Interpretative reading: recognizing the unusual and inferring resistance mechanisms from resistance phenotypes

Fernández-de-Bobadilla M, Serrano-Tomás MI, Sánchez-Díaz AM, Avendaño-Ortiz J, Coque TM, Ruiz-Garbajosa P, del Campo R, Cantón R. A long-term survey of Serratia spp. bloodstream infections revealed an increase of antimicrobial resistance involving adult population

Serratia spp. is a well-recognized pathogen in neonates; however, limited data are available in adults. We studied microbiological and clinical characteristics of Serratia spp. causing bloodstream infections (BSI) in our institution (January 2005-July 2020). Overall, 141 BSI episodes affecting 139 patients were identified and medical records reviewed. Antimicrobial susceptibility was recovered from our informatics system and 118 isolates from 116 patients were available for further microbiological studies. Whole genome sequencing (WGS) was completed in 107 isolates. Incidence of Serratia BSI was 0.3/1000 overall admissions (range 0.12-0.60), with maximum prevalence (27 episodes, 19.1%) during 2017-2018. Relevant patients' clinical characteristics were 71.9% ≥60 years (n = 100), with high comorbidity rates (49%, ≥2), 23 (74.2%) of them died within 1 month of the BSI episode. WGS identified all isolates as Serratia marcescens when Kraken bioinformatics taxonomic tool was used despite some which were identified as Serratia nematodiphila (32/118) or Serratia ureilytica (5/118) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Nevertheless, when using MASH distance, Serratia nevei (63/107), S. ureilytica (38/107), and S. marcescens (6/107) were assigned. Carbapenemase (blaVIM-1) and extended-spectrum β-lactases (ESBL) (blaSHV-12) genes were found in seven and three isolates, respectively, one of them expressing both genes. The worldwide-disseminated IncL/M scaffold plasmid was identified in six VIM producers. Four genotypes were established based on their virulence factors and resistome. Serratia spp. emerged as a relevant nosocomial pathogen causing BSI in elderly patients in our hospital, particularly in recent years with a remarkable increase in antibiotic resistance. ESBL and carbapenemases production related to plasmid dissemination are particularly noteworthy.IMPORTANCESerratia spp. is the third most frequent pathogen involved in outbreaks at neonatal facilities and is primarily associated with bacteremia episodes. In this study, we characterized all causing bloodstream infection (BSI) in patients admitted to our hospital during a 16-year period (2005-2020). Despite having no neonatal intensive care unit in our hospital, this study revealed that Serratia spp. is a relevant pathogen causing BSI in elderly patients with high comorbidity rates. A significant increase of antimicrobial resistance was detected over time, particularly in 2020 and coinciding with the coronavirus disease (COVID-19) pandemic and nosocomial spread of multidrug-resistant Serratia spp. isolates. extended-spectrum β-lactases and carbapenemases genes associated with plasmid dissemination, typically detected in other Enterobacterales species, were also identified, reinforcing the role of Serratia spp. in the antimicrobial resistance landscape. Additionally, this work highlights the need to reclassify the species of Serratia, since discrepancies were observed in the identification when using different tools.

Epidemiology and microbiology of recurrent UTI in women in the community in Oxfordshire, UK

Background

Recurrent urinary tract infection (rUTI) contributes to significant morbidity and antibiotic usage.

Objectives

To characterize the age of women experiencing rUTI, the microbiology of rUTIs, and the risk of further rUTIs in Oxfordshire, UK.

Patients and methods

We retrospectively analysed de-identified linked microbiology and hospital admissions data (Infections in Oxfordshire Research Database), between 2008 and 2019, including positive urine cultures from women aged ≥16 years in community settings. We defined rUTI as ≥2 positive urine cultures within 6 months or ≥3 within 12 months.

Results

Of 201 927 women with urine culture performed, 84 809 (42%) had ≥1 positive culture, and 15 617 (18%) of these experienced ≥1 rUTI over a median (IQR) follow-up of 6 (3-9) years. Women with rUTI were 17.0 (95% CI: 16.3-17.7) years older on average. rUTI was commonest (6204; 40%) in those aged 70-89 years. Post-rUTI, the risk of further UTI within 6 months was 29.4% (95% CI: 28.7-30.2). Escherichia coli was detected in 65% of positive cultures. Among rUTIs where the index UTI was E. coli associated, the second UTI was also E. coli associated in 81% of cases.

Conclusions

rUTIs represent a substantial healthcare burden, particularly in women >60 years. One-third of women experiencing rUTI have a further microbiologically confirmed UTI within 6 months.

#AMRrounds: a systematic educational approach for navigating bench to bedside antimicrobial resistance

Antimicrobial resistance (AMR) continues to serve as a major global health crisis. Clinicians practising in this modern era are faced with ongoing challenges in the therapeutic management of patients suffering from antimicrobial-resistant infections. A strong educational understanding and synergistic application of clinical microbiology, infectious disease and pharmacological concepts can assist the adventuring clinician in the navigation of such cases. Important items include mobilizing laboratory testing for pathogen identification and susceptibility data, harnessing an understanding of intrinsic pathogen resistance, acknowledging epidemiological resistance trends, recognizing acquired AMR mechanisms, and consolidating these considerations when constructing an ideal pharmacological plan. In this article, we outline a novel framework by which to systematically approach clinical AMR, encourage AMR-related education and optimize therapeutic decision-making in AMR-related illnesses.

Molecular characterization of multidrug-resistant non-typeable Haemophilus influenzae with high-level resistance to cefuroxime, levofloxacin, and trimethoprim-sulfamethoxazole

BACKGROUND

Non-typeable Haemophilus influenzae (NTHi) has become the major cause of invasive H. influenzae diseases in the post-H. influenzae type b vaccine era. The emergence of multidrug-resistant (MDR) NTHi is a growing public health problem. Herein, we investigated the molecular basis of MDR in NTHi. The isolated NTHi were subjected to antimicrobial susceptibility testing for 12 agents. Whole genome and plasmid sequencing were conducted and analyzed to identify significant genetic variations and plasmid-encoded genes conferred antibiotic resistance.

RESULTS

Thirteen (50%) MDR NTHi isolates were obtained; of these, 92.3% were non-susceptible to ampicillin, 30.8% to amoxicillin-clavulanate, 61.5% to cefuroxime, 61.5% to ciprofloxacin/levofloxacin, 92.3% to trimethoprim-sulfamethoxazole, 30.8% to tetracycline, and 7.7% to azithromycin. Eight ampicillin-resistant isolates were β-lactamase positive; of these, 6 carried bla_TEM-1 and 2 carried bla_ROB-1, whereas 4 were β-lactamase negative. Genetic variations in mrdA, mepA, and pbpG were correlated with amoxicillin-clavulanate non-susceptibility, whereas variations in ftsI and lpoA conferred cefuroxime resistance. Five variations in gyrA, 2 in gyrB, 3 in parC, 1 in parE, and 1 in the parC-parE intergenic region were associated with levofloxacin/ciprofloxacin non-susceptibility. Among these genes, 8 variations were linked to high-level levofloxacin resistance. Six variations in folA were associated with trimethoprim-sulfamethoxazole resistance. Plasmid-bearing tet(B) and mef(A) genes were responsible for tetracycline and azithromycin resistance in 4 and 1 MDR isolates, respectively.

CONCLUSIONS

This study clarified the molecular epidemiology of MDR in NTHi. This can benefit the monitoring of drug resistance trends in NTHi and the adequate medical management of patients with NTHi infection.

β-LacFamPred: An online tool for prediction and classification of β-lactamase class, subclass, and family

β-Lactams are a broad class of antimicrobial agents with a high safety profile, making them the most widely used class in clinical, agricultural, and veterinary setups. The widespread use of β-lactams has induced the extensive spread of β-lactamase hydrolyzing enzymes known as β-lactamases (BLs). To neutralize the effect of β-lactamases, newer generations of β-lactams have been developed, which ultimately led to the evolution of a highly diverse family of BLs. Based on sequence homology, BLs are categorized into four classes: A-D in Ambler's classification system. Further, each class is subdivided into families. Class B is first divided into subclasses B1-B3, and then each subclass is divided into families. The class to which a BL belongs gives a lot of insight into its hydrolytic profile. Traditional methods of determining the hydrolytic profile of BLs and their classification are time-consuming and require resources. Hence we developed a machine-learning-based in silico method, named as β-LacFamPred, for the prediction and annotation of Ambler's class, subclass, and 96 families of BLs. During leave-one-out cross-validation, except one all β-LacFamPred model HMMs showed 100% accuracy. Benchmarking with other BL family prediction methods showed β-LacFamPred to be the most accurate. Out of 60 penicillin-binding proteins (PBPs) and 57 glyoxalase II proteins, β-LacFamPred correctly predicted 56 PBPs and none of the glyoxalase II sequences as non-BLs. Proteome-wide annotation of BLs by β-LacFamPred showed a very less number of false-positive predictions in comparison to the recently developed BL class prediction tool DeepBL. β-LacFamPred is available both as a web-server and standalone tool at http://proteininformatics.org/mkumar/blacfampred and GitHub repository https://github.com/mkubiophysics/B-LacFamPred respectively.

The role of the microbiology laboratory in the diagnosis of multidrug-resistant Gram-negative bacilli infections. The importance of the determination of resistance mechanisms

Early diagnosis and treatment has an important impact on the morbidity and mortality of infections caused by multidrug-resistant bacteria. Multidrug-resistant gram-negative bacilli (MR-GNB) constitute the main current threat in hospitals and especially in intensive care units (ICU). The role of the microbiology laboratory is essential in providing a rapid and effective response. This review updates the microbiology laboratory procedures for the rapid detection of BGN-MR and its resistance determinants. The role of the laboratory in the surveillance and control of outbreaks caused by these bacteria, including typing techniques, is also studied. The importance of providing standardized resistance maps that allow knowing the epidemiological situation of the different units is emphasized. Finally, the importance of effective communication systems for the transmission of results and decision making in the management of patients infected by BGN-MR is reviewed.

Characterisation of Yersinia enterocolitica strains isolated from wildlife in the northwestern Italian Alps

Introduction

Yersiniosis is a zoonosis causing gastroenteritis, diarrhoea, and occasionally reactive arthritis and septicaemia. Cases are often linked to meat consumption and the most common aetiological agent is the Gram-negative bacilliform Yersinia enterocolitica bacterium. The occurrence of Yersinia spp. among wild animals has mostly been studied in wild boar, but it has seldom been in other species.

Material and Methods

A total of 1,868 faecal samples from animals found dead or hunted were collected between 2015 and 2018 in the Valle d’Aosta region of the northwestern Italian Alps. Alpine ibex faecal samples were collected during a health monitoring program in 2018. Bacteria were isolated via PCR and confirmed as Y. enterocolitica biochemically. Strain antimicrobial susceptibility was tested by Kirby–Bauer disc diffusion, and the presence of virulence factors and antimicrobial resistance genes was investigated using whole-genome sequencing.

Results

Yersinia enterocolitica strains of biotype 1A were detected in six faecal samples from red deer (0.93%), roe deer (0.49%) and red foxes (0.7%). Strains found in beech martens (3.57%) and Alpine ibex (2.77%) belonged to biotypes 1B and 5, respectively and harboured the pYPTS01 plasmid that had only been detected in Y. pseudotuberculosis PB1/+. All the isolates were resistant to ampicillin and erythromycin.

Conclusion

The biovar 1A strains exhibited different virulence factors and behaved like non-pathogenic commensals. The strain from an Alpine ibex also harboured the self-transmissible pYE854 plasmid that can mobilise itself and the pYPTS01 plasmid to other strains. The beech marten could be considered a sentinel animal for Y. enterocolitica. Phenotypic resistance may account for the ability of all the strains to resist β-lactams.

Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods

Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article reviews common antimicrobial susceptibility testing (AST) methods and relevant issues concerning the advantages and disadvantages of each method. Although accurate, classic technologies used in clinical microbiology to profile antimicrobial susceptibility are time-consuming and relatively expensive. As a result, physicians often prescribe empirical antimicrobial therapies and broad-spectrum antibiotics. Although recently developed AST systems have shown advantages over traditional methods in terms of testing speed and the potential for providing a deeper insight into resistance mechanisms, extensive validation is required to translate these methodologies to clinical practice. With a continuous increase in antimicrobial resistance, additional efforts are needed to develop innovative, rapid, accurate, and portable diagnostic tools for AST. The wide implementation of novel devices would enable the identification of the optimal treatment approaches and the surveillance of antibiotic resistance in health, agriculture, and the environment, allowing monitoring and better tackling the emergence of AMR.

Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex

Serratia marcescens is an important nosocomial pathogen causing various opportunistic infections, such as urinary tract infections, bacteremia and sometimes even hospital outbreaks. The recent emergence and spread of multidrug-resistant (MDR) strains further pose serious threats to global public health. This bacterium is also ubiquitously found in natural environments, but the genomic differences between clinical and environmental isolates are not clear, including those between S. marcescens and its close relatives. In this study, we performed a large-scale genome analysis of S. marcescens and closely related species (referred to as the 'S. marcescens complex'), including more than 200 clinical and environmental strains newly sequenced here. Our analysis revealed their phylogenetic relationships and complex global population structure, comprising 14 clades, which were defined based on whole-genome average nucleotide identity. Clades 10, 11, 12 and 13 corresponded to S. nematodiphila, S. marcescens sensu stricto, S. ureilytica and S. surfactantfaciens, respectively. Several clades exhibited distinct genome sizes and GC contents and a negative correlation of these genomic parameters was observed in each clade, which was associated with the acquisition of mobile genetic elements (MGEs), but different types of MGEs, plasmids or prophages (and other integrative elements), were found to contribute to the generation of these genomic variations. Importantly, clades 1 and 2 mostly comprised clinical or hospital environment isolates and accumulated a wide range of antimicrobial resistance genes, including various extended-spectrum β-lactamase and carbapenemase genes, and fluoroquinolone target site mutations, leading to a high proportion of MDR strains. This finding suggests that clades 1 and 2 represent hospital-adapted lineages in the S. marcescens complex although their potential virulence is currently unknown. These data provide an important genomic basis for reconsidering the classification of this group of bacteria and reveal novel insights into their evolution, biology and differential importance in clinical settings.

Antimicrobial Susceptibility of Enterotoxigenic Escherichia coli from Diarrhoeic Neonatal Calves in Spain

Simple Summary

Neonatal calf diarrhoea, a worldwide concern for cattle production, can be caused by viral, bacterial and protozoan enteropathogens: the enterotoxigenic Escherichia coli (ETEC) is one of the most important. The use of antimicrobials for treating neonatal calf diarrhoea cases is still a common practice among veterinary surgeons, although its use is only justified in bacterial infections evolving towards a systemic disease. Since the indiscriminate use of antimicrobials for treating diarrhoeic calves increases the risk for the appearance of antimicrobial resistances, restrictions on the use of antimicrobials in veterinary practice were implemented. The aim of this study was to characterize the antimicrobial susceptibility of ETEC strains obtained from diarrhoeic calves. Our results are alarming since all ETEC strains were resistant to three or more families of antimicrobials; in addition, a high number of strains were resistant to most first-line antimicrobials used in veterinary practice. Only ceftiofur, cefoperazone, cefquinome and gentamicin presented efficacy against most ETEC strains. Thus, empirical treatment of calf scours caused by ETEC is usually ineffective. Our results reveal that performing antimicrobial susceptibility tests in each NCD outbreak is needed for establishing an effective treatment and avoiding the emergence of new resistance mechanisms.

Abstract

Enterotoxigenic Escherichia coli (ETEC) is one of the major pathogens involved in neonatal calf diarrhoea (NCD) causing high economic losses in dairy farms. Antibiotic treatment is common in cases of systemic illness caused by NCD, but antimicrobial susceptibility tests (AST) are usually not performed. Thus, the aim of this study was to characterize the antimicrobial susceptibility of ETEC strains obtained from calves with diarrhoea between 2018–2020. Faecal samples (n = 420) were analyzed to detect the typical ETEC virulence factors F5 and STa. Positive samples were cultured to identify and isolate ETEC strains (n = 41) and ASTs were performed. Our results are alarming since ETEC strains resistant to three or more families of antimicrobials were detected in all isolates. Only four antibiotics (ceftiofur, cefoperazone, cefquinome and gentamicin) presented efficacy against more than 90% of the ETEC strains, while the other ten antibiotics were effective against less than 40% of the strains. In addition, a high number of strains were resistant to most first-line antimicrobials used in veterinary practice. For this reason, when ETEC infection is suspected, an AST must always be performed to select the most appropriate antimicrobial in each case and to avoid the emergence of new resistance mechanisms.

Multicenter surveillance of in vitro activities of cefepime-zidebactam, cefepime-enmetazobactam, omadacycline, eravacycline, and comparator antibiotics against Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii complex causing bloodstream infection in Taiwan, 2020

OBJECTIVES

: To determine the in vitro activities of novel and comparator antibiotics against gram-negative bacteria (GNB) in Taiwan.

METHODS

: Isolates of Escherichia coli (n = 335), Klebsiella pneumoniae (n = 316; 144 isolates with hyperviscosity characteristics), Pseudomonas aeruginosa (n = 271), Acinetobacter baumannii complex species (n = 187), and non-typhoidal Salmonella species (n = 226), Shigella species (n = 13) from miscellaneous culture sources were collected in 2020 in Taiwan. The MICs of the isolates to test antibiotics were determined using the broth microdilution method. GeneXpert was used to detect genes encoding carbapenemases among the carbapenem-non-susceptible (NS) Enterobacterales isolates.

RESULTS

: The MIC values of the cefepime-enmetazobactam combination against extended-spectrum β-lactamase-producing E. coli and K. pneumoniae isolates (MIC₉₀ ≤ 0.5 mg/L), bla_KPC-harboring E. coli isolates (0.25 mg/L; n = 2), and 80% of bla_OXA-48-like gene-harboring K. pneumoniae isolates (≤2 mg/L) were low. The MIC ranges of the cefepime-zidebactam against carbapenemase-producing Enterobacterales isolates (irrespective of the carbapenemase type [MIC₉₀ ≤ 4 mg/L]) and carbapenem-NS or ceftolozane-tazobactam-NS P. aeruginosa isolates (MIC₉₀ value, 8 mg/L) were significantly lower than those of the cefepime-enmetazobactam.

CONCLUSIONS

: The efficacy of novel antibiotics against important drug-resistant GNB must be monitored and validated during the clinical treatment of patients.

Prevalence of Antibiotic Resistance Over Time in a Third-Level University Hospital

This study evaluated the spread and possible changes in resistance patterns of ESKAPE bacteria to first-choice antibiotics from 2015 to 2019 at a third-level university hospital after persuasive stewardship measures were implemented. Isolates were divided into three groups (group 1, low drug-resistant; group 2, multidrug/extremely drug-resistant; and group 3, pan-resistant bacteria) and a chi-squared test (χ²) was applied to determine differences in their distributions. Among the 2,521 isolates, Klebsiella pneumoniae was the most frequently detected (31.1%). From 2015 to 2019, the frequency of isolates in groups 2 and 3 decreased from 70.1% to 48.6% (χ² = 63.439; p < 0.0001). Stratifying isolates by bacterial species, for K. pneumoniae, the frequency of PDR isolates decreased from 20% to 1.3% (χ² = 15.885; p = 0.003). For Acinetobacter baumannii, a statistically significant decrease was found in groups 2 and 3: from 100% to 83.3% (χ² = 27.721; p < 0.001). Also, for Pseudomonas aeruginosa and Enterobacter spp., the frequency of groups 2 and 3 decreased from 100% to 28.3% (χ² = 225.287; p < 0.001) and from 75% to 48.7% (χ² = 15.408; p = 0.003), respectively. These results indicate that a program consisting of persuasive stewardship measures, which were rolled out during the time frame of our study, may be useful to control drug-resistant bacteria in a hospital setting.

New Insight on Antibiotic Resistance and Virulence of Escherichia coli from Municipal and Animal Wastewater

Antibiotic resistance of the indicator microorganism Escherichia coli was investigated in isolates from samples collected during the course of one year from two wastewater treatment plants treating municipal and animal wastes in Slovakia, respectively. The genes of antibiotic resistance and virulence factors in selected resistant E. coli isolates were described. A high percentage of the isolates from municipal and animal wastewater were resistant to ampicillin, streptomycin, tetracycline, ceftiofur, ceftriaxone, and enrofloxacin. In the selected E. coli isolates, we detected the following phenotypes: ESBL (20.4% in animal wastewater; 7.7% in municipal wastewater), multidrug-resistant (17% of animal and 32% of municipal isolates), high resistance to quinolones (25% of animal and 48% of municipal samples), and CTX-M (7.9% of animal and 17.3% of municipal isolates). We confirmed an integro-mediated antibiotic resistance in 13 E. coli strains from municipal and animal wastewater samples, of which the Tn3 gene and virulence genes cvaC, iutA, iss, ibeA, kps, and papC were detected in six isolates. One of the strains of pathogenic E. coli from the animal wastewater contained genes ibeA with papC, iss, kpsII, Int1, Tn3, and Cit. In addition, one bla_IMP gene was found in the municipal wastewater sample. This emphasises the importance of using the appropriate treatment methods to reduce the counts of antibiotic-resistant microorganisms in wastewater effluent.

Evidence of Another Anthropic Impact on Iguana delicatissima from the Lesser Antilles: The Presence of Antibiotic Resistant Enterobacteria

The improper use of antibiotics by humans may promote the dissemination of resistance in wildlife. The persistence and spread of acquired antibiotic resistance and human-associated bacteria in the environment, while representing a threat to wildlife, can also be exploited as a tool to monitor the extent of human impact, particularly on endangered animal species. Hence, we investigated both the associated enterobacterial species and the presence of acquired resistance traits in the cloacal microbiota of the critically endangered lesser Antillean iguana (Iguana delicatissima), by comparing two separate populations living in similar climatic conditions but exposed to different anthropic pressures. A combination of techniques, including direct plating, DNA sequencing and antimicrobial susceptibility testing allowed us to characterize the dominant enterobacterial populations, the antibiotic resistant strains and their profiles. A higher frequency of Escherichia coli was found in the samples from the more anthropized site, where multi-drug resistant strains were also isolated. These results confirm how human-associated bacteria as well as their antibiotic-resistance determinants may be transferred to wildlife, which, in turn, may act as a reservoir of antibiotic resistance.

Reporting antimicrobial susceptibilities and resistance phenotypes in Staphylococcus spp.: a nationwide proficiency study

Objectives

To evaluate the proficiency of microbiology laboratories in Spain in antimicrobial susceptibility testing (AST) of Staphylococcus spp.

Materials and methods

Eight Staphylococcus spp. with different resistance mechanisms were selected: six Staphylococcus aureus (CC-01/mecA, CC-02/mecC, CC-03/BORSA, CC-04/MLSBi, CC-06/blaZ and CC-07/linezolid resistant, cfr); one Staphylococcus epidermidis (CC-05/linezolid resistant, 23S rRNA mutation); and one Staphylococcus capitis (CC-08/daptomycin non-susceptible). Fifty-one laboratories were asked to report: (i) AST system used; (ii) antimicrobial MICs; (iii) breakpoints used (CLSI or EUCAST); and (iv) clinical category. Minor, major and very major errors (mEs, MEs and VMEs, respectively) were determined.

Results

The greatest MIC discrepancies found were: (i) by AST method: 19.4% (gradient diffusion); (ii) by antimicrobial agent: daptomycin (21.3%) and oxacillin (20.6%); and (iii) by isolate: CC-07/cfr (48.0%). The greatest error rates were: (i) by AST method: gradient diffusion (4.3% and 5.1% VMEs, using EUCAST and CLSI, respectively); (ii) by breakpoint: 3.8% EUCAST and 2.3% CLSI; (iii) by error type: mEs (0.8% EUCAST and 1.0% CLSI), MEs (1.8% EUCAST and 0.7% CLSI) and VMEs (1.2% EUCAST and 0.6% CLSI); (iii) by antimicrobial agent: VMEs (4.7% linezolid and 4.3% oxacillin using EUCAST); MEs (14.3% fosfomycin, 9.1% tobramycin and 5.7% gentamicin using EUCAST); and mEs (22.6% amikacin using EUCAST).

Conclusions

Clinical microbiology laboratories should improve their ability to determine the susceptibility of Staphylococcus spp. to some antimicrobial agents to avoid reporting false-susceptible or false-resistant results. The greatest discrepancies and errors were associated with gradient diffusion, EUCAST breakpoints and some antimicrobials (mEs for aminoglycosides; MEs for fosfomycin, aminoglycosides and oxacillin; and VMEs for linezolid and oxacillin).

Characteristics of High-Level Aminoglycoside-Resistant Enterococcus faecalis Isolated from Bulk Tank Milk in Korea

Enterococci, which are considered environmental mastitis-causing pathogens, have easily acquired aminoglycoside-resistant genes that encode various aminoglycoside-modifying enzymes (AME). Therefore, this study was conducted to compare the distribution of high-level aminoglycoside-resistant (HLAR) and multidrug-resistant (MDR) Enterococcus faecalis (E. faecalis) bacteria isolated from bulk tank milk in four dairy companies in Korea. Moreover, it analyzed the characteristics of their antimicrobial resistance genes and virulence factors. Among the 301 E. faecalis bacteria studied, 185 (61.5%) showed HLAR with no significant differences among the dairy companies. Furthermore, 129 (69.7%) of the 185 HLAR E. faecalis showed MDR without significant differences among companies. In contrast, HLAR E. faecalis from companies A, B, and C were significantly higher in resistance to the four classes than those in company D, which had the highest MDR ability against the three antimicrobial classes (p < 0.05). In addition, in the distribution of AME genes, 72 (38.9%) and 36 (19.5%) of the isolates carried both aac(6')Ie-aph(2″)-la and ant(6)-Ia genes, and the ant (6)-Ia gene alone, respectively, with significant differences among the companies (p < 0.05). In the distribution of virulence genes, the ace (99.5%), efa A (98.9%), and cad 1 (98.4%) genes were significantly prevalent (p < 0.05). Thus, our results support that an advanced management program by companies is required to minimize the dissemination of antimicrobial resistance and virulence factors.

A proposed scheme for the monitoring of antibiotic resistance in veterinary pathogens of food animals in the UK

BACKGROUND

Antibiotic resistance in bacteria is a global threat to both animal and public health, and detecting its occurrence is an important component of control strategies. Monitoring programmes for antibiotic resistance are currently in place in food-producing animals in the European Union covering the zoonotic bacteria Salmonella enterica, Campylobacter coli and Campylobacter jejuni and the indicator bacteria Escherichia coli, Enterococcus faecalis and Enterococcus faecium. However, there is no equivalent pan-European statutory monitoring programme covering the antibiotic susceptibility of veterinary bacterial pathogens in food animals. This paper considers that issue and aims to facilitate and stimulate further discussion.

METHODS

Recommendations, proposed by the authors from the scientific literature and following expert discussion at international meetings, are presented for monitoring the susceptibility of key veterinary pathogens.

RESULTS

The selected veterinary pathogens comprise Actinobacillus pleuropneumoniae, Bordetella bronchiseptica, E. coli, Histophilus somni, Mannheimia haemolytica, Pasteurella multocida, Staphylococcus aureus and Streptococcus spp. from the major food animal species cattle, pigs and poultry. The organisms are tested using harmonised panels of antibiotics over specified dilution ranges in a broth microdilution method.

CONCLUSION

The selected antibiotics and their respective dilution ranges are presented together with the underlying rationale for inclusion; the ranges chosen are suitable for incorporation into three microtitre plates, with each organism tested using a single plate. The recommendations are being implemented in 2020 in the UK for monitoring of the susceptibility of veterinary bacterial pathogens.

Development of a Multiplex Real-Time PCR Assay for Predicting Macrolide and Tetracycline Resistance Associated with Bacterial Pathogens of Bovine Respiratory Disease

Antimicrobial resistance (AMR) in bovine respiratory disease (BRD) is an emerging concern that may threaten both animal and public health. Rapid and accurate detection of AMR is essential for prudent drug therapy selection during BRD outbreaks. This study aimed to develop a multiplex quantitative real-time polymerase chain reaction assay (qPCR) to provide culture-independent information regarding the phenotypic AMR status of BRD cases and an alternative to the gold-standard, culture-dependent test. Bovine clinical samples (297 lung and 111 nasal) collected in Nebraska were subjected to qPCR quantification of macrolide (MAC) and tetracycline (TET) resistance genes and gold-standard determinations of AMR of BRD pathogens. Receiver operating characteristic curve analysis was used to classify AMR based on the qPCR results. For lung tissues, the qPCR method showed good agreement with the gold-standard test for both MACs and TETs, with a sensitivity of 67–81% and a specificity higher than 80%. For nasal swabs, qPCR results passed validation criteria only for TET resistance detection, with a sensitivity of 88%, a specificity of 80% and moderate agreement. The culture-independent assay developed here provides the potential for more rapid AMR characterization of BRD cases directly from clinical samples at equivalent accuracy and higher time efficiency compared with the gold-standard, culture-based test.

DeepBL: a deep learning-based approach for in silico discovery of beta-lactamases

Beta-lactamases (BLs) are enzymes localized in the periplasmic space of bacterial pathogens, where they confer resistance to beta-lactam antibiotics. Experimental identification of BLs is costly yet crucial to understand beta-lactam resistance mechanisms. To address this issue, we present DeepBL, a deep learning-based approach by incorporating sequence-derived features to enable high-throughput prediction of BLs. Specifically, DeepBL is implemented based on the Small VGGNet architecture and the TensorFlow deep learning library. Furthermore, the performance of DeepBL models is investigated in relation to the sequence redundancy level and negative sample selection in the benchmark dataset. The models are trained on datasets of varying sequence redundancy thresholds, and the model performance is evaluated by extensive benchmarking tests. Using the optimized DeepBL model, we perform proteome-wide screening for all reviewed bacterium protein sequences available from the UniProt database. These results are freely accessible at the DeepBL webserver at http://deepbl.erc.monash.edu.au/.

Antibiotic resistance and virulence of Escherichia coli strains isolated from animal rendering plant

Processing of animal carcasses and other animal wastes in rendering plants is a significant source of antibiotic resistant microorganisms. The main goal of this study was to investigate the resistance to 18 antibacterial agents including β-lactams, fluoroquinolones, colistin and virulence factors (iss, tsh, cvaC, iutA, papC, kps and ibeA genes) in 88 Escherichia coli strains isolated from a rendering plant over 1 year period. ESBL (Extended-spectrum beta-lactamases) and plasmid-mediated Amp were screened by interpretative reading of MIC. ESBL phenotype was detected in 20.4% of samples and high level of resistance to fluoroquinolone was found in 27.2% of strains. Cephalosporinase CTX-M1, cephamycinase CMY-2, integrase 1 and transposon 3 genes were detected by PCR. Furthermore, there were found three CMY-2 producing E. coli with O25b-ST131, resistant to the high level of enrofloxacin and containing the gene encoding the ferric aerobactin receptor (iutA). One enrofloxacin resistant E. coli strain possessed iss, ibeA, kps and papC virulence genes also with CMY-2, integrase1 and Tn3. ST131 E. coli with CMY-2 has a zoonotic potential and presents a serious health risk to humans.

The use of aminoglycosides in animals within the EU: development of resistance in animals and possible impact on human and animal health: a review

Aminoglycosides (AGs) are important antibacterial agents for the treatment of various infections in humans and animals. Following extensive use of AGs in humans, food-producing animals and companion animals, acquired resistance among human and animal pathogens and commensal bacteria has emerged. Acquired resistance occurs through several mechanisms, but enzymatic inactivation of AGs is the most common one. Resistance genes are often located on mobile genetic elements, facilitating their spread between different bacterial species and between animals and humans. AG resistance has been found in many different bacterial species, including those with zoonotic potential such as Salmonella spp., Campylobacter spp. and livestock-associated MRSA. The highest risk is anticipated from transfer of resistant enterococci or coliforms (Escherichia coli) since infections with these pathogens in humans would potentially be treated with AGs. There is evidence that the use of AGs in human and veterinary medicine is associated with the increased prevalence of resistance. The same resistance genes have been found in isolates from humans and animals. Evaluation of risk factors indicates that the probability of transmission of AG resistance from animals to humans through transfer of zoonotic or commensal foodborne bacteria and/or their mobile genetic elements can be regarded as high, although there are no quantitative data on the actual contribution of animals to AG resistance in human pathogens. Responsible use of AGs is of great importance in order to safeguard their clinical efficacy for human and veterinary medicine.

The Gut Microbiota of the Egyptian Mongoose as an Early Warning Indicator of Ecosystem Health in Portugal

The Egyptian mongoose is a carnivore mammal species that in the last decades experienced a tremendous expansion in Iberia, particularly in Portugal, mainly due to its remarkable ecological plasticity in response to land-use changes. However, this species may have a disruptive role on native communities in areas where it has recently arrived due to predation and the potential introduction of novel pathogens. We report reference information on the cultivable gut microbial landscape of widely distributed Egyptian mongoose populations (Herpestes ichneumon, n = 53) and related antimicrobial tolerance across environmental gradients. The panel of isolated species is consistent with the typical protein-based diet of a carnivore: Firmicutes predominate (89% of individuals), while Clostridiales, Enterobacteriales, and Lactobacillales are the major classes. Forty-one individuals (77.4%) harbour Clostridium spp. A spatial influence on mongooses’ microbiota is confirmed by nonmetric multidimensional scaling analysis, with a significant contribution of municipality to their microbiota composition. Antimicrobial susceptibility testing of mongoose commensal bacteria to 28 compounds evidences xenobiotic tolerance of Escherichia coli (E. coli), enterococci, Salmonella Spartel and Mbandaka serotypes and Pseudomonas bacteria, among others. The common isolation of antimicrobial tolerant microbiota from the mongoose’s gut suggests this species is exposed to anthropogenic influence and is affected by forestry and agricultural-related practices, reflecting its easy adaptation to ecological gradients across agroecosystems. We thus propose regular microbial and phenotypic resistance profiling of widely distributed mongooses as a sentinel tool for xenobiotics’ lifecycle and ecosystem health in Portugal.

Recommendations of the Spanish Antibiogram Committee (COESANT) for selecting antimicrobial agents and concentrations for in vitro susceptibility studies using automated systems

Automated antimicrobial susceptibility testing devices are widely implemented in clinical microbiology laboratories in Spain, mainly using EUCAST (European Committee on Antimicrobial Susceptibility Testing) breakpoints. In 2007, a group of experts published recommendations for including antimicrobial agents and selecting concentrations in these systems. Under the patronage of the Spanish Antibiogram Committee (Comité Español del Antibiograma, COESANT) and the Study Group on Mechanisms of Action and Resistance to Antimicrobial Agents (GEMARA) from the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), and aligned with the Spanish National Plan against Antimicrobial Resistance (PRAN), a group of experts have updated this document. The main modifications from the previous version comprise the inclusion of new antimicrobial agents, adaptation of the ranges of concentrations to cover the EUCAST breakpoints and epidemiological cut-off values (ECOFFs), and the inference of new resistance mechanisms. This proposal should be considered by different manufacturers and users when designing new panels or cards. In addition, recommendations for selective reporting are also included. With this approach, the implementation of EUCAST breakpoints will be easier, increasing the quality of antimicrobial susceptibility testing data and their microbiological interpretation. It will also benefit epidemiological surveillance studies as well as the clinical use of antimicrobials aligned with antimicrobial stewardship programs.

A pilot study using environmental screening to determine the prevalence of Mycobacterium avium subspecies paratuberculosis (MAP) and antimicrobial resistance (AMR) in Irish cattle herds

Background

Dairy and beef cattle can be reservoirs of many pathogens, including Salmonella and Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne’s disease (JD). Farm environments may provide potential entry points for the transmission of infectious agents into the food chain. Antibiotics are used to treat a wide variety of infections on farms, and administration of antimicrobial agents to cattle is considered to be a driving factor for antimicrobial resistance (AMR). Control of JD and AMR are priority for animal health initiatives in Ireland. A national JD pilot programme was introduced by Animal Health Ireland in 2014, while the national action plan launched by Department of Health and Department of Agriculture, Food and Marine introduced in 2017 aims to improve the surveillance of AMR. The current investigation was undertaken as a pilot study to determine the proportion of herds positive for MAP, Salmonella species (Salmonella spp), commensal Escherichia coli (E. coli), Extended-spectrum beta-lactamase (ESBL) AmpC β-lactamase and carbapenemase-producing E. coli from 157 environmental faecal samples in Irish farms.

Results

MAP was detected in 10.2% of samples collected; on culture in 4 (4.9%) of the dairy herds and from 1 (1.3%) of the beef/suckler herds, and by PCR in 10 (12.3%) and 6 (7.9%) of these herds respectively. All culture positive herds were also positive by PCR. An additional 11 herds were positive by PCR only. Salmonella was not detected, while commensal E. coli were isolated from 70.7% of the samples (111/157) with 101 of these isolates shown to be fully susceptible to all antimicrobials tested. Of the 27 presumptive ESBL AmpC β-lactamase producing E. coli detected, one isolate was resistant to ten antimicrobials, nine isolates were resistant to nine antimicrobials, and four isolates were resistant to eight antimicrobials. Carbapenemase-producing E. coli were not isolated.

Conclusions

The results highlight the importance of monitoring farm environments for Johne’s disease. This disease is a growing concern for dairy and beef producers in Ireland, and sampling the farm environment may offer a useful means to rapidly screen for the presence of MAP. Non-pathogenic common enteric commensal and multiple-drug-resistant E. coli may contribute to AMR acting as a reservoir and transferring resistance to other species/pathogens in the environment.

Quantification and Multidrug Resistance Profiles of Vancomycin-Resistant Enterococci Isolated from Two Wastewater Treatment Plants in the Same Municipality

Wastewater treatment plants (WWTPs) are points of control for the environmental dissemination of antimicrobial resistant bacteria. Vancomycin-resistant enterococci (VRE) were used as indicators of antimicrobial resistance (AMR) in two WWTPs (biologically aerated filter (BAF) and conventional activated sludge (CAS)) in the same municipality. The removal and abundance of enterococci and VRE as well as the species and antimicrobial resistance profiles of VRE were assessed. Enterococci and VRE from the primary and final effluents were enumerated. Results were assessed from an ecological context. VRE was not selected for by either WWTP but the BAF system outperformed the CAS system for the removal of enterococci/VRE. Enterococcus faecalis (n = 151), E. faecium (n = 94) and E. casseliflavus/E. gallinarum (n = 59) were the dominant VRE species isolated. A decrease in levofloxacin resistance in enterococci was observed in the BAF WWTP. An increase in nitrofurantoin resistant (p < 0.001) and a decrease in quinupristin/dalfopristin (p = 0.003) and streptomycin (p = 0.022) resistant enterococci were observed in the CAS WWTP, corresponding to a shift of VRE from E. faecalis to E. faecium. Wastewater treatment processes can be managed to limit the dissemination of antimicrobial resistance determinants into the surrounding environment.

Virulence and antibiotic resistance profile of avian Escherichia coli strains isolated from colibacillosis lesions in central of Algeria

Background and Aim

Avian pathogenic Escherichia coli cause extensive mortality in poultry flocks, leading to extensive economic losses. To date, in Algeria, little information has been available on virulence potential and antibiotics resistance of avian E. coli isolates. Therefore, the aim of this study was the characterization of virulence genes and antibiotic resistance profile of Algerian E. coli strains isolated from diseased broilers.

Materials and Methods

In this study, 43 avian E. coli strains isolated from chicken colibacillosis lesions at different years were analyzed to determine their contents in 10 virulence factors by polymerase chain reaction, antimicrobial susceptibility to 22 antibiotics belonging to six different chemical classes and genomic diversity by pulsed-field gel electrophoresis (PFGE).

Results

Mainly E. coli isolates (58.1%) carried two at six virulence genes and the most frequent virulence gene association detected were ompT (protectin), hlyF (hemolysin) with 55.8% (p<0.001), and iroN, sitA (iron acquisition/uptake systems), and iss (protectin) with 41.8% (p<0.001). Some strains were diagnosed as virulent according to their virulence gene profile. Indeed, 23.25% of the isolates harbored iroN, ompT, hlyF, iss, and sitA combination, 14% ompT, hlyF, and frz_orf4 (sugar metabolism), and 11,6% iroN, hlyF, ompT, iss, iutA (iron acquisition/uptake systems), and frz _orf4. The chicken embryo lethality assay performed on five isolates confirmed the potential virulence of these strains. All isolates submitted to PFGE analysis yielded different genetic profiles, which revealed their diversity. Overall, 97.2% of the isolates were resistant to at least one antibiotic and 53.5% demonstrated multi-antimicrobial resistance to three different antimicrobial classes. The highest resistance levels were against nalidixic acid (83.4%), amoxicillin and ampicillin (83.3%), ticarcillin (80.5%), pipemidic acid (75%), and triméthoprim-sulfamethoxazole (66.6%). For beta-lactam class, the main phenotype observed belonged to broad-spectrum beta-lactamases. However, extended-spectrum beta-lactamase associated with three at six virulence factors was also detected in 13 isolates. Two of them were attested virulent as demonstrated in the embryo lethality test which constitutes a real public threat.

Conclusion

It would be imperative in avian production to discourage misuse while maintaining constant vigilance guidelines and regulations, to limit and rationalize antimicrobial use.

An outbreak of ST307 extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae in a rehabilitation center: An unusual source and route of transmission

OBJECTIVE

Nosocomial outbreaks due to multidrug-resistant microorganisms in rehabilitation centers have rarely been reported. We report an outbreak of extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae (ESBL-K. pneumoniae) on a single ward in a rehabilitation center in Rotterdam, The Netherlands.

DESIGN

Outbreak description.

SETTING

A 40-bed ward of a rehabilitation center in the Netherlands.

METHODS

In October 2016, 2 patients were found to be colonized by genetically indistinguishable ESBL-K. pneumoniae isolates. Therefore, an outbreak management team was installed, by whom a contact tracing plan was made. In addition to general outbreak measures, specific measures were formulated to allow continuation of the rehabilitation process. Also, environmental cultures were taken. Multiple-locus variable-number tandem-repeat analysis and amplification fragment-length polymorphism were used to determine strain relatedness. Selected isolates were subjected to whole-genome multilocus sequence typing.

RESULTS

The outbreak lasted 8 weeks. In total, 14 patients were colonized with an ESBL-K. pneumoniae, of whom 11 patients had an isolate belonging to sequence type 307. Overall, 163 environmental cultures were taken. Several sites of a household washing machine were repeatedly found to be contaminated with the outbreak strain. This machine was used to wash lifting slings and patient clothing contaminated with feces. The outbreak was contained after taking the machine temporarily out of service and implementing a reinforced and adapted protocol on the use of this machine.

CONCLUSION

We conclude that in this outbreak, the route of transmission of the outbreak strain via the household washing machine played a major role.

Structural Insights into Catalytic Relevances of Substrate Poses in ACC-1

ACC-1 is a plasmid-encoded class C β-lactamase identified in clinical isolates of Klebsiella pneumoniae, Proteus mirabilis, Salmonella enterica, and Escherichia coli ACC-1-producing bacteria are susceptible to cefoxitin, whereas they are resistant to oxyimino cephalosporins. Here, we depict crystal structures of apo ACC-1, adenylylated ACC-1, and acylated ACC-1 complexed with cefotaxime and cefoxitin. ACC-1 has noteworthy structural alterations in the R2 loop, the Ω loop, and the Phe119 loop located along the active-site rim. The adenylate covalently bonded to the nucleophilic serine reveals a tetrahedral phosphorus mimicking the deacylation transition state. Cefotaxime in ACC-1 has a proper conformation for the substrate-assisted catalysis in that its C-4 carboxylate and N-5 nitrogen are adequately located to facilitate the deacylation reaction. In contrast, cefoxitin in ACC-1 has a distinct conformation, in which those functional groups cannot contribute to catalysis. Furthermore, the orientation of the deacylating water relative to the acyl carbonyl group in ACC-1 is unfavorable for nucleophilic attack.

Outbreaks of Serratia marcescens and Serratia rubidaea bacteremia in a central Kathmandu hospital following the 2015 earthquakes

Background

Human infections with Serratia spp. are generally limited to Serratia marcescens and the Serratia liquefaciens complex. There is little data regarding the infections caused by the remaining Serratia spp., as they are seldom isolated from clinical specimens.

Methods

In this health care setting in Kathmandu, Nepal routine blood culture is performed on all febrile patients with a temperature >38°C or when there is clinical suspicion of bacteremia. During 2015 we atypically isolated and identified several Serratia spp. We extracted clinical data from these cases and performed whole genome sequencing on all isolates using a MiSeq system (Ilumina, San Diego, CA, USA).

Results

Between June and November 2015, we identified eight patients with suspected bacteremia that produced a positive blood culture for Serratia spp., six Serratia rubidaea and five Serratia marcescens. The S. rubidaea were isolated from three neonates and were concentrated in the neonatal intensive care unit between June and July 2015. All patients were severely ill and one patient died. Whole genome sequencing confirmed that six Nepalese S. rubidaea sequences were identical and indicative of a single-source outbreak.

Conclusions

Despite extensive screening we were unable to identify the source of the outbreak, but the inferred timeline suggested that these atypical infections were associated with the aftermath of two massive earthquakes. We speculate that deficits in hygienic behavior, combined with a lack of standard infection control, in the post-earthquake emergency situation contributed to these unusual Serratia spp. outbreaks.

Recognizing and Overcoming Resistance to New Beta-Lactam/Beta-Lactamase Inhibitor Combinations

PURPOSE OF REVIEW

To describe the mechanisms and clinical relevance of emergent resistance to three recently introduced beta-lactamase inhibitor combinations (BLICs) active against resistant Gram-negative organisms: ceftolozane-tazobactam, ceftazidime-avibactam, and meropenem-vaborbactam.

RECENT FINDINGS

Despite their recent introduction into practice, clinical reports of resistance to BLICs among typically susceptible organisms have already emerged, in some cases associated with therapeutic failure. The resistance mechanisms vary by agent, including mutations in beta-lactamase active sites, upregulation of efflux pumps, and alterations in the structure or expression of porin channels. These changes may confer cross-resistance or, rarely, increased susceptibility to related agents. Clinicians need to be aware of the potential for initial or emergent resistance to BLICs and ensure appropriate antimicrobial susceptibility testing is performed. Dose optimization and novel combinations of agents may play a role in preventing and managing resistance. Recently approved BLICs have provided important new therapeutic options against resistant Gram-negative organisms, but are already coming up against emergent resistance. Awareness of the potential for resistance, early detection, and dose optimization may be important in preserving the utility of these agents.

Activity of ceftazidime/avibactam against problem Enterobacteriaceae and Pseudomonas aeruginosa in the UK, 2015-16

Background

Ceftazidime/avibactam combines an established oxyimino-cephalosporin with the first diazabicyclooctane β-lactamase inhibitor to enter clinical use. We reviewed its activity against Gram-negative isolates, predominantly from the UK, referred for resistance investigation in the first year of routine testing, beginning in July 2015.

Methods

Isolates were as received from referring laboratories; there is a bias to submit those with suspected carbapenem resistance. Identification was by MALDI-TOF mass spectroscopy, and susceptibility testing by BSAC agar dilution. Carbapenemase genes were sought by PCR; other resistance mechanisms were inferred using genetic data and interpretive reading.

Results

Susceptibility rates to ceftazidime/avibactam exceeded 95% for: (i) Enterobacteriaceae with KPC, GES or other Class A carbapenemases; (ii) Enterobacteriaceae with OXA-48-like enzymes; and (iii) for ESBL or AmpC producers, even when these had impermeability-mediated ertapenem resistance. Almost all isolates with metallo-carbapenemases were resistant. Potentiation of ceftazidime by avibactam was seen for 87% of ceftazidime-resistant Enterobacteriaceae with 'unassigned' ceftazidime resistance mechanisms, including two widely referred groups of Klebsiella pneumoniae where no synergy was seen between cephalosporins and established β-lactamase inhibitors. Potentiation here may be a diazabicyclooctane/cephalosporin enhancer effect. Activity was seen against Pseudomonas aeruginosa with derepressed AmpC, but not for those with efflux-mediated resistance.

Conclusions

Of the available β-lactams or inhibitor combinations, ceftazidime/avibactam has the widest activity spectrum against problem Enterobacteriaceae, covering all major types except metallo-carbapenemase producers; against P. aeruginosa it has a slightly narrower spectrum than ceftolozane/tazobactam, which also covers efflux-type resistance.

Preliminary readings of antimicrobial susceptibility panels: A simple, fast and inexpensive way to detect bacterial resistance and enhance antibiotic treatment of bloodstream infections

Increasing incidence of resistant bacteria needs faster identification (ID) and antibiotic susceptibility testing (AST) in order to improve antimicrobial treatment of severe infections. We propose a preliminary reading of the AST MicroScan® panels coupled with mass spectrometry ID. A total of 157 bacterial clinical isolates were processed for routine ID and AST (in 22 cases, ID and AST were performed directly from positive blood culture bottles). For gram-negatives, data from the initial and final readings were recorded and compared [89.9% category agreement (CA), 6.9% very major errors (VME)]. In adition all the 32 ESBL producers were detected at 5.3-8.6 hours. For Staphylococcus aureus, all the 16 MRSA isolates were detected at 4.5 to 7.5 hours. Thus, we find our preliminary readings approach as a simple, inexpensive and reliable way to detect and identify the most prevalent resistant bacteria in our institution on the same day that ID/AST is performed.

Serratia marcescens Infections in Neonatal Intensive Care Units (NICUs)

Serratia marcescens belongs to the family Enterobacteriaceae, which is commonly found in water, soil, animals, insects, plants. Although S. marcescens displays relatively low virulence, it causes nosocomial infections and outbreaks in severely immunocompromised or critically ill patients, particularly in settings such as intensive care units (ICUs), especially neonatal units (NICUs). This microorganism gives rise to a wide range of clinical manifestations in newborns: from asymptomatic colonization to keratitis, conjunctivitis, urinary tract infections, pneumonia, surgical wound infections, sepsis, bloodstream infection and meningitis. The most frequent site of infection is the bloodstream, followed by the respiratory apparatus and the gastrointestinal tract. Strains of S. marcescens involved in epidemic events have frequently proved to be multi-resistant. Indeed, this species displays intrinsic resistance to several classes of antibiotics. Often, the specific source of the infection cannot be identified. However, the contaminated hands of healthcare workers are believed to be a major vehicle of its transmission. In neonatal intensive care units, colonized or infected newborns are the main potential source of S. marcescens, particularly in the respiratory apparatus, but also in the gastrointestinal tract. The early identification of colonized or infected patients and the prompt implementation of infection control measures, particularly rigorous hand hygiene and contact precautions, are essential in order to curb the spread of infection.

Detection of carbapenem resistance genes in Pseudomonas aeruginosa isolates with several phenotypic susceptibility profiles

Introduction: Pseudomonas aeruginosa display several resistance mechanisms to carbapenems and such variety makes it difficult to infer from the antibiogram. The aim of this study was to determine the carbapenem resistance genes in P. aeruginosa isolates with different profiles of phenotypic susceptibility to these antibiotics. Materials and methods: From a microbial collection of P. aeruginosa isolates from infected patients, 40 isolates with different carbapenem resistance profiles were selected. The carbapenemases genes, and expression of the OprD porin, the MexAB-OprM efflux pump and the β-lactamase AmpC were determined. Results: From a total of 40 isolates evaluted, in 21 (52.5%) any mechanism of resistance evaluated were detected. In the meropenem-resistant group, overexpression of AmpC (n = 1) and decreased expression of MexAB-OprM (n = 2) and OprD (n = 1) were found. A decrease in the expression of MexAB-OprM was observed in imipenem-resistant group (n = 3) and mutations in the gene encoding the OprD porin (n = 1). Finally, the presence of carbapenemases (VIM, n= 3, KPC-2 / VIM, n = 1) was detected in imipenem-meropenem resistant isolates. Conclusion: The phenotypic susceptibility profiles in P. aeruginosa isolates were not explained by the molecular mechanisms explored, with the exception of carbapenemase-producing isolates. These results evidence the complexity of the antibiotic resistance mechanisms involved in this bacterium.

Increasing Prevalence of Group III Penicillin-Binding Protein 3 Mutations Conferring High-Level Resistance to Beta-Lactams Among Nontypeable Haemophilus influenzae Isolates from Children in Korea

This study investigated the roles of β-lactamase and penicillin-binding protein 3 (PBP3) alterations in the development of recent antimicrobial resistance in nontypeable Haemophilus influenzae (NTHi) isolated from Korean children. Nasopharyngeal NTHi isolates from children at a tertiary children's hospital were tested for antimicrobial susceptibility using E-test. β-lactamase production was screened by the paper disc test, and polymerase chain reaction amplification of bla_TEM and bla_ROB-1 was performed. The ftsI gene was amplified to identify PBP3 alteration. Of the 53 NTHi isolates, 69.8% were ampicillin nonsusceptible. The nonsusceptibility rates for cefaclor were 81.1%, cefpodoxime 69.8%, and amoxicillin/clavulanate 32.1%. About 60.3% and 32.1% of the isolates were genetically β-lactamase-nonproducing ampicillin-resistant (gBLNAR) and genetically β-lactamase-producing amoxicillin/clavulanate-resistant (gBLPACR) strains, respectively. Group III amino acid substitutions comprised 65.6% of the gBLNAR strains and 70.6% of the gBLPACR strains. MIC₅₀ for amoxicillin/clavulanate, cefaclor, cefuroxime, cefpodoxime, and cefixime were more than 2-80 times higher in the gBLNAR and gBLPACR strains compared with gBLPAR strains. Group III gBLNAR strains had significantly higher ampicillin, amoxicillin/clavulanate, cefpodoxime, and cefixime minimum inhibitory concentrations than group II strains. Group III gBLNAR and gBLPACR NTHi strains are highly prevalent in Korea, raising the alarm about increasing β-lactam resistance in NTHi.

Activity of RX-04 Pyrrolocytosine Protein Synthesis Inhibitors against Multidrug-Resistant Gram-Negative Bacteria

Pyrrolocytosines RX-04A to -D are designed to bind to the bacterial 50S ribosomal subunit differently from currently used antibiotics. The four analogs had broad anti-Gram-negative activity: RX-04A-the most active analog-inhibited 94.7% of clinical Enterobacteriaceae, Acinetobacter baumannii, and Pseudomonas aeruginosa at 0.5 to 4 μg/ml, with no MICs of >8 μg/ml. MICs for multidrug-resistant (MDR) carbapenemase producers were up to 2-fold higher than those for control strains; values were highest for one Serratia isolate with porin and efflux lesions. mcr-1 did not affect MICs.

Bacteriuria is not associated with surgical site infection in patients undergoing cardiovascular surgery

BACKGROUND

Despite absence of evidence, in practice, asymptomatic bacteriuria is perceived as a risk factor for surgical site infection (SSI) among patients with cardiac surgery. We aimed to identify whether an association exists between the preoperative presence of asymptomatic bacteriuria or urinary tract infection and SSI in patients undergoing cardiovascular surgery.

METHODS

This is an analytical study with a retrospective cohort of patients undergoing coronary revascularization or valve replacement surgery. We identified cases of bacteriuria, urinary tract infection, and cardiovascular SSI and adjusted the results according to exposure to antibiotics and known risk factors for SSI using a multivariate logistic regression analysis.

RESULTS

A total of 840 patients were included in the study, of whom 33 (3.9%) had asymptomatic bacteriuria and 13 (1.5%) had urinary tract infections. The incidence of SSI was 9.5% (80 patients), with 2.3% of cases having mediastinitis. In the multivariate analysis, asymptomatic bacteriuria (relative risk, 0.83; 95% confidence interval, 0.26-2.56; P = .74) and urinary tract infection (relative risk, 2.54; 95% confidence interval, 0.60-10.69; P = .20) were not risk factors for SSI. Traditional risk factors were found to increase the risk of SSI.

CONCLUSIONS

The presence of bacteriuria is not a risk factor for presenting SSI in cardiovascular surgery. Screening with urinalysis or urine culture would not be recommended for patients undergoing cardiac surgery.

Activity of ceftolozane/tazobactam against surveillance and 'problem' Enterobacteriaceae, Pseudomonas aeruginosa and non-fermenters from the British Isles

Background

We assessed the activity of ceftolozane/tazobactam against consecutive isolates collected in the BSAC Bacteraemia Surveillance from 2011 to 2015 and against 'problem' isolates sent to the UK national reference laboratory from July 2015, when routine testing began.

Methods

Susceptibility testing was by BSAC agar dilution with resistance mechanisms identified by PCR and interpretive reading.

Results

Data were reviewed for 6080 BSAC surveillance isolates and 5473 referred organisms. Ceftolozane/tazobactam had good activity against unselected ESBL producers in the BSAC series, but activity was reduced against ertapenem-resistant ESBL producers, which were numerous among reference submissions. AmpC-derepressed Enterobacter spp. were widely resistant, but Escherichia coli with raised chromosomal AmpC frequently remained susceptible, as did Klebsiella pneumoniae with acquired DHA-1-type AmpC. Carbapenemase-producing Enterobacteriaceae were mostly resistant, except for ceftazidime-susceptible isolates with OXA-48-like enzymes. Ceftolozane/tazobactam was active against 99.8% of the BSAC Pseudomonas aeruginosa isolates; against referred P. aeruginosa it was active against 99.7% with moderately raised efflux, 94.7% with strongly raised efflux and 96.6% with derepressed AmpC. Resistance in P. aeruginosa was largely confined to isolates with metallo-β-lactamases (MBLs) or ESBLs. MICs for referred Burkholderia spp. and Stenotrophomonas maltophilia were 2-4-fold lower than those of ceftazidime.

Conclusions

Ceftolozane/tazobactam is active against ESBL-producing Enterobacteriaceae; gains against other problem Enterobacteriaceae groups were limited. Against P. aeruginosa it overcame the two most prevalent mechanisms (up-regulated efflux and derepressed AmpC) and was active against 51.9% of isolates non-susceptible to all other β-lactams, rising to 80.9% if ESBL and MBL producers were excluded.

Clonality, virulence and antimicrobial resistance of enteroaggregative Escherichia coli from Mirzapur, Bangladesh

Purpose

This study investigates the virulence and antimicrobial resistance in association with common clonal complexes (CCs) of enteroaggregative Escherichia coli (EAEC) isolated from Bangladesh. The aim was to determine whether specific CCs were more likely to be associated with putative virulence genes and/or antimicrobial resistance.

Methodology

The presence of 15 virulence genes (by PCR) and susceptibility to 18 antibiotics were determined for 151 EAEC isolated from cases and controls during an intestinal infectious disease study carried out between 2007–2011 in the rural setting of Mirzapur, Bangladesh (Kotloff KL, Blackwelder WC, Nasrin D, Nataro JP, Farag TH et al.Clin Infect Dis 2012;55:S232–S245). These data were then analysed in the context of previously determined serotypes and clonal complexes defined by multi-locus sequence typing.

Results

Overall there was no association between the presence of virulence or antimicrobial resistance genes in isolates of EAEC from cases versus controls. However, when stratified by clonal complex (CC) one CC associated with cases harboured more virulence factors (CC40) and one CC harboured more resistance genes (CC38) than the average. There was no direct link between the virulence gene content and antibiotic resistance. Strains within a single CC had variable virulence and resistance gene content indicating independent and multiple gene acquisitions over time.

Conclusion

In Bangladesh, there are multiple clonal complexes of EAEC harbouring a variety of virulence and resistance genes. The emergence of two of the most successful clones appeared to be linked to either increased virulence (CC40) or antimicrobial resistance (CC38), but increased resistance and virulence were not found in the same clonal complexes.

Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease

Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle mortality in the United States. Whole-genome sequencing offers a culture-independent alternative to current bacterial identification methods, but requires a library of bacterial reference genomes for comparison. To contribute new bacterial genome assemblies and evaluate genetic diversity and variation in antimicrobial resistance genotypes, whole-genome sequencing was performed on bovine respiratory disease–associated bacterial isolates (Histophilus somni, Mycoplasma bovis, Mannheimia haemolytica, and Pasteurella multocida) from dairy and beef cattle. One hundred genomically distinct assemblies were added to the NCBI database, doubling the available genomic sequences for these four species. Computer-based methods identified 11 predicted antimicrobial resistance genes in three species, with none being detected in M. bovis. While computer-based analysis can identify antibiotic resistance genes within whole-genome sequences (genotype), it may not predict the actual antimicrobial resistance observed in a living organism (phenotype). Antimicrobial susceptibility testing on 64 H. somni, M. haemolytica, and P. multocida isolates had an overall concordance rate between genotype and phenotypic resistance to the associated class of antimicrobials of 72.7% (P < 0.001), showing substantial discordance. Concordance rates varied greatly among different antimicrobial, antibiotic resistance gene, and bacterial species combinations. This suggests that antimicrobial susceptibility phenotypes are needed to complement genomically predicted antibiotic resistance gene genotypes to better understand how the presence of antibiotic resistance genes within a given bacterial species could potentially impact optimal bovine respiratory disease treatment and morbidity/mortality outcomes.

In vitro susceptibility and resistance phenotypes in contemporary Enterobacter isolates in a university hospital in Crete, Greece

Aim: To study the evolution in the susceptibility of Enterobacter spp. in Crete, Greece from 2010 to 2015. Methods: Non-duplicate isolates were studied using automated systems. Phenotypic confirmatory tests were applied. Results: A total of 939 Enterobacter isolates were included. Colistin was the most active antibiotic (97.9%) followed by imipenem (96.1%), gentamicin (95.7%), tigecycline (91.8%), cefepime (89.4%), chloramphenicol (85.8%), fosfomycin (85.5%), trimethoprim/sulfamethoxazole (83.3%) and piperacillin/tazobactam (73.3%). Antibiotic resistance did not increase during the study period for most antibiotics. Lower susceptibility was observed among multidrug-resistant strains and carbapenem-nonsusceptible isolates. AmpC was the most common resistant mechanism (21%); carbapenemases (3.7%) and aminoglycoside-modifying enzymes (6.5%) were also detected. Conclusion: A significant proportion of Enterobacter spp. was resistant to several antibiotics, most notably β-lactams.

In-vitro activity of several antimicrobial agents against methicillin-resistant Staphylococcus aureus (MRSA) isolates expressing aminoglycoside-modifying enzymes: potency of plazomicin alone and in combination with other agents

This study investigated the in-vitro activity of clinically relevant aminoglycosides and new antimicrobial agents-plazomicin, ceftobiprole and dalbavancin-against 55 methicillin-resistant Staphylococcus aureus (MRSA) isolates producing aminoglycoside-modifying enzymes (AMEs). The checkerboard method was used to assess synergism between plazomicin and four antibiotics (fosfomycin, ceftobiprole, cefoxitin and meropenem), and time-kill assays were performed for the most active combinations. Among the aminoglycosides tested, plazomicin was the most active agent against MRSA, with >90% of isolates being inhibited at a minimum inhibitory concentration (MIC) of ≤1 mg/L. MIC₅₀ and MIC₉₀ values for ceftobiprole and dalbavancin were 2 and 4 mg/L, and 0.125 and 0.125 mg/L, respectively. The most prevalent AME gene was aac(6')Ie-aph(2″)Ia (87.3%), followed by ant(4')Ia (52.7%) and aph(3')IIIa (52.7%). Plazomicin activity was not affected by the type or number of enzymes detected. In checkerboard and time-kill assays, indifference was the most common result achieved for the antibiotic combinations. Notably, no antagonism was observed with any combination tested. Overall, plazomicin in combination with meropenem had the highest synergistic effect, demonstrating synergy against seven isolates in the checkerboard assay and three isolates in time-kill curves. In conclusion, plazomicin showed potent activity against aminoglycoside-resistant MRSA isolates, regardless of the number and type of AMEs present. These findings indicate the potential utility of plazomicin in combination with meropenem for the treatment of MRSA infections.

Antibiogramj: A tool for analysing images from disk diffusion tests

BACKGROUND AND OBJECTIVES

Disk diffusion testing, known as antibiogram, is widely applied in microbiology to determine the antimicrobial susceptibility of microorganisms. The measurement of the diameter of the zone of growth inhibition of microorganisms around the antimicrobial disks in the antibiogram is frequently performed manually by specialists using a ruler. This is a time-consuming and error-prone task that might be simplified using automated or semi-automated inhibition zone readers. However, most readers are usually expensive instruments with embedded software that require significant changes in laboratory design and workflow.

METHODS

Based on the workflow employed by specialists to determine the antimicrobial susceptibility of microorganisms, we have designed a software tool that, from images of disk diffusion tests, semi-automatises the process. Standard computer vision techniques are employed to achieve such an automatisation.

RESULTS

We present AntibiogramJ, a user-friendly and open-source software tool to semi-automatically determine, measure and categorise inhibition zones of images from disk diffusion tests. AntibiogramJ is implemented in Java and deals with images captured with any device that incorporates a camera, including digital cameras and mobile phones. The fully automatic procedure of AntibiogramJ for measuring inhibition zones achieves an overall agreement of 87% with an expert microbiologist; moreover, AntibiogramJ includes features to easily detect when the automatic reading is not correct and fix it manually to obtain the correct result.

CONCLUSIONS

AntibiogramJ is a user-friendly, platform-independent, open-source, and free tool that, up to the best of our knowledge, is the most complete software tool for antibiogram analysis without requiring any investment in new equipment or changes in the laboratory.

Microbiological Quality and Prevalence of β-Lactam Antibiotic Resistance Genes in Oysters ( Crassostrea rhizophorae )

The microbiological quality of oysters reflects the microbiological quality of their habitats because they are filter feeders. The objective of this study was to assess the bacterial composition of the edible oyster Crassostrea rhizophorae in urban and preserved estuaries. Particularly, we assessed the presence of pathogenic bacteria, investigated antibiotic susceptibility in bacterial isolates, and quantified β-lactam antibiotic resistance genes (bla_TEM, bla_SHV, and bla_KPC) via quantitative PCR of oyster DNA. Our results detected total coliforms, Escherichia coli , and enterobacteria in the oysters from urban estuaries, which is indicative of poor water quality. In addition, our detection of the eaeA and stxA2 virulence genes in 16.7% of E. coli isolates from oysters from this region suggests the presence of multiantibiotic-resistant enteropathogenic and enterohemorrhagic E. coli strains. During periods of low precipitation, increased contamination by E. coli (in winter) and Vibrio parahaemolyticus (in autumn) was observed. In contrast, cultivated oysters inhabiting monitored farms in preserved areas had low levels of bacterial contamination, emphasizing that oyster culture monitoring enhances food quality and makes oysters fit for human consumption. Distinct antibiotic resistance profiles were observed in bacteria isolated from oysters collected from different areas, including resistance to β-lactam antibiotics. The presence of the bla_TEM gene in 91.3% of oyster samples indicated that microorganisms in estuarine water conferred the capability to produce β-lactamase. To our knowledge, this is the first study to directly quantify and detect β-lactam antibiotic resistance genes in oysters. We believe our study provides baseline data for bacterial dynamics in estuarine oysters; such knowledge contributes to developing risk assessments to determine the associated hazards and consequences of consuming oysters from aquatic environments containing pathogenic bacteria that may possess antibiotic resistance genes.

Towards better antimicrobial susceptibility testing: impact of the Journal of Antimicrobial Chemotherapy

Susceptibility testing of bacteria is one of the most important tests performed in a clinical microbiology laboratory. Improvements in laboratory techniques, especially the move towards standardized susceptibility testing, has provided better consistency and accuracy of testing. When used in conjunction with the most recently developed interpretative criteria, the result is better prediction of the outcome of antimicrobial therapy for infected patients. Throughout the last four decades this Journal has published numerous articles evidencing improvements and new techniques, a valuable source of information for microbiology laboratories.