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Changes in hospitals’ daily practice due to COVID-19 pandemic may have an impact on antimicrobial resistance (AMR). We aimed to assess this possible impact as captured by the Greek Electronic System for the Surveillance of Antimicrobial Resistance (WHONET-Greece). Routine susceptibility data of 17,837 Gram-negative and Gram-positive bacterial isolates from blood and respiratory specimens of hospitalized patients in nine COVID-19 tertiary hospitals were used in order to identify potential differences in AMR trends in the last three years, divided into two periods, January 2018–March 2020 and April 2020–March 2021. Interrupted time-series analysis was used to evaluate differences in the trends of non-susceptibility before and after the changes due to COVID-19. We found significant differences in the slope of non-susceptibility trends of Acinetobacter baumannii blood and respiratory isolates to amikacin, tigecycline and colistin; of Klebsiella pneumoniae blood and respiratory isolates to meropenem and tigecycline; and of Pseudomonas aeruginosa respiratory isolates to imipenem, meropenem and levofloxacin. Additionally, we found significant differences in the slope of non-susceptibility trends of Staphylococcus aureus isolates to oxacillin and of Enterococcus faecium isolates to glycopeptides. Assessing in this early stage, through surveillance of routine laboratory data, the way a new global threat like COVID-19 could affect an already ongoing pandemic like AMR provides useful information for prompt action.

Monophasic Salmonella typhimurium is of increasing importance worldwide. Here we present the available data regarding monophasic S. typhimurium from 2007 to 2019 in Greece, in order to assess its public health impact. Surveillance data, data on antimicrobial resistance, molecular typing by pulsed-field gel electrophoresis (PFGE), and results of the investigation of monophasic S. typhimurium outbreaks were analyzed. Overall, 403 cases were identified, 329 (81.6%) sporadic and 74 (18.4%) related to two community outbreaks in 2017. A total of 305 isolates from sporadic cases tested for antimicrobial resistance revealed resistance to ampicillin, streptomycin, sulphamethoxazole, and tetracycline (41.3%). Some 23.3% were further resistant to trimethoprim and 5.2% were also resistant to chloramphenicol. Outbreak 1 in 2017 with 37 identified cases was attributed to the consumption of raw milk from a vending machine and isolates were resistant to ampicillin, streptomycin, sulphamethoxazole, tetracycline, and trimethoprim. Outbreak 2 also with 37 cases was attributed to the consumption of pork and isolates were resistant to the five above mentioned antibiotics plus chloramphenicol. The number of human monophasic S. typhimurium isolates is low, however, since 2009, it has been among the five most frequently identified serotypes in Greece. Investigation of the outbreaks revealed that other vehicles apart from pork may be implicated in the occurrence of outbreaks.

Background Antimicrobial resistance (AMR) changes over time and continuous monitoring provides insight on trends to inform both empirical treatment and public health action. Aims To survey trends in relative isolation frequency (RIF) and AMR among key bloodstream pathogens using data from the Greek Electronic System for the Surveillance of AMR (WHONET-Greece). Methods This observational study looked into routine susceptibility data of 50,488 blood culture isolates from hospitalised patients in 25 tertiary hospitals, participating in the WHONET-Greece for trends over time between January 2010 and December 2017. Only the first isolate per species from each patient was included. Hospital wards and intensive care units (ICUs) were analysed separately. Results During the study, the RIF of Acinetobacter baumannii increased in wards, as did the proportion of A. baumannii isolates, which were non-susceptible to most antibiotics in both wards and ICUs. Coincidently, Klebsiella pneumoniae RIF declined while the respective rates of non-susceptible isolates to carbapenems and gentamicin increased. Pseudomonas aeruginosa RIF remained stable but decreasing proportions of non-susceptible isolates to all studied antibiotics, except imipenem were observed. Escherichia coli RIF increased as did the proportion of isolates non-susceptible to third-generation cephalosporins, carbapenems and fluoroquinolones. Concerning Staphylococcus aureus, a decline in the percentage of meticillin resistant isolates in ICUs was found, while the percentages of Enterococcus faecium isolates with non-susceptibility to vancomycin stayed stable. Conclusions Recognising these trends over time is important, since the epidemiology of AMR is complex, involving different ‘bug and drug’ combinations. This should be taken into consideration to control AMR.

The objective of the study is to report a multidrug-resistant outbreak of Providencia stuartii that occurred in inpatients in the Athens area in 2012 resulting from a very successful transmissible A/C multidrug-resistant plasmid. Thirteen multidrug-resistant P. stuartii clinical isolates from 5 hospitals were studied. Molecular typing was performed by pulsed-field gel electrophoresis. Antibiotic resistance genes and their genetic surround were detected by PCR and sequencing. Plasmid analysis included conjugation experiments using liquid cultures, sizing by S1 digestion, and incompatibility replicon typing by PCR. Isolates were grouped into 2 distinct clonal types A and B, exhibiting similarity less than 70%. Isolates of type A were recovered from patients hospitalized in 4 different hospitals with no obvious epidemiological linkage, while isolates of type B were recovered from patients treated in a single hospital. Both clonal types harbored a conjugative plasmid of 130 bp and IncA/C replicon type carrying 5 β-lactamase genes bla(SHV-5), bla(VEB-1), bla(VIM-1), bla(OXA-10), and bla(TEM-1) and aminoglycosides resistant determinants. All β-lactamase genes were included in stable structures as IS26, IS1999, and In-e541. The current plasmid seemed to have many common determinants with previously reported plasmids derived from P. stuartii and Proteus mirabilis clinical isolates and exhibited the ability to circulate in nosocomial bacterial populations.

We describe the outbreak of a pan-susceptible Klebsiella pneumoniae strain in a neonatal intensive care unit. A total of 7 neonates developed bacteraemia (37% attack rate), of whom 3 died (43% case fatality rate). A birth weight < 1500 g was the only statistically significant risk factor. Despite an extensive environmental investigation, the source was not identified.

Eleven Salmonella spp. isolates with the antigenic type 11:z41:e,n,z15 - not referred to in the 9th edition of the White-Kauffman–Le Minor Scheme - were identified at the National Reference Laboratory for Salmonella in Greece. Their pulsed-field gel electrophoresis profiles were indistinguishable. No apparent epidemiological link has yet been identified; the results of a case–case study are pending.

Acquisition of carbapenemase-producing Klebsiella pneumoniae (CP-Kp) strains poses a major threat to critically ill patients. The objectives of this study were to describe the epidemiology of CP-Kp isolates as well as the clinical outcome associated with the corresponding infections and to identify risk factors for mortality of intensive care unit (ICU) patients in a Greek hospital. A prospective, observational study was conducted in a nine-bed general ICU over a 2-year period (April 2010–March 2012). Imipenem-resistant K. pneumoniae isolates recovered from clinical samples of ICU patients were prospectively collected and studied for the presence of carbapenemases. Isolates were submitted to molecular typing using pulsed-field gel electrophoresis (PFGE). In total, 61 CP-Kp isolates (48 KPC-producers and 13 VIM-producers) were recovered from 58 ICU patients. The majority of KPC-producers were classified into a single PFGE type, indicating potent clonal dissemination. Among the 32 infected patients, bacteraemia was diagnosed in 16. Tigecycline + colistin was the most common combination antimicrobial regimen. Infection-attributable mortality was 43.8%. Regarding mortality risk factors, non-survivors were older (P = 0.080), all of them presented with septic shock (P = 0.010) and they had higher Sepsis-related Organ Failure Assessment (SOFA) scores at infection onset (P = 0.004) compared with survivors. Appropriate definitive treatment and combination regimens were not associated with patient survival. In conclusion, CP-Kp infections are associated with limited treatment options and high in-hospital mortality. Effective measures for preventing dissemination of respective isolates in the hospital setting are required.

VIM-1-producing Klebsiella pneumoniae strains, increasingly isolated in Greece since 2002, constitute the majority of multiresistant clinical isolates of this species found in most Greek hospitals ([9][1]). Moreover, following reports on Klebsiella pneumoniae carbapenemase (KPC)-producing isolates

Recently, multiresistant Salmonella enterica serovar 1,4,[5],12:i:-, a monophasic variant of S. Typhimurium (1,4,[5],12:i:1,2) emerged, and is now among the most common serovars isolated from humans in many countries. In Greece, monophasic Typhimurium which was recorded for the first time in human isolates in 2007 (0.3% of total isolates), increased sharply thereafter, and since 2009 is the third most frequent serovar. In the present study, 119 S. enterica 1,4,[5],12:i:- strains of human, animal and food origin, isolated during the period between 2006 and 2011, were examined. Strains verified as monophasic Typhimurium variants by polymerase chain reaction (PCR) (97 strains), were further characterised by phenotypic (antibiotic resistance and phage typing) and molecular (pulsed-field gel electrophoresis - PFGE) methods. The results indicate that multiple clones of multiresistant monophasic Typhimurium are circulating in Greece. The most frequently encountered clone in humans and pigs was that of phage type DT120, R-type ASSuTSpTm and PFGE profile STYMXB.0010, while in poultry other clones were detected. The data indicate that pigs may be a reservoir of this clone in Greece. .

Nosocomial infections and antibiotic resistance are regarded as critical issues both in clinical medicine as well as in Public health, thus understanding their epidemiology is a priority in the health sector. Our research aims at demonstrating that data mining techniques, such as regression, classification and association rules and assist in discovering interesting patterns in the epidemiological trends of antibiotic resistance in Greek Hospitals. In this work, we present a novel framework which integrates data from multiple hospitals and discovers association rules stored in a data warehouse. Furthermore, this data warehouse is used as a source for extracting interesting and valid predictions by applying techniques such as regression and classification. Our system is fully operational and treats real-world data from the WHONET, a software installed on the majority of Greek member hospitals of the ”Greek System for Surveillance of Antimicrobial Resistance” network. The contributions of the proposed framework are i. a standardized workflow for the seamless integration of data produced in various hospitals into a consistent data warehouse and b. the use of a mechanisms to predict hidden future behavior on large datasets, using regression and classification algorithms, which can provide significant surveillance warnings.

Objectives To follow the epidemic of KPC-2-producing Klebsiella pneumoniae in Greece. Methods KPC-2-producing isolates (n = 378) were collected during January 2009-April 2010 in 40 Greek hospitals. bla(KPC) and bla(VIM) were detected by PCR. Carbapenemase production was confirmed by spectrophotometry. Sequences flanking bla(KPC-2) and their plasmid carriers were studied. Isolates were typed by PFGE and multilocus sequence typing (MLST). Results All 378 isolates were bla(KPC-2) positive; 18 also carried bla(VIM-1/VIM-4). Higher isolation frequencies were observed in Athens and Crete. Isolates were classified into 13 PFGE types and 11 sequence types (STs). ST258 was predominant (n = 322), followed by ST147 (n = 20), ST383 (n = 9), ST133 (n = 6), ST274 (n = 4) and ST323 (n = 3). Of the remaining isolates, seven were distributed into five STs (11, 17, 340 and the novel 494 and 495) and seven were not typed. bla(KPC-2) could not be transferred from ST258 isolates, in contrast to isolates of ST17, ST133, ST147, ST274, ST494 and ST495. All bla(KPC-2)-encoding plasmids were of similar size (∼100 kb) and showed indistinguishable restriction fragment length polymorphism (RFLP) patterns except those from the ST340 isolates. Sequences flanking bla(KPC-2) revealed that the Tn4401a isoform was present in plasmids from all STs except ST340 containing Tn4401b. Co-production of VIM enzymes was observed in isolates of ST147, ST323 and ST383. Conclusions Apart from the epidemic of KPC-2-producing K. pneumoniae belonging to ST258 in Greece, diffusion of bla(KPC-2) to at least 10 additional STs has taken place. Notably, strains from three of the latter STs (147, 323 and 383) were found to carry both bla(KPC-2) and bla(VIM).

Staphylococcus aureus was isolated in 88 (30. 8%) of 286 adult patients suffering from various skin and soft-tissue infections examined in the outpatient department of a 650 bed tertiary-care hospital of Athens, Greece between January 2006 and December 2007. Twenty-seven (30.7%) of the S. aureus infections were caused by methicillin-resistant S. aureus (MRSA). All MRSA isolates were also resistant to tetracycline, fucidic acid and kanamycin, but were sensitive to gentamicin and tobramycin, as well as to to cotrimoxazole, chloramphenicol, quinolones, clindamycin and erythromycin. All isolates belonged to staphylococcal cassette chromosome mec elements (SCCmec) type IV, and were found to carry the lukF-PV and lukS genes coding for Panton-Valentine leukocidin (PVL). Pulsed-field gel electrophoresis (PFGE) and spa-typing revealed high genetic similarity among all MRSA isolates and with the PFGE pattern of the well-described ST80 clone that seems to be spreading through Europe. The high prevalence of MRSA among S. aureus infections in the community signify that empiric therapy in Greece, when clinically indicated, should exclude β-lactam antibiotics. Moreover, the establishment of an active screening for PVL-positive community-acquired (CA)-MRSA carriage and the adoption of a search and destroy strategy for CA-MRSA in all patients admitted with purulent skin and soft-tissue is of high priority in Greece as well as in all European countries which face high rates of CA-MRSA infection.

One of the most considerable functions in a hospital's infection control program is the surveillance of antibiotic resistance. Several traditional methods used to measure it do not provide adequate and promising results for further analysis. Data mining techniques, such as the association rules, have been used in the past and successfully led to discovering interesting patterns in public health data. In this work, we present the architecture of a novel framework which integrates data from multiple hospitals, discovers association rules, stores them in a data warehouse for future analysis and provides anytime accessibility through an intuitive Web interface. We implemented the proposed architecture as a Web application and evaluated it using data from the WHONET software installed in many Greek hospitals that belong to "the Greek System for Surveillance of Antimicrobial Resistance" network. The contribution of the proposed framework is considered to be a standardized workflow aiming at the integration of data produced by various hospitals into a consistent data warehouse and the use of a mechanism that detects hidden and previously unknown patterns on large datasets, in terms of association rules, which can provide surveillance warnings.

We investigated the characteristics of 20 community acquired methicillin resistant Staphylococcus aureus (MRSA) strains isolated in a paediatric hospital in Athens. Eighteen of these, all isolated from skin and soft tissue infections, carried the Panton-Valentine leukocidin (PVL) determinants. They all were found resistant to fusidic acid, tetracycline and kanamycin, and displayed a PFGE pattern identical to that of the well-described ST80 CA-MRSA clone circulating in various European countries.