beta-Lactamases responsible for resistance to expanded-spectrum cephalosporins in Klebsiella pneumoniae, Escherichia coli, and Proteus mirabilis isolates recovered in South Africa

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.

Dynamics of Antimicrobial Resistance Carriage in Koalas (Phascolarctos Cinereus) and Pteropid Bats (Pteropus Poliocephalus) Before, During and After Wildfires

In the 2019-2020 summer, wildfires decimated the Australian bush environment and impacted wildlife species, including koalas (Phascolarctos cinereus) and grey headed flying fox pups (Pteropid bats, Pteropus poliocephalus). Consequently, hundreds of koalas and thousands of bat pups entered wildlife hospitals with fire-related injuries/illness, where some individuals received antimicrobial therapy. This study investigated the dynamics of antimicrobial resistance (AMR) in pre-fire, fire-affected and post-fire koalas and Pteropid bat pups. PCR and DNA sequencing were used to screen DNA samples extracted from faeces (koalas and bats) and cloacal swabs (koalas) for class 1 integrons, a genetic determinant of AMR, and to identify integron-associated antibiotic resistance genes. Class 1 integrons were detected in 25.5% of koalas (68 of 267) and 59.4% of bats (92 of 155). Integrons contained genes conferring resistance to aminoglycosides, trimethoprim and beta-lactams. Samples were also screened for blaTEM (beta-lactam) resistance genes, which were detected in 2.6% of koalas (7 of 267) and 25.2% of bats (39 of 155). Integron occurrence was significantly higher in fire-affected koalas in-care compared to wild pre-fire koalas (P < 0.0001). Integron and blaTEM occurrence were not significantly different in fire-affected bats compared to pre-fire bats (P > 0.05), however, their occurrence was significantly higher in fire-affected bats in-care compared to wild fire-affected bats (P < 0.0001 and P = 0.0488 respectively). The observed shifts of AMR dynamics in wildfire-impacted species flags the need for judicious antibiotic use when treating fire-affected wildlife to minimise unwanted selective pressure and negative treatment outcomes associated with carriage of resistance genes and antibiotic resistant bacteria.

Review and analysis of the overlapping threats of carbapenem and polymyxin resistant E. coli and Klebsiella in Africa

BACKGROUND

Carbapenem-resistant Enterobacterales are among the most serious antimicrobial resistance (AMR) threats. Emerging resistance to polymyxins raises the specter of untreatable infections. These resistant organisms have spread globally but, as indicated in WHO reports, the surveillance needed to identify and track them is insufficient, particularly in less resourced countries. This study employs comprehensive search strategies with data extraction, meta-analysis and mapping to help address gaps in the understanding of the risks of carbapenem and polymyxin resistance in the nations of Africa.

METHODS

Three comprehensive Boolean searches were constructed and utilized to query scientific and medical databases as well as grey literature sources through the end of 2019. Search results were screened to exclude irrelevant results and remaining studies were examined for relevant information regarding carbapenem and/or polymyxin(s) susceptibility and/or resistance amongst E. coli and Klebsiella isolates from humans. Such data and study characteristics were extracted and coded, and the resulting data was analyzed and geographically mapped.

RESULTS

Our analysis yielded 1341 reports documenting carbapenem resistance in 40 of 54 nations. Resistance among E. coli was estimated as high (> 5%) in 3, moderate (1-5%) in 8 and low (< 1%) in 14 nations with at least 100 representative isolates from 2010 to 2019, while present in 9 others with insufficient isolates to support estimates. Carbapenem resistance was generally higher among Klebsiella: high in 10 nations, moderate in 6, low in 6, and present in 11 with insufficient isolates for estimates. While much less information was available concerning polymyxins, we found 341 reports from 33 of 54 nations, documenting resistance in 23. Resistance among E. coli was high in 2 nations, moderate in 1 and low in 6, while present in 10 with insufficient isolates for estimates. Among Klebsiella, resistance was low in 8 nations and present in 8 with insufficient isolates for estimates. The most widespread associated genotypes were, for carbapenems, blaOXA-48, blaNDM-1 and blaOXA-181 and, for polymyxins, mcr-1, mgrB, and phoPQ/pmrAB. Overlapping carbapenem and polymyxin resistance was documented in 23 nations.

CONCLUSIONS

While numerous data gaps remain, these data show that significant carbapenem resistance is widespread in Africa and polymyxin resistance is also widely distributed, indicating the need to support robust AMR surveillance, antimicrobial stewardship and infection control in a manner that also addresses broader animal and environmental health dimensions.

Extended-Spectrum β-Lactamases (ESBL) Producing Bacteria in Animals

Animals have been identified as potential reservoirs and vectors of resistance genes, with studies showing that Gram-negative bacteria can acquire resistance through the horizontal transmission of resistance genes on plasmids. It is important to understand the distribution of antimicrobial-resistant bacteria and their drug-resistant genes in animals. Previous review articles mostly focused on a single bacterium or a single animal. Our objective is to compile all ESBL-producing bacteria isolated from various animals in recent years and provide a comprehensive viewpoint. Using a thorough PubMed literature search spanning from 1 January 2020 to 30 June 2022, studies exploring extended-spectrum beta-lactamase (ESBL) producing bacteria in animals were included. ESBL-producing bacteria are present in animals from various countries around the world. The most common sources of these bacteria were farm animals, and the most frequently isolated bacteria were Escherichia coli and Klebsiella pneumoniae. The most detected ESBL genes were blaTEM, blaSHV, and blaCTX-M. The presence of ESBL-producing bacteria in animals highlights the importance of the One Health approach to address the issue of antibiotic resistance. Further research is needed to better understand the epidemiology and mechanisms of the spread of ESBL-producing bacteria in animal populations and their potential impact on human and animal health.

Prevalence and Risk Factors Associated with Multidrug Resistance and Extended-Spectrum β-lactamase Producing E. coli Isolated from Healthy and Diseased Cats

Household cats have been identified as potential antimicrobial resistance (AMR) reservoirs, and the extended-spectrum β-lactamases (ESBL) producing E. coli circulating among cats has been more frequently reported globally, but the factors linked to its colonization remain poorly understood. Thus, the objectives of this study were to determine E. coli shedding and the occurrence of multidrug resistant (MDR)- and ESBL-producing E. coli, as well as to determine risk factors associated with colonization of MDR and ESBL-producing E. coli isolated from both healthy and diseased cats in the Eastern Province of Saudi Arabia. In a cross-sectional study, 2000 swabs were collected from five anatomical regions (anus, skin, ear canal, nares, and conjunctival sac) of 209 healthy and 191 diseased cats that were admitted to a veterinary clinic in the Eastern Province of Saudi Arabia. In addition, each cat owner filled out a questionnaire about their cat's demographics, management, health status, and antimicrobial usage. E. coli was detected in 165 (41.3%) of all cats, including 59 (28.2%) healthy and 106 (55.5%) diseased cats. In total, 170 E. coli isolates were found in healthy (35.3%) and diseased (64.7%) cats. Susceptibility testing revealed that 123 (72.4%) of the E. coli isolates were resistant to at least one of the tested antimicrobials. Overall, 17.6% (30/170) of E. coli isolates were MDR, with 10 (5.9%) and 20 (11.8%) isolates found in healthy and diseased cats, respectively. However, only 12 (7.1%) E. coli isolates were resistant to cefotaxime and harbored the bla_CTX-M gene (ESBL-producer), with seven (4.1%) in healthy and five (2.9%) in diseased cats. Risk factor analysis showed that the odds of MDR and ESBL-producing E. coli were (20 and 17) and (six and eight) times higher when the family and cats were previously treated with antimicrobials, respectively. The presence of a child in the cat's family was also linked to an increased risk of MDR E. coli colonization (OR = 3.4). In conclusion, a high frequency of MDR and ESBL-producing E. coli was detected among healthy and diseased cats in Saudi Arabia, raising concerns about transmission to humans and supporting the need of a "One Health" approach to address the potential threats of cats as AMR reservoirs.

Finding of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales in wild game meat originating from several European countries: predominance of Moellerella wisconsensis producing CTX-M-1, November 2021

IntroductionMeat can be a vehicle for food-borne transmission of antimicrobial resistant bacteria and antimicrobial resistance genes. The occurrence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales has been observed in meat from livestock production but has not been well studied in meat from wild game.AimWe aimed to investigate, particularly in central Europe, to what extent ESBL-producing Enterobacterales may be present in wild game meat.MethodsA total of 111 samples of different types of game meat supplied by butchers, hunters, retail stores and a large game-processing establishment in Europe were screened for ESBL-producing Enterobacterales using a selective culture medium. Isolates were genotypically and phenotypically characterised.ResultsThirty-nine samples (35% of the total) yielded ESBL-producing Enterobacterales, with most (35/39) supplied by the game-processing establishment. Isolates included 32 Moellerella wisconsensis, 18 Escherichia coli and one Escherichia marmotae. PCR screening identified bla CTX-M-1 (n = 31), bla CTX-M-32 (n = 8), bla CTX-M-65 (n = 4), bla CTX-M-15 (n = 3), bla CTX-M-8 (n = 1), bla CTX-M-14 (n = 1), bla CTX-M-55 (n = 1), and bla SHV-12 (n = 2). Most E. coli belonged to phylogenetic group A (n = 7) or B1 (n = 9), but several isolates belonged to extraintestinal pathogenic E. coli (ExPEC) sequence types (ST)58 (n = 4), ST68 (n = 1) and ST540 (n = 1). Whole genome sequencing of six selected isolates localised bla CTX-M-1 on megaplasmids in four M. wisconsensis and bla CTX-M-32 on IncN_1 plasmids in one M. wisconsensis and one E. marmotae. Forty-eight isolates (94%) exhibited a multidrug-resistance phenotype.ConclusionWe found a high occurrence of ESBL-producing Enterobacterales in wild game meat, suggesting wildlife habitat pollution and possible microbial contamination events occurring during skinning or cutting carcasses.

Detection and characterization of ESBL-producing Escherichia coli and additional co-existence with mcr genes from river water in northern Thailand

Background

Extended-spectrum β-lactamase producing Escherichia coli (ESBL-producing E. coli) have emerged, causing human and animal infections worldwide. This study was conducted to investigate the prevalence and molecular genetic features of ESBL-producing and multidrug-resistant (MDR) E. coli in river water.

Methods

A total of 172 E. coli samples were collected from the Kok River and Kham River in Chiang Rai, Thailand, during a 10-month period (2020-2021).

Results

We detected 45.3% of E. coli to be MDR. The prevalence of ESBL-producers was 22%. Among those ESBL-producing strains, CTX-M-15 (44.7%) was predominantly found, followed by CTX-M-55 (26.3%), CTX-M-14 (18.4%), and CTX-M-27 (10.5%). The bla _TEM-1 and bla _TEM-116 genes were found to be co-harbored with the bla _CTX-M genes. Mobile elements, i.e., ISEcp1 and Tn3, were observed. Twelve plasmid replicons were found, predominantly being IncF (76.3%) and IncFIB (52.6%). Whole genome sequencing of ten selected isolates revealed the co-existence of ESBL with mcr genes in two ESBL-producing E. coli. A wide diversity of MLST classifications was observed. An mcr-1.1-pap2 gene cassette was found to disrupt the PUF2806 domain-containing gene, while an mcr-3.4 contig on another isolate contained the nimC/nimA-mcr-3.4-dgkA core segment.

Discussion

In conclusion, our data provides compelling evidence of MDR and ESBL-producing E. coli, co-existing with mcr genes in river water in northern Thailand, which may be disseminated into other environments and so cause increased risks to public health.

Genetic Diversity, Biofilm Formation, and Antibiotic Resistance of Pseudomonas aeruginosa Isolated from Cow, Camel, and Mare with Clinical Endometritis

Pseudomonas aeruginosa is a ubiquitous opportunistic bacterium that causes diseases in animals and humans. This study aimed to investigate the genetic diversity, antimicrobial resistance, biofilm formation, and virulence and antibiotic resistance genes of P. aeruginosa isolated from the uterus of cow, camel, and mare with clinical endometritis and their drinking water. Among the 180 uterine swabs and 90 drinking water samples analysed, 54 (20%) P. aeruginosa isolates were recovered. Isolates were identified biochemically to the genus level by the automated Vitek 2 system and genetically by the amplification of the gyrB gene and the sequencing of the 16S rRNA gene. Multilocus sequence typing identified ten different sequence types for the P. aeruginosa isolates. The identification of ST2012 was significantly (p ≤ 0.05) higher than that of ST296, ST308, ST111, and ST241. The isolates exhibited significantly (p ≤ 0.05) increased resistance to piperacillin (77.8%), ciprofloxacin (59.3%), gentamicin (50%), and ceftazidime (38.9%). Eight (14.8%) isolates showed resistance to imipenem; however, none of the isolates showed resistance to colistin. Multidrug resistance (MDR) was observed in 24 isolates (44.4%) with a multiple antibiotic resistance index ranging from 0.44 to 0.77. MDR was identified in 30 (33.3%) isolates. Furthermore, 38.8% and 9.2% of the isolates exhibited a positive extended-spectrum-β-lactamase (ESBL) and metallo-β-lactamase (MBL) phenotype, respectively. The most prevalent β-lactamase encoding genes were bla_TEM and bla_CTX-M, however, the bla_IPM gene was not detected in any of the isolates. Biofilm formation was observed in 49 (90.7%) isolates classified as: 11.1% weak biofilm producers; 38.9% moderate biofilm producers; 40.7% strong biofilm producers. A positive correlation was observed between the MAR index and biofilm formation. In conclusion, the results highlighted that farm animals with clinical endometritis could act as a reservoir for MDR and virulent P. aeruginosa. The emergence of ESBLs and MBLs producing P. aeruginosa in different farm animals is a public health concern. Therefore, surveillance programs to monitor and control MDR P. aeruginosa in animals are required.

Antimicrobial resistance profiles of Escherichia coli and prevalence of extended‐spectrum beta‐lactamase‐producing Enterobacteriaceae in calves from organic and conventional dairy farms in Switzerland

This study compared the antimicrobial resistance (AMR) among commensal Escherichia coli in the fecal microbiota of young calves raised on organic and on conventional dairy farms in Switzerland. Further, fecal carriage of extended‐spectrum beta‐lactamase (ESBL) producing Enterobacteriaceae was assessed for calves from both farming systems. Where possible, data on antimicrobial usage (AMU) were obtained. Antimicrobial susceptibility testing was performed on a total of 71 isolates using the disk diffusion method. ESBL producers were characterized by polymerase chain reaction‐based multilocus sequence typing and sequencing of the bla_ESBL genes. Organically raised calves were significantly more likely to harbor E. coli that showed AMR to ampicillin (odds ratio [OR]: 2.78, 95% confidence interval [CI]: 1.02–7.61, p = 0.046), streptomycin (OR: 3.22, 95% CI: 1.17–8.92, p = 0.046), kanamycin (OR: 11.3, 95% CI: 2.94–43.50, p < 0.001), and tetracycline (OR: 3.25, 95% CI: 1.13–9.31, p = 0.028). Calves with reported AMU were significantly more likely to harbor E. coli with resistance to ampicillin (OR: 3.91, 95% CI: 1.03–14.85, p = 0.045), streptomycin (OR: 4.35, 95% CI: 1.13–16.7, p = 0.045), and kanamycin (OR: 8.69, 95% CI: 2.01–37.7, p = 0.004). ESBL‐producing Enterobacteriaceae (18 E. coli and 3 Citrobacter braakii) were detected exclusively among samples from conventionally farmed calves (OR: infinity [∞], 95% CI: 2.3–∞, p < 0.0013). The observations from this study suggest that AMR is highly prevalent among commensal E. coli in young dairy calves, irrespective of the farm management system, with proportions of certain resistance phenotypes higher among organic calves. By contrast, the occurrence of ESBL producers among young dairy calves may be linked to factors associated with conventional farming.

Characterization of ESBL-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Clinical Samples in a Northern Portuguese Hospital: Predominance of CTX-M-15 and High Genetic Diversity

Background: Enterobacteriaceae are major players in the spread of resistance to β-lactam antibiotics through the action of CTX-M β-lactamases. We aimed to analyze the diversity and genetic characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae isolates from patients in a Northern Portuguese hospital. Methods: A total of 62 cefotaxime/ceftazidime-resistant E. coli (n = 38) and K. pneumoniae (n = 24) clinical isolates were studied. Identification was performed by MALDI-TOF MS. Antimicrobial susceptibility testing against 13 antibiotics was performed. Detection of ESBL-encoding genes and other resistance genes, phylogenetic grouping, and molecular typing (for selected isolates) was carried out by PCR/sequencing. Results: ESBL activity was detected in all 62 E. coli and K. pneumoniae isolates. Most of the ESBL-producing E. coli isolates carried a bla_CTX-M gene (37/38 isolates), being bla_CTX-M-15 predominant (n = 32), although bla_CTX-M-27 (n = 1) and bla_CTX-M-1 (n = 1) were also detected. Two E. coli isolates carried the bla_KPC2/3 gene. The lineages ST131-B2 and ST410-A were detected among the ESBL-producing blood E. coli isolates. Regarding the 24 ESBL-producing K. pneumoniae isolates, 18 carried a bla_CTX-M gene (bla_CTX-M-15, 16 isolates; bla_CTX-M-55, 2 isolates). All K. pneumoniae isolates carried bla_SHV genes, including ESBL-variants (bla_SHV-12 and bla_SHV-27, 14 isolates) or non-ESBL-variants (bla_SHV-11 and bla_SHV-28, 10 isolates); ten K. pneumoniae isolates also carried the bla_KPC2/3 gene and showed imipenem-resistance. ESBL-positive E. coli isolates were ascribed to the B₂ phylogenetic group (82%), mostly associated with ST131 lineage and, at a lower rate, to ST410/A. Regarding K. pneumoniae, the three international lineages ST15, ST147, and ST280 were detected among selected isolates. Conclusions: Different ESBL variants of CTX-M (especially CTX-M-15) and SHV-type (specially SHV-12) were detected among CTX/CAZ^RE. coli and K. pneumoniae isolates, in occasions associated with carbapenemase genes (bla_KPC2/3 gene).

Antimicrobial Resistance Genes and Diversity of Clones among Faecal ESBL-Producing Escherichia coli Isolated from Healthy and Sick Dogs Living in Portugal

The purpose of this study was to analyse the prevalence and genetic characteristics of ESBL and acquired-AmpC (qAmpC)-producing Escherichia coli isolates from healthy and sick dogs in Portugal. Three hundred and sixty-one faecal samples from sick and healthy dogs were seeded on MacConkey agar supplemented with cefotaxime (2 µg/mL) for cefotaxime-resistant (CTX^R) E. coli recovery. Antimicrobial susceptibility testing for 15 antibiotics was performed and the ESBL-phenotype of the E. coli isolates was screened. Detection of antimicrobial resistance and virulence genes, and molecular typing of the isolates (phylogroups, multilocus-sequence-typing, and specific-ST131) were performed by PCR (and sequencing when required). CTX^RE. coli isolates were obtained in 51/361 faecal samples analysed (14.1%), originating from 36/234 sick dogs and 15/127 healthy dogs. Forty-seven ESBL-producing E. coli isolates were recovered from 32 sick (13.7%) and 15 healthy animals (11.8%). Different variants of bla_CTX-M genes were detected among 45/47 ESBL-producers: bla_CTX-M-15 (n = 26), bla_CTX-M-1 (n = 10), bla_CTX-M-32 (n = 3), bla_CTX-M-55 (n = 3), bla_CTX-M-14 (n = 2), and bla_CTX-M-variant (n = 1); one ESBL-positive isolate co-produced CTX-M-15 and CMY-2 enzymes. Moreover, two additional CTX^R ESBL-negative E. coli isolates were CMY-2-producers (qAmpC). Ten different sequence types were identified (ST/phylogenetic-group/β-lactamase): ST131/B2/CTX-M-15, ST617/A/CTX-M-55, ST3078/B1/CTX-M-32, ST542/A/CTX-M-14, ST57/D/CTX-M-1, ST12/B2/CTX-M-15, ST6448/B1/CTX-M-15 + CMY-2, ST5766/A/CTX-M-32, ST115/D/CMY-2 and a new-ST/D/CMY-2. Five variants of CTX-M enzymes (CTX-M-15 and CTX-M-1 predominant) and eight different clonal complexes were detected from canine ESBL-producing E. coli isolates. Although at a lower rate, CMY-2 β-lactamase was also found. Dogs remain frequent carriers of ESBL and/or qAmpC-producing E. coli with a potential zoonotic role.

Extended-spectrum β-lactamases: an update on their characteristics, epidemiology and detection

Extended-spectrum β-lactamase (ESBL)-producing Gram-negative pathogens are a major cause of resistance to expanded-spectrum β-lactam antibiotics. Since their discovery in the early 1980s, they have spread worldwide and an are now endemic in Enterobacterales isolated from both hospital-associated and community-acquired infections. As a result, they are a global public health concern. In the past, TEM- and SHV-type ESBLs were the predominant families of ESBLs. Today CTX-M-type enzymes are the most commonly found ESBL type with the CTX-M-15 variant dominating worldwide, followed in prevalence by CTX-M-14, and CTX-M-27 is emerging in certain parts of the world. The genes encoding ESBLs are often found on plasmids and harboured within transposons or insertion sequences, which has enabled their spread. In addition, the population of ESBL-producing Escherichia coli is dominated globally by a highly virulent and successful clone belonging to ST131. Today, there are many diagnostic tools available to the clinical microbiology laboratory and include both phenotypic and genotypic tests to detect β-lactamases. Unfortunately, when ESBLs are not identified in a timely manner, appropriate antimicrobial therapy is frequently delayed, resulting in poor clinical outcomes. Several analyses of clinical trials have shown mixed results with regards to whether a carbapenem must be used to treat serious infections caused by ESBLs or whether some of the older β-lactam-β-lactamase combinations such as piperacillin/tazobactam are appropriate. Some of the newer combinations such as ceftazidime/avibactam have demonstrated efficacy in patients. ESBL-producing Gram-negative pathogens will continue to be major contributor to antimicrobial resistance worldwide. It is essential that we remain vigilant about identifying them both in patient isolates and through surveillance studies.

2003-2019: explosive spread of enterobacteria producing extended-spectrum beta-lactamases in Bangui Central African Republic

Introduction

the spread of enterobacteria producing extended-broad-spectrum beta-lactamases (ESBL) is a global public health-problem. In a study carried in 2003-2005 at the Pasteur Institute in Bangui, 450 enterobacteria were identified in clinical isolates, of which 17 were ESBL (prevalence: 3.78%). The aim of this study was to update this data.

Methods

from May 2018 to April 2019, a total of 941 enterobacteria were isolated and identified under identical conditions of recruitment and with the same techniques used in the previous study: phenotypic identification using Api 20E strips (bioMérieux SA, Marcy-l'Etoile, France) and antimicrobial drug susceptibility using the disk diffusion method (Bio-Rad antibiotic discs, Marnes la Coquette, France). Resistance genes were identified by polymerase chain reaction (PCR) and sequencing.

Results

from May 2018 to April 2019, a total of 941 enterobacteria were isolated of which 478 were ESBL, thus amounting to a prevalence of 50.80%. The genetic profiles of the bla CTX-M resistance genes exhibited the emergence of the CTX-M28 variant (CTX-M1 group) and variants of the M2 and M9 groups. There was also a notable increase, from 35 to 64%, in the ESBL with a bla SHV gene.

Conclusion

this study documents a 13 fold increase in the prevalence of ESBL derived from clinical isolates of the bacteriology laboratory of the Institute Pasteur in Bangui, by comparing its data with that of the publication by Frank et al. 2006. Together with this increase a significant diversification of the circulating CTX-M resistance genes was noticed.

Antimicrobial Resistance in Humans, Animals, Water and Household Environs in Rural Andean Peru: Exploring Dissemination Pathways through the One Health Lens

Antimicrobial resistance (AMR) is a global public health threat, especially for low and middle-income countries (LMIC) where the threat has not been fully identified. Our study aims to describe E. coli AMR in rural communities to expand our knowledge on AMR bacterial contamination. Specifically, we aim to identify and describe potential dissemination routes of AMR-carrying bacteria in humans (children’s stools), community water sources (reservoirs and household sources), household environments (yard soil) and domestic animals of subsistence farmers in rural Andean areas. Our cross-sectional study was conducted in rural households in the region of Cajamarca, Peru. A total of 266 samples were collected. Thirty-four point six percent of reservoir water and 45% of household water source samples were positive for thermotolerant coliforms. Of the reservoir water samples, 92.8% were positive for E. coli, and 30.8% displayed resistance to at least one antibiotic, with the highest resistance to tetracycline. E. coli was found in 57.1% of the household water sources, 18.6% of these isolates were multidrug-resistant, and displayed the highest resistance to tetracycline (31.3%). Among samples from the children’s drinking water source, 32.5% were positive for thermotolerant coliforms, and 57.1% of them were E. coli. One third of E. coli isolates were multidrug-resistant and displayed the highest AMR to tetracycline (41.6%) and ampicillin (25%). Thermotolerant coliforms were found in all the soil samples, 43.3% of the isolates were positive for E. coli, 34.3% of the E. coli isolates displayed AMR to at least one antibiotic, and displayed the highest AMR to tetracycline (25.7%). We determined thermotolerant coliforms in 97.5% of the child feces samples; 45.3% of them were E. coli, 15.9% displayed multidrug resistance, and displayed the highest resistance to ampicillin (34.1%). We identified thermotolerant coliforms in 67.5% of the animal feces samples. Of those, 38.7% were E. coli, and 37.7% were resistant to at least one antibiotic. For all the samples, the prevalence of resistance to at least one antibiotic in the E. coli and Klebsiella spp. isolates was almost 43% and the prevalence of MDR in the same isolates was nearly 9%, yet the latter nearly doubled (15.9%) in children’s stools. Our results provide preliminary evidence for critical pathways and the interconnectedness of animal, human and environmental transmission but molecular analysis is needed to track dissemination routes properly.

Migratory Wild Birds as a Potential Disseminator of Antimicrobial-Resistant Bacteria around Al-Asfar Lake, Eastern Saudi Arabia

Migratory wild birds acquire antimicrobial-resistant (AMR) bacteria from contaminated habitats and then act as reservoirs and potential spreaders of resistant elements through migration. However, the role of migratory wild birds as antimicrobial disseminators in the Arabian Peninsula desert, which represents a transit point for birds migrating all over Asia, Africa, and Europe not yet clear. Therefore, the present study objective was to determine antimicrobial-resistant bacteria in samples collected from migratory wild birds around Al-Asfar Lake, located in Al-Ahsa Oasis, Eastern Saudi Arabia, with a particular focus on Escherichia coli virulence and resistance genes. Cloacal swabs were collected from 210 migratory wild birds represent four species around Al-Asfar. E. coli, Staphylococcus, and Salmonella spp. have been recovered from 90 (42.9%), 37 (17.6%), and 5 (2.4%) birds, respectively. Out of them, 19 (14.4%) were a mixed infection. All samples were subjected to AMR phenotypic characterization, and results revealed (14-41%) and (16-54%) of E. coli and Staphylococcus spp. isolates were resistant to penicillins, sulfonamides, aminoglycoside, and tetracycline antibiotics. Multidrug-resistant (MDR) E. coli and Staphylococcus spp. were identified in 13 (14.4%) and 7 (18.9%) isolates, respectively. However, none of the Salmonella isolates were MDR. Of the 90 E. coli isolates, only 9 (10%) and 5 (5.6%) isolates showed the presence of eaeA and stx2 virulence-associated genes, respectively. However, both eaeA and stx2 genes were identified in four (4.4%) isolates. None of the E. coli isolates carried the hlyA and stx1 virulence-associated genes. The E. coli AMR associated genes bla_CTX-M, bla_TEM, bla_SHV, aac(3)-IV, qnrA, and tet(A) were identified in 7 (7.8%), 5 (5.6%), 1 (1.1%), 8 (8.9%), 4 (4.4%), and 6 (6.7%) isolates, respectively. While the mecA gene was not detected in any of the Staphylococcus spp. isolates. Regarding migratory wild bird species, bacterial recovery, mixed infection, MDR, and AMR index were relatively higher in aquatic-associated species. Overall, the results showed that migratory wild birds around Al-Asfar Lake could act as a reservoir for AMR bacteria enabling them to have a potential role in maintaining, developing, and disseminating AMR bacteria. Furthermore, results highlight the importance of considering migratory wild birds when studying the ecology of AMR.

Animal petting zoos as sources of Shiga toxin-producing Escherichia coli, Salmonella and extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae

Animal petting zoos and farm fairs provide the opportunity for children and adults to interact with animals, but contact with animals carries a risk of exposure to zoonotic pathogens and antimicrobial-resistant bacteria. The aim of this study was to assess the occurrence of Shiga toxin-producing Escherichia coli (STEC), Salmonella, extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae and methicillin-resistant Staphylococcus aureus (MRSA) in animal faeces from six animal petting zoos and one farm fair in Switzerland. Furthermore, hygiene facilities on the venues were evaluated. Of 163 faecal samples, 75 contained stx1, stx2 or stx1/stx2 genes, indicating the presence of STEC. Samples included faeces from sika deer (100%), sheep (92%), goats (88%), mouflons (80%), camels (62%), llamas (50%), yaks (50%), pigs (29%) and donkeys (6%), whereas no stx genes were isolated from faeces of calves, guinea pigs, hens, ostriches, ponies, zebras or zebus. Salmonella enterica subsp. enterica serovar Stourbridge (S. Stourbridge) was detected in faecal samples from camels. A total of four ESBL-producing E. coli strains were isolated from faeces of goats, camels and pigs. PCR and sequencing identified the presence of bla_CTX-M-15 in three and bla_CTX-M-65 in one E. coli. Antimicrobial resistance profiling using the disk diffusion method revealed two multidrug-resistant (MDR) E. coli with resistance to ciprofloxacin, gentamicin and azithromycin, all of which are critically important drugs for human medicine. Multilocus sequence typing identified E. coli ST162, E. coli ST2179, extraintestinal high-risk E. coli ST410 and E. coli ST4553, which belongs to the emerging extraintestinal clonal complex (CC) 648. No MRSA was detected. On all animal petting venues, there were inadequacies with regard to access to hygiene information and handwashing hygiene facilities. This study provides data that underscore the importance of hygiene measures to minimize the risk of transmission of zoonotic pathogens and MDR, ESBL-producing E. coli to visitors of animal petting venues.

The Mobile Colistin Resistance Gene, mcr-1.1, Is Carried on IncX4 Plasmids in Multidrug Resistant E. coli Isolated from Rainbow Trout Aquaculture

Colistin, a last resort antibiotic, is important for controlling infections with carbapenem-resistant Enterobacteriaceae. The recent emergence of mobile-colistin-resistance (mcr) genes has threatened the effectiveness of colistin. Aquaculture is hypothesized to be a major contributor to the evolution and dissemination of mcr. However, data on mcr in aquaculture are limited. Here, the occurrence of mcr-1 was assessed in Rainbow Trout in Lebanon, a country with developing antimicrobial stewardship and an established use of colistin for medical and farming purposes. mcr-1 was detected in 5 Escherichia coli isolated from fish guts. The isolates were classified as multidrug-resistant and their colistin minimum inhibitory concentration ranged between 16 and 32 μg/mL. Whole genome sequencing analysis showed that mcr-1 was carried on transmissible IncX4 plasmids and that the isolates harbored more than 14 antibiotic resistance genes. The isolates belonged to ST48 and ST101, which have been associated with mcr and can occur in humans and fish. The mcr-1-positive E. coli persisted in 6-day biofilms, but there was a potential fitness cost. Given the status of infrastructure in Lebanon, there is a high potential for the dissemination of mcr via aquatic environments. Urgent actions are needed to control mcr and to enhance antimicrobial stewardship in Lebanon.

Spectrum of Bacterial Colonization in Patients Hospitalized for Treatment of Multidrug-Resistant Tuberculosis

This study investigated the bacterial colonization in patients admitted for treatment of drug-resistant tuberculosis in a specialized TB hospital. Identification and antimicrobial susceptibility testing of bacterial isolates (n = 62) from nasal, groin, and rectal swabs [patient cohort (n = 37)] were determined by the VITEK-MS system. Resistance gene analysis was by PCR and DNA sequencing. Molecular typing of Klebsiella pneumoniae isolates was by Multilocus Sequencing Typing (MLST). Patients (n = 13/37; 35%) were colonized by multidrug-resistant (MDR) bacteria (ESBL and MRSA) on admission. Of the 24 patients who were not colonized by MDR bacteria on admission, 46% (17/37) became colonized by MDR bacteria within 1 month of admission, mostly with ESBL-producing Enterobacteriales and resistance to aminoglycosides and fluoroquinolones. ESBL Escherichia coli (41/62; 66%) and K. pneumoniae (14/62; 23%) predominated. Genes encoding for ESBLs (bla_CTX-M-14, bla_CTX-M-15, bla_SHV-28, bla_OXA-1, and bla_OXY-2) and plasmid-mediated quinolone resistant genes (qnrB1, qnrB4, and qnrB10) were detected. MLST revealed genetic diversity among the K. pneumoniae isolates from hospitalized patients. This study provides insight into bacterial pathogen colonization in hospitalized TB patients with the first occurrence of the qnrB4 and qnrB10 genes and co-expression of genes: qnrB4+aac(6')-lb-cr, qnrB10+aac(6')-lb-cr, qnrB4+qnrS1, and qnrB10+qnrS1 in fluoroquinolone-resistant E. coli isolates within South Africa. However, the source and colonization routes of these isolates could not be determined.

Antimicrobial Resistance Pattern of Escherichia coli Isolated from Frozen Chicken Meat in Bangladesh

Escherichia coli is known as one of the most important foodborne pathogens in humans, and contaminated chicken meat is an important source of foodborne infection with this bacterium. The occurrence of extended-spectrum β-lactamase (ESBL)-producing E. coli (ESBL-Ec), in particular, in chicken meat is considered a global health problem. This study aimed to determine the magnitude of E. coli, with special emphasis on ESBL-Ec, along with their phenotypic antimicrobial resistance pattern in frozen chicken meat. The study also focused on the determination of ESBL-encoding genes in E. coli. A total of 113 frozen chicken meat samples were purchased from 40 outlets of nine branded supershops in five megacities in Bangladesh. Isolation and identification of E. coli were done based on cultural and biochemical properties, as well as PCR assay. The resistance pattern was determined by the disc diffusion method. ESBL-encoding genes were determined by multiplex PCR. The results showed that 76.1% of samples were positive for E. coli, of which 86% were ESBL producers. All the isolates were multidrug-resistant (MDR). Resistance to 9-11 and 12-13 antimicrobial classes was observed in 38.4% and 17.4% isolates, respectively, while only 11.6% were resistant to 3-5 classes. Possible extensive drug resistance (pXDR) was found in 2.3% of isolates. High single resistance was observed for oxytetracycline (93%) and amoxicillin (91.9%), followed by ampicillin (89.5%), trimethoprim-sulfamethoxazole, and pefloxacin (88.4%), and tetracycline (84.9%). Most importantly, 89.6% of isolates were resistant to carbapenems. All the isolates were positive for the blaTEM gene. However, the blaSHV and blaCTX-M-2 genes were identified in two ESBL-non producer isolates. None of the isolates carried the blaCTX-M-1 gene. This study provided evidence of the existence of MDR and pXDR ESBL-Ec in frozen chicken meat in Bangladesh, which may pose a risk to human health if the meat is not properly cooked or pickled raw only. This emphasizes the importance of the implementation of good slaughtering and processing practices by the processors.

Antimicrobial susceptibility and distribution of extended-spectrum β-lactamases, AmpC β-lactamases and carbapenemases among Proteus, Providencia and Morganella isolated from global hospitalised patients with intra-abdominal and urinary tract infections: Results of the Study for Monitoring Antimicrobial Resistance Trends (SMART), 2008-2011

OBJECTIVES

The increasing trend of β-lactam resistance among Enterobacteriaceae is a worldwide problem. This study investigated isolates of the tribe Proteeae (Proteus, Providencia and Morganella) causing intra-abdominal and urinary tract infections from the worldwide Study for Monitoring Antimicrobial Resistance Trends (SMART) collected from 2008-2011.

METHODS

Antimicrobial susceptibility testing was performed on isolates with an ertapenem minimum inhibitory concentration >0.5mg/L or those phenotypically producing extended-spectrum β-lactamases (ESBLs). ESBLs, AmpC β-lactamases and carbapenemases were detected by multiplex PCR.

RESULTS

A total of 142 isolates, including Proteus mirabilis (n=121), Proteus vulgaris (n=3), Providencia stuartii (n=5), Providencia rettgeri (n=6) and Morganella morganii (n=7), were analysed. Proteus mirabilis was generally susceptible to ertapenem (∼90%) compared with imipenem (≤25%). The most common ESBLs were CTX-M types (n=64), followed by TEM (n=27) and SHV (n=7). CTX-M-1, CTX-M-2 and CTX-M-15 were the dominant CTX-M-type ESBLs in P. mirabilis isolates. CMY (n=14), which included CMY-2 (n=6), was the most common AmpC β-lactamase, followed by DHA (n=6) and FOX (n=4). NDM (n=7), which included NDM-1 (n=4), was the most common carbapenemase, followed by KPC (n=2). Isolates from hospital-associated infections had more complicated β-lactamase combinations than isolates from community-acquired infections.

CONCLUSION

The global emergence and spread of β-lactamase-producing Proteeae isolates are major issues in tackling antimicrobial resistance. Continuous monitoring of antimicrobial resistance trends and developing further resistance surveillance are necessary.

Characterization of ESBL-Producing Salmonella enterica Serovar Infantis Infection in Humans, Lima, Peru

Salmonella enterica serovar Infantis is causing an increasing number of infections worldwide. Our aim was to describe the characteristics of S. enterica serovar Infantis among patients attended in a hospital of Lima, Peru. Fifty cases of salmonellosis were seen during October 2015-May 2017; Salmonella Infantis was detected in 36% (n = 18) of them, displacing Enteritidis and Typhimurium (n = 13, 26%, each). Seventeen cases caused by Salmonella Infantis were presented as diarrheal illnesses; only one extraintestinal case (bacteremia) was seen in a 1-year-old infant. This serovar is resistant to multiple groups of antimicrobials, showing only fully susceptibility to carbapenems. Compared with Infantis, other serovars analyzed (mainly Enteritidis and Typhimurium) showed a lower frequency of resistance to antimicrobials such as trimethoprim-sulfamethoxazole, ampicillin, and chloramphenicol. The antibiotic with the highest frequency of resistance was ciprofloxacin. Further studies are needed to evaluate the routes of transmission and measures of control of this multidrug-resistant Salmonella.

Antimicrobial resistant and extended-spectrum ß-lactamase (ESBL) producing Escherichia coli isolated from fecal samples of African dromedary camels

This study was conducted to determine the distribution of antimicrobial resistance among Escherichia coli isolated from feces of healthy dromedary camels in Kenya. A total of 162 fecal samples were cultivated for E. coli. Samples were also subcultivated to detect E. coli with extended-spectrum ß-lactamases (ESBLs). Antimicrobial susceptibility testing (AST) was performed by disk diffusion using a panel of 16 antimicrobials. In addition, isolates were screened for the presence of the plasmid-mediated colistin resistance genes mcr-1 to mcr-5.

Samples from 20 (12.4%) of the camels contained antimicrobial resistant (AMR) E. coli, and 85% of the AMR isolates were multidrug resistant (MDR). The highest frequency of resistance was observed to tetracycline (11.7%), followed by ampicillin and streptomycin (both 10.5%), and sulfamethoxazole/trimethoprim (9.9%). Two (1.2%) of the isolates showed intermediate resistance to cefazolin and streptomycin, respectively. All the isolates were susceptible to amoxycillin/clavulanic acid, ciprofloxacin, fosfomycin, aztreonam and kanamycin, and 86.4% of the isolates were susceptible to all 16 antimicrobials used in this study. The prevalence of fecal carriage of ESBL producing E. coli was 0.6%. PCR and amplicon sequencing showed that the ESBL producer belonged to E. coli phylogenetic group A, sequence type (ST) 48, and harbored bla_CTX-M-15. None of the isolates contained mcr genes. The results indicate that dromedary camels in Kenya may be reservoirs of AMR E. coli, including ESBL producers, that could potentially be transmitted to humans by direct contact or via the food chain.

The Occurrence and Characterization of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolated from Clinical Diagnostic Specimens of Equine Origin

Escherichia coli isolates were recovered from clinical specimens of equine patients admitted to the Texas A&M Veterinary Medical Teaching Hospital over a five-year period. Ceftiofur resistance was used as a marker for potential extended-spectrum beta-lactamase (ESBL)-activity, and of the 48 ceftiofur-resistant E. coli isolates, 27.08% (n = 13) were phenotypically ESBL-positive. Conventional PCR analysis followed by the _large-scalebla Finder multiplex PCR detected the ESBL genes, CTX-M-1 and SHV, in seven out of the 13 isolates. Moreover, beta-lactamase genes of TEM-1-type, BER-type (AmpC), and OXA-type were also identified. Sequencing of these genes resulted in identification of a novel TEM-1-type gene, called bla_TEM-233, and a study is currently underway to determine if this gene confers the ESBL phenotype. Furthermore, this report is the first to have found E. coli ST1308 in horses. This subtype, which has been reported in other herbivores, harbored the SHV-type ESBL gene. Finally, one out of 13 E. coli isolates was PCR-positive for the carbapenemase gene, bla_IMP-1 despite the lack of phenotypically proven resistance to imipenem. With the identification of novel ESBL gene variant and the demonstrated expansion of E. coli sequence types in equine patients, this study underscores the need for more investigation of equines as reservoirs for ESBL-producing pathogens.

A ten-year review of ESBL and non-ESBL Escherichia coli bloodstream infections among children at a tertiary referral hospital in South Africa

Introduction

There are few studies describing Escherichia coli (E. coli) bloodstream infection (BSI) among children in Africa, yet E.coli is increasing in importance as a cause of antibiotic resistant infection in paediatric settings.

Methods

In this retrospective, descriptive study aspects of E. coli BSI epidemiology are described over a 10-year period including incidence risk, risk factors for extended-spectrum β-lactamase (ESBL)-producing E. coli BSI, antibiotic susceptibility of the bacterial isolates and outcome including risk factors for severe disease.

Results

There were 583 new E. coli BSI episodes among 217,483 admissions, an overall incidence risk of 2.7 events/1,000 hospital admissions. Of 455 of these E. coli BSI episodes that were analysed, 136 (29.9%) were caused by ESBL-producing isolates. Risk factors for ESBL-producing E. coli BSI included hospitalization in the 28-day period preceding E. coli BSI episodes, having an underlying chronic illness other than HIV infection at the time of the E. coli BSI and having a temperature of 38° Celsius or higher at the time of the E. coli BSI. None of the E. coli isolates were resistant to carbapenems or colistin. The mortality rate was 5.9% and admission to the intensive care unit was required in 12.3% of BSI episodes. Predictors of severe disease included age less than 1 month, hospitalization in the 28-day period preceding E. coli BSI and BSI without a definable focus.

Conclusions

These findings extend our understanding of E. coli BSI in a sub-Saharan African setting, provide useful information that can guide empiric treatment choices for community- and hospital-acquired BSI and help inform prevention strategies.

Yersinia enterocolitica: Prevalence, virulence, and antimicrobial resistance from retail and processed meat in Egypt

Background and Aim:

The objectives of this study were to investigate the prevalence of Yersinia enterocolitica in retail chicken meat, ground and processed beef meat, determine their virulence-associated genes, antimicrobial susceptibility pattern, molecular detection of extended-spectrum β-lactamases, and their capability of biofilm formation in vitro.

Materials and Methods:

A total of 210 samples (120 retail chicken meat, 30 ground beef, 30 beef burger, and 30 sausage samples) were collected from different retail chicken outlets and markets located at Mansoura city between December 2016 and April 2017. Meat samples were examined bacteriologically for the existence of Y. enterocolitica; bacterial colonies that displayed positive biochemical properties were subjected to polymerase chain reaction targeting 16 rRNA gene. Y. enterocolitica isolates were tested for their susceptibility to six antimicrobial agents using disk diffusion method. Uniplex PCR was used for screening Y. enterocolitica isolates for the presence of two virulence chromosome-associated genes (ail and yst), and β-lactamases (bla_TEM and bla_SHV). The capability of Y. enterocolitica to form biofilms was detected by tube method.

Results:

Thirty Y. enterocolitica isolates (14.29%) were recovered including 19 (15.83%) isolates from chicken meat, 3 (10%) from ground beef, 5 (16.67%) from beef burger, and 3 (10%) from sausage samples. Regarding ail gene, it was detected in 6.67% (2/30), while yst gene detected in 20% (6/30) Y. enterocolitica isolates. About 80%, 70%, 63.33%, and 50% of Y. enterocolitica isolates were sensitive to ciprofloxacin, gentamicin, cefotaxime, and streptomycin, respectively, while 83.33% of Y. enterocolitica isolates were resistant to both ampicillin and cephalothin. Interestingly, 21 (70%) isolates had the capability of biofilms formation in vitro. Among the multidrug-resistant (MDR) strains, a significant difference (p<0.05) was found between MDR and biofilm formation. However, biofilm formation was correlated with the resistance of the isolates to β-lactam antimicrobials and the presence of β-lactam-resistant genes.

Conclusion:

The presence of Y. enterocolitica in chicken meat, ground and processed beef meat represents a significant health risk for meat consumers, which reflects the contamination of slaughterhouses and processing operations, therefore, strict hygienic measures should be applied to minimize carcasses contamination.

Antimicrobial Susceptibility and Molecular Epidemiology of Proteus mirabilis Isolates from Three Hospitals in Northern Taiwan

Of all the Proteus spp., Proteus mirabilis is the most common species identified in clinical specimens and is a leading agent of complicated urinary tract infection. This study was undertaken to understand the antimicrobial susceptibility, prevalence of antibiotic resistance genes, and molecular typing of P. mirabilis isolates collected from three hospitals in northern Taiwan. The results showed that the collected isolates of P. mirabilis were susceptible to most antibiotics except cefazolin and tigecycline. Many resistance genes were detected in the collected isolates, of which TEM genes were the most common. Resistance to third- or fourth-generation cephalosporins was related to the presence of at least one of the tested extended-spectrum β-lactamase (ESBL) or AmpC genes. The presence of the VEB-1 gene seemed to be a good predictor for both cefepime and ceftazidime resistance, which was further supported by quantitative polymerase chain reaction results. Of the four imipenem-resistant P. mirabilis isolates, three isolates could hydrolyze imipenem by mass spectrometry analysis. Molecular typing by pulsed-field gel electrophoresis showed that the pulsotyping of the selected P. mirabilis isolates was heterogeneous. By analyzing the relationship of antimicrobial resistance and the presence of resistance genes, revision of the Clinical and Laboratory Standards Institute cefepime and ceftazidime MIC breakpoints for Enterobacteriaceae to predict ESBL producers might possibly be needed.

First report on extended-spectrum beta-lactamase (ESBL) producing Escherichia coli from European free-tailed bats (Tadarida teniotis) in Portugal: A one-health approach of a hidden contamination problem

The main aim of this study was to characterize the diversity of extended-spectrum beta-lactamases (ESBLs) in Escherichia coli isolates from European free tailed-bats (Tadarida teniotis) in Portugal. ESBL-producing E. coli isolates were recovered from 14 of 146 faecal samples (9.6%) and a total of 19 isolates were completely characterized. The more prevalent beta-lactamase genes detected were bla_CTX-M-1 (57.9%) and bla_CTX-M-3 (36.8%), followed by bla_SHV (31.6%), bla_TEM (21.1%), bla_OXA (10.5%) and bla_CTX-M-9 (10.5%). Among other associated resistance genes studied, tet(A) and tet(B) were predominant and fimA was the main virulence factor detected. Phylogroups D (47.4%) and A (31.6%) were the more prevalent, followed by group B2 (21.1%). Bats are reservoirs of antimicrobial-resistant bacteria and resistance determinants and is important in further studies to identify the main sources of pollution in the environment, such as water or insects that may contain these multiresistant organisms.

First Description of Colistin and Tigecycline-Resistant Acinetobacter baumannii Producing KPC-3 Carbapenemase in Portugal

Herein, we describe a case report of carbapenem-resistant Acinetobacter baumannii and Klebsiella pneumoniae isolates that were identified from the same patient at a Tertiary University Hospital Centre in Portugal. Antimicrobial susceptibility and the molecular characterization of resistance and virulence determinants were performed. PCR screening identified the presence of the resistance genes bla_KPC-3, bla_TEM-1 and bla_SHV-1 in both isolates. The KPC-3 K. pneumoniae isolate belonged to the ST-14 high risk clone and accumulated an uncommon resistance and virulence profile additional to a horizontal dissemination capacity. In conclusion, the molecular screening led to the first identification of the A. baumannii KPC-3 producer in Portugal with a full antimicrobial resistance profile including tigecycline and colistin.

Molecular Detection of New SHV β-lactamase Variants in Clinical Escherichia coli and Klebsiella pneumoniae Isolates from Egypt

The emergence of multidrug-resistant (MDR) pathogens was reported worldwide. Herein, SHV extended-spectrum β-lactamase (SHV-ESBL) variants detection was investigated in MDR E. coli and K. pneumoniae isolates recovered from human subjects (n = 144), one day-old chicks (n = 36) and broiler clinical samples (n = 90). All examined samples were positive for E. coli (n = 246/270; 91.11%) and Klebsiella pneumoniae (n = 24/270; 8.89%). Antimicrobial susceptibility testing was performed on E. coli and K. pneumoniae. SHV-ESBL producing isolates were defined followed by SHV-ESBL amino acids sequence and proteins structure-function analyses. Phylogenetic analysis of 11 MDR isolates resistant to at least 6 β-lactams was designed to determine their genetic relationship with those previously identified in Egypt. SHV-ESBL variants were detected in 28% and 16% of E. coli and K. pneumoniae isolates, respectively. Among the 11 SHV-ESBL producing isolates, one isolate displayed 100% blaSHV-12 similarity with three point mutations, while the other 10 isolates displayed amino acid substitutions at previously non-reported sites. Amino acid sequence analyses of these 10 isolates displayed 96-100% identity to blaSHV-10 (2 isolates with 3-6 point mutations), blaSHV-18 (one isolate with 4 point mutations), blaSHV-58 (4 isolates with 4-5 point mutations), and blaSHV-91 (3 isolates with 3-7 point mutations). These mutations altered SHV-enzyme pocket dimensions and its binding sites chargeability. The blaSHV phylogeny analysis revealed occurrence of variants in closely related lineages with blaSHV-5 and blaSHV-12 with possibility of blaSHV gene transfer between human and birds. The occurrence of these variants in Egypt could help in epidemiological studies and could explain the emergent resistance to β-lactams.

The prevalence and diversity of AmpC β-lactamase genes in plasmids from aquatic systems

This study aimed to investigate the presence and diversity of AmpC β-lactamase and integrase genes among DNA (genomic and plasmid) from bacterial populations in selected aquatic systems. Following an enrichment step, DNA was isolated and subjected to polymerase chain reaction (PCR) and digital droplet PCR. The intI1 gene and AmpC β-lactamase genes were present in genomic and plasmid DNA from all sites in the Mooi, Crocodile and Marico Rivers, with the exception of intI1 in the Marico River. Digital droplet PCR demonstrated that copy numbers varied considerably (0.0 to 29.38 copies per picogram of DNA). Some samples in which ampC was not detected, intI1 was present. Amplicons of ampC genes were subjected to restriction digest using HindIII. Samples where the restriction markers were absent were purified by cloning followed by plasmid extraction, PCR amplification, and sequencing of individual AmpC gene fragments. Phylogenetic analysis identified all positive AmpC genes as Class C β-lactamases, comprising of ampC, CMY- and ACT-families. Detecting AmpC and intl1 genes on plasmids suggests a high risk of horizontal gene transfer and potential dissemination of these and other antibiotic resistance genes surrounding immediate aquatic environments. Consequences of β-lactamase diversity in aquatic ecosystems are relatively unexplored in South African aquatic ecosystems.

Extended-spectrum β-lactamase-producing Escherichia coli in wastewaters and refugee camp in Lebanon

AIM

To evaluate the effects of population influx of refugees on the prevalence of extended-spectrum β-lactamase-producing Escherichia coli in wastewater networks in Lebanon.

MATERIALS & METHODS

Pulsed-field gel electrophoresis, multilocus sequence typing and antibiotic resistance genes typing were performed.

RESULTS

53.1% of isolates recovered from Al-Qaa refugee camp were positive for the tested resistant determinants compared with 49.1% from river effluents. All isolates carried aac(6)-1b and/or aac(3)-II; none carried armA, rmtB, ant(4')-Iia, aph(3')-Ia or carbapenemases. CTX-M-15, TEM-1, OXA-1, CMY-2 and SHV-12 were detected. Single and/or double substitutions were detected in GyrA and ParC. Phylogenetic group B2 and ST6470 were the most prevalent. Pulsed-field gel electrophoresis revealed 19 XbaI patterns and 17 pulsotypes.

CONCLUSION

The introduction of novel resistance patterns into the wastewater network requires effective control.

Clonal Diversity, Virulence Potential and Antimicrobial Resistance of Escherichia coli Causing Community Acquired Urinary Tract Infection in Switzerland

Objectives: The aim of this study was to assess the clonal structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli (UPEC) isolates causing community acquired urinary tract infection (CAUTI) in unselected primary care patients in Switzerland. Methods: We performed multilocus sequence typing, virulence factor determination, and phenotypic and genotypic antimicrobial resistance testing on 44 non-duplicate UPEC isolates. Results: Twenty-seven different sequence types (STs) were identified. Major UPEC clones were represented by 19 (43.2%) of the isolates, including E. coli ST131, ST69 (both 13.6%), ST73 (6.8%), ST10 (4.5%), ST127, ST140, (both 2.3%). Five (11.4%) isolates belonged to ST141. Aggregate virulence factor (VF) scores were highest among isolates belonging to ST127 and ST141. Overall, 50% of the isolates were susceptible to all 12 antimicrobials tested, and all isolates remained susceptible to fosfomycin and nitrofurantoin. Resistance to sulfamethoxazole and ciprofloxacin were found in 31.8, and 15.9% of the isolates, respectively. Plasmid-mediated resistance genes were detected in ST69 and ST131 and included aac(6')-Ib-cr (2.3% of all isolates) blaCTX-M-14 and blaCTX-M-15 (9%), and mph(A) (13.6%). None of the isolates tested positive for mcr-1 or mcr-2. Conclusions: Our results show that CAUTI in Switzerland is caused by a wide variety of UPEC STs for which fosfomycin remains a good treatment option. We suggest that ST141 is an emerging clone associated with UTI in the community, and warrants closer attention. Moreover, the high rate of E. coli harboring mph(A) from patients without a history of antimicrobial therapy or hospitalization indicates that UPEC is an important reservoir for mph(A).

High frequency of B2 phylogroup among non-clonally related fecal Escherichia coli isolates from wild boars, including the lineage ST131

Wild boars are worldwide distributed mammals which population is increasing in many regions, like the Iberian Peninsula, leading to an increased exposition to humans. They are considered reservoirs of different zoonotic pathogens and have been postulated as potential vectors of antimicrobial-resistant (AMR) bacteria. This study aimed to determine the prevalence of antimicrobial resistance and phylogenetic distribution of Escherichia coli from wild boar feces. Antimicrobial resistance and integron content was genetically characterized and E. coli of B2 phylogroup was further analyzed by molecular typing and virulence genotyping. The prevalence of AMR E. coli was low, with only 7.5% of isolates being resistant against at least one antimicrobial, mainly ampicillin, tetracycline and/or sulfonamide. An unexpected elevated rate of B2 phylogroup (47.5%) was identified, most of them showing unrelated pulsed-field-gel-electrophoresis patterns. ST131/B2 (fimH 22 sublineage), ST28/B2, ST1170/B2, ST681/B2 and ST625/B2 clones, previously described in extraintestinal infections in humans, were detected in B2 isolates, and carried one or more genes associated with extraintestinal pathogenic E. coli (ExPEC). This study demonstrated a low prevalence of antimicrobial resistance in E. coli from wild boars, although they are not exempt of AMR bacteria, and a predominance of genetically diverse B2 phylogroup, including isolates carrying ExPEC which may contribute to the spread of virulence determinants among different ecosystems.

Isolation and characterization of antimicrobial-resistant Escherichia coli from national horse racetracks and private horse-riding courses in Korea

Limited information is available regarding horse-associated antimicrobial resistant (AR) Escherichia (E.) coli. This study was designed to evaluate the frequency and characterize the pattern of AR E. coli from healthy horse-associated samples. A total of 143 E. coli (4.6%) were isolated from 3,078 samples collected from three national racetracks and 14 private horse-riding courses in Korea. Thirty of the E. coli isolates (21%) showed antimicrobial resistance to at least one antimicrobial agent, and four of the AR E. coli (13.3%) were defined as multi-drug resistance. Most of the AR E. coli harbored AR genes corresponding to their antimicrobial resistance phenotypes. Four of the AR E. coli carried class 1 integrase gene (intI1), a gene associated with multi-drug resistance. Pulsed-field gel electrophoretic analysis showed no genetic relatedness among AR E. coli isolated from different facilities; however, cross-transmissions between horses or horses and environments were detected in two facilities. Although cross-transmission of AR E. coli in horses and their environments was generally low, our study suggests a risk of transmission of AR bacteria between horses and humans. Further studies are needed to evaluate the risk of possible transmission of horse-associated AR bacteria to human communities through horse riders and horse-care workers.

Evolution and Epidemiology of Multidrug-Resistant Klebsiella pneumoniae in the United Kingdom and Ireland

Klebsiella pneumoniae is a human commensal and opportunistic pathogen that has become a leading causative agent of hospital-based infections over the past few decades. The emergence and global expansion of hypervirulent and multidrug-resistant (MDR) clones of K. pneumoniae have been increasingly reported in community-acquired and nosocomial infections. Despite this, the population genomics and epidemiology of MDR K. pneumoniae at the national level are still poorly understood. To obtain insights into these, we analyzed a systematic large-scale collection of invasive MDR K. pneumoniae isolates from hospitals across the United Kingdom and Ireland. Using whole-genome phylogenetic analysis, we placed these in the context of previously sequenced K. pneumoniae populations from geographically diverse countries and identified their virulence and drug resistance determinants. Our results demonstrate that United Kingdom and Ireland MDR isolates are a highly diverse population drawn from across the global phylogenetic tree of K. pneumoniae and represent multiple recent international introductions that are mainly from Europe but in some cases from more distant countries. In addition, we identified novel genetic determinants underlying resistance to beta-lactams, gentamicin, ciprofloxacin, and tetracyclines, indicating that both increased virulence and resistance have emerged independently multiple times throughout the population. Our data show that MDR K. pneumoniae isolates in the United Kingdom and Ireland have multiple distinct origins and appear to be part of a globally circulating K. pneumoniae population.

Klebsiella pneumoniae is a major human pathogen that has been implicated in infections in healthcare settings over the past few decades. Antimicrobial treatment of K. pneumoniae infections has become increasingly difficult as a consequence of the emergence and spread of strains that are resistant to multiple antimicrobials. To better understand the spread of resistant K. pneumoniae, we studied the genomes of a large-scale population of extensively antimicrobial-resistant K. pneumoniae in the United Kingdom and Ireland by utilizing the fine resolution that whole-genome sequencing of pathogen genomes provides. Our results indicate that the K. pneumoniae population is highly diverse and that, in some cases, resistant strains appear to have spread across the country over a few years. In addition, we found evidence that some strains have acquired antimicrobial resistance genes independently, presumably in response to antimicrobial treatment.

Population structure of multidrug resistant Klebsiella oxytoca within hospitals across the UK and Ireland identifies sharing of virulence and resistance genes with K. pneumoniae

Klebsiella oxytoca, a member of the Enterobacteriaceae, is a gram-negative pathogenic bacterium of environmental origin, which can cause infection in healthcare settings. Outbreaks of multidrug-resistant K. oxytoca infection have been increasingly reported in hospitalized patients. Despite the growing importance of this pathogen, there is limited knowledge about the population structure and epidemiology of antimicrobial resistant K. oxytoca. We investigated the population structure and genomic basis of antimicrobial resistance of 41 multidrug resistant K. oxytoca isolates recovered from bloodstream infections across the UK and Ireland. Our results show that K. oxytoca has a highly diverse population, which is composed of several distinct clades, and we identified one recent expansion of a clone within our dataset. Although the K. oxytoca genomes are clearly distinct from the genomes of a global collection of Klebsiella pneumoniae complex, pre-dominantly composed of K. pneumoniae, we found evidence for sharing of core genes through recombination, as well as the exchange of accessory antimicrobial resistance and virulence factor genes between the species. Our findings also suggest that the different K. oxytoca clades have acquired antimicrobial resistance and virulence factor genes independently. This highlights the clinical and therapeutic importance of genetic flexibility in K. oxytoca and the relevance of this in its role as an opportunistic pathogen.

Characterization of CTX-M enzymes, quinolone resistance determinants, and antimicrobial residues from hospital sewage, wastewater treatment plant, and river water

Multidrug-resistant (MDR) bacteria are widespread in hospitals and have been increasingly isolated from aquatic environments. The aim of the present study was to characterize extended-spectrum β-lactamase (ESBL) and quinolone-resistant Enterobacteriaceae from a hospital effluent, sanitary effluent, inflow sewage, aeration tank, and outflow sewage within a wastewater treatment plant (WWTP), as well as river water upstream and downstream (URW and DRW, respectively), of the point where the WWTP treated effluent was discharged. β-lactamase (bla) genes, plasmid-mediated quinolone resistance (PMQR), and quinolone resistance-determining regions (QRDRs) were assessed by amplification and sequencing in 55 ESBL-positive and/or quinolone-resistant isolates. Ciprofloxacin residue was evaluated by high performance liquid chromatography. ESBL-producing isolates were identified in both raw (n=29) and treated (n=26) water; they included Escherichia coli (32), Klebsiella pneumoniae (22) and Klebsiella oxytoca (1). Resistance to both cephalosporins and quinolone was observed in 34.4% of E. coli and 27.3% of K. pneumoniae. Resistance to carbapenems was found in 5.4% of K. pneumoniae and in K. oxytoca. Results indicate the presence of bla_CTX-M (51/55, 92.7%) and bla_SHV (8/55, 14.5%) ESBLs, and bla_GES (2/55, 3.6%) carbapenemase-encoding resistance determinants. Genes conferring quinolone resistance were detected at all sites, except in the inflow sewage and aeration tanks. Quinolone resistance was primarily attributed to amino acid substitutions in the QRDR of GyrA (47%) or to the presence of PMQR (aac-(6')-Ib-cr, oqxAB, qnrS, and/or qnrB; 52.9%) determinants. Ciprofloxacin residue was absent only from URW. Our results have shown strains carrying ESBL genes, PMQR determinants, and mutations in the gyrA QRDR genes mainly in hospital effluent, URW, and DRW samples. Antimicrobial use, and the inefficient removal of MDR bacteria and antibiotic residue during sewage treatment, may contribute to the emergence and spreading of resistance in the environment, making this a natural reservoir.

Molecular Characteristics and Antibiotic Resistance Profiles of Klebsiella Isolates in Mthatha, Eastern Cape Province, South Africa

The increase in the incidence of extended-spectrum β-lactamase- (ESBL-) producing Klebsiella species has become a serious problem worldwide, because of their incrimination in antibiotic resistance. The objective of this study is to investigate the resistance genes responsible for ESBL-producing Klebsiella species and carbapenemase-producing Klebsiella (CRE) isolated in Mthatha and to study their epidemiology. A prospective, descriptive study of 202 nonrepetitive samples from patients was obtained from Nelson Mandela Academic Hospital. The cultured Klebsiella isolates were subjected to antimicrobial susceptibility tests and the polymerase chain reaction of bla_CTX-M, bla_TEM, bla_SHV, bla_KPC, and bla_NDM genes. Overall K. pneumoniae were the majority with 169 (83.7%) species isolates, followed by K. oxytoca with 29 (14.4%), while K. ozaenae and Raoultella ornithinolytica were 2 (0.9%) each. The prevalence of ESBL production in all Klebsiella species was 117 (57.9%). ESBL-genotypic resistance is driven in Mthatha by bla_SHV 121 (77.1%) followed by bla_TEM 105 (66.9%) and bla_CTX-M at 89 (56.7%). The most common ESBL genotype combination among the Klebsiella was bla_TEM + bla_SHV + bla_CTX-M at 79 (50.3%). There is a steady increase in the rate of ESBL genes in the last five years.

Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae

Background

Klebsiella pneumoniae is a gram-negative bacterial species capable of occupying a broad range of environmental and clinical habitats. Known as an opportunistic pathogen, it has recently become a major causative agent of clinical infections worldwide. Despite growing knowledge about the highly diverse population of K. pneumoniae, the evolution and clinical significance of environmental K. pneumoniae, as well as the relationship between clinical and environmental K. pneumoniae, are poorly defined.

Methods

We isolated and sequenced K. pneumoniae from in-patients in a single hospital in Thailand, as well as hospital sewage, and surrounding canals and farms within a 20-km radius.

Results

Phylogenetic analysis of 77 K. pneumoniae (48 clinical and 29 non-clinical isolates) demonstrated that the two groups were intermixed throughout the tree and in some cases resided in the same clade, suggesting recent divergence from a common ancestor. Phylogenetic comparison of the 77 Thai genomes with 286 K. pneumoniae from a global collection showed that Thai isolates were closely related to the clinical sub-population of the global collection, indicating that Thai clinical isolates belonged to globally circulating lineages. Dating of four Thai K. pneumoniae clades indicated that they emerged between 50 and 150 years ago. Despite their phylogenetic relatedness, virulence factors and β-lactamase resistance genes were more numerous in clinical than in environmental isolates. Our results indicate that clinical and environmental K. pneumoniae are closely related, but that hospitals may select for isolates with a more resistant and virulent genotype.

Conclusions

These findings highlight the clinical relevance of environmental K. pneumoniae isolates.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-017-0397-1) contains supplementary material, which is available to authorized users.

Extended-spectrum β-lactamase producing Enterobacteriaceae in bulk tank milk from German dairy farms

Although the dairy farm environment is a known source of extended-spectrum β-lactamase (ESBL)-producing bacteria, surveillance data on ESBL in the milk production chain are still scarce. This study aimed at estimating the dimensions of the problem for public health and animal welfare by surveying ESBL-producing Enterobacteriaceae in raw bulk tank milk in Germany. Samples from 866 dairy farms, comprising about 1% of the total number of dairy farms in Germany, were first screened for presence of cefotaxime-resistant bacteria by selective enrichment. Suspect colonies were identified phenotypically and further characterized by biochemical and molecular methods, including analysis of resistance genes and clonal diversity in ESBL-producing isolates. Bulk tank milk from 82 (9.5%) farms yielded Enterobacteriaceae with confirmed ESBL-production. The most frequent ESBL-producing species was Escherichia coli (75.6%), followed by Citrobacter spp. (9.6%), Enterobacter cloacae (6.1%), and Klebsiella oxytoca (3.7%), a few isolates belonged to other species within the genera Hafnia, Raoutella and Serratia. The majority of isolates (95.1%) harbored the β-lactamase blaCTX-M gene, which has gained increased importance among ESBL-producing strains worldwide; the CTX-M group 1 was found to be the dominating (88.4%) phylogenetic group. All ESBL-positive Escherichia coli isolates were clonally heterogeneous, as determined by pulsed-field gel electrophoresis. The results from this survey demonstrate that ESBL-producing bacteria are distributed widely in the dairy farm environment in Germany. Therefore, raw milk is a potential source of exposure for the consumer, which is of increasing importance considering the trend of farmer-to-consumer direct marketing. Furthermore, dairy farm staff have an increased likelihood of exposure to ESBL-producing bacteria. Finally, ESBL-producing bacteria may also be transferred via waste milk to calves, thus further spreading antibiotic resistance in the farm environment.

Detection of blaOXA-23-like and blaNDM-1 in Acinetobacter baumannii from the Eastern Region, Saudi Arabia

Acinetobacter baumannii is currently considered as one of the most common successful pathogens in the healthcare system due to its ability to quickly develop resistance. Ten carbapenem-resistant A. calcoaceticus-baumannii complex were isolated from the eastern region, Saudi Arabia in 2014. All isolates were resistant to ciprofloxacin, however, 8 of 10 isolates were tigecycline resistant. Susceptibility test was also carried out for three aminoglycosides, resistance to gentamicin was 80%, amikacin was 90%, and tobramycin was 50%. Colistin susceptibility was seen in all isolates. The 10 isolates harbored bla_OXA-23-like and ISAba1 and 9 of them also carried bla_ADC. Three isolates of 10 harbored bla_NDM-1 coding for NDM metallo-β-lactamase (MBL) with coexistence of bla_ADC together with either bla_GES or bla_TEM or both. Those three isolates exhibited negative Etest MBL screening test. Pulsed-field gel electrophoresis revealed the high clonal variability of the isolates, although two isolates were indistinguishable. The risk of dissemination of carbapenem resistance through presence of ISAba1 upstream of OXA-23-like in all isolates raises the concern about emergence of higher carbapenem prevalence rates in the future in our region. This study also demonstrated the importance of molecular surveillance to provide accurate and reliable data about the resistance rates of A. baumannii. Finally, the high incidence of NDM-1 among our isolates requires a routine surveillance to monitor the future prevalence of this enzyme in the region.

Prevalence of Extended-Spectrum-β-Lactamase-Producing Escherichia coli in Imported Frozen Freshwater Fish in Eastern Province of Saudi Arabia

Background:

The prevalence of extended-spectrum β-lactamase (ESBL) production and antimicrobial susceptibility testing in the Escherichia coli in frozen freshwater fish imported into Saudi Arabia have not been investigated.

Objective:

The aim of this study was to investigate the prevalence of ESBL-producing E. coli in frozen freshwater fish imported into Saudi Arabia and retailed in various supermarkets and food stores in the Eastern Province of Saudi Arabia.

Materials and Methods:

A total of 405 imported freshwater fish samples: Catfish (n = 65); mrigal (n = 45); tilapia (n = 135); carfoo (n = 50); rohu (n = 75); and milkfish (n = 35) were purchased from supermarkets and screened for ESBL-producing E. coli using ESBL chromogenic selective agar. The phenotypically confirmed ESBL isolates were further tested for antimicrobial susceptibility testing against 21 antimicrobial agents and amplification of bla_TEM, bla_SHV, and bla_CTX-M genes using polymerase chain reaction.

Results:

A total of 110 out of the 405 (27.2%) freshwater fish samples were found to be positive for ESBL producing E. coli and yielded 224 confirmed isolates. The highest rates of multi-drug resistant patterns to antimicrobial agents were observed in E. coli isolated from catfish, mrigal, and tilapia imported from Thailand and milkfish imported from Vietnam. The most prevalent ESBL gene found in the samples was bla_CTX-M, which was detected in tilapia (100%, n = 30) imported from Thailand and carfoo (100%, n = 5), milkfish (60%, n = 24), catfish (52.3%, n = 34), and tilapia imported from India (34.8%, n = 24).

Conclusion:

The results confirmed the imported frozen freshwater fish is pool reservoir of antibiotic resistance and ESBL producing E. coli.