective media for the screening of resistant organisms. The phenotypic detection of extended-spectrum beta-lactamase (ESBL), AmpC, metallo-beta-lactamase (MBL), and Klebsiella pneumoniae carbapenemase (KPC) production was performed using the beta-lactamase inhibitors ethylenediaminetetraacetic acid, phenylboronic acid, and cloxacillin. A temocillin disk was used for OXA-48. Multiplex PCRs were used for the genotypic detection of ESBL and carbapenemase genes, and sequencing was performed to identify CTX-M-15. The medical records of each subject were reviewed on a regular basis in order to assess the risk factors associated with MDR Enterobacteriaceae fecal carriage.

RESULTS

Over the study period, 76.5% of the recruited elderly persons were at least one-time carriers. A total of 178 isolates were obtained. Phenotypic testing revealed that 91.5% of them were ESBL producers, 4% were AmpC producers, 2.8% were co-producers of ESBL and AmpC, and 1.7% were co-producers of OXA-48 and ESBL. Recent antibiotic intake was found to be the only independent risk factor associated with the fecal carriage of MDR Enterobacteriaceae.

CONCLUSIONS

The high prevalence of MDR Enterobacteriaceae detected in this study and the emergence of carbapenem resistance is alarming. Efficient infection control measures and antibiotic stewardship programs are urgently needed in these settings in order to limit the spread of resistant strains.

Increased Hydrolysis of Oximino-β-Lactams by CMY-107, a Tyr199Cys Mutant Form of CMY-2 Produced by Escherichia coli

The cephalosporinase CMY-107, a Tyr199Cys mutant form of CMY-2 encoded by an IncI self-transferable plasmid carried by an Escherichia coli clinical strain, was characterized. The enzyme hydrolyzed oximino-cephalosporins and aztreonam more efficiently than CMY-2 did.

Escherichia coli of sequence type 3835 carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12

New Delhi metallo-β-lactamase (NDM) represents a serious challenge for treatment and public health. A carbapenem-resistant Escherichia coli clinical strain WCHEC13-8 was subjected to antimicrobial susceptibility tests, whole genome sequencing and conjugation experiments. It was resistant to imipenem (MIC, >256 μg/ml) and meropenem (MIC, 128 μg/ml) and belonged to ST3835. bla NDM-1 was the only carbapenemase gene detected. Strain WCHEC13-8 also had a plasmid-borne AmpC gene (bla CMY-42) and two extended-spectrum β-lactamase genes (bla CTX-M-15 and bla SHV-12). bla NDM-1 and bla SHV-12 were carried by a 54-kb IncX3 self-transmissible plasmid, which is identical to plasmid pNDM-HF727 from Enterobacter cloacae. bla CMY-42 was carried by a 64-kb IncI1 plasmid and bla CTX-M-15 was located on a 141-kb plasmid with multiple F replicons (replicon type: F36:A4:B1). bla CMY-42 was in a complicated context and the mobilisation of bla CMY-42 was due to the transposition of ISEcp1 by misidentifying its right-end boundary. Genetic context of bla NDM-1 in strain WCHEC13-8 was closely related to those on IncX3 plasmids in various Enterobacteriaceae species in China. In conclusion, a multidrug-resistant ST3835 E. coli clinical strain carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12 was identified. IncX3 plasmids may be making a significant contribution to the dissemination of bla NDM among Enterobacteriaceae in China.