A novel mcr colistin resistance gene was identified in a strain of Salmonella enterica, monophasic variant of serovar Typhimurium (4,5,12:i:- ), isolated from a pig at slaughter in Italy in 2013, and ...in Escherichia coli strains collected during routine diagnostic of post-weaning diarrhoea in pigs from Spain and Belgium in 2015 and 2016. Immediate implementation of mcr-screening including this novel gene variant is required for Salmonella and E. coli from humans and food-producing animals in Europe.
Streptococcus suis is a pathogen associated with severe diseases in pigs and humans. Human infections have a zoonotic origin in pigs. To assess circulating strains, we characterized the serotypes, ...sequence types, and antimicrobial susceptibility of 78 S. suis isolates from diseased farmed pigs in Italy during 2017-2019. Almost 60% of infections were caused by serotypes 1/2 and 9. All but 1 of the serotype 2 and 1/2 isolates were confined to a single cluster, and serotype 9 isolates were distributed along the phylogenetic tree. Besides sequence type (ST) 1, the serotype 2 cluster included ST7, which caused severe human infections in China in 1998 and 2005. A large proportion of serotype 9 isolates, assigned to ST123, were resistant to penicillin. The emergence of this clone threatens the successful treatment of S. suis infection. Characterizing S. suis isolates from pigs will promote earlier detection of emerging clones.
The transmission of antimicrobial resistance bacteria from animals to humans has become an important concern. The extended-spectrum beta-lactamase (ESBL) -AmpC- producing Escherichia coli (ESBL-AmpC ...EC) and quinolones resistant E. coli are of particular interest. The present study aimed to evaluate the load and prevalence of antibiotic-resistant commensal E. coli along the goose production cycle on 2 free-range farms in central Italy. On A farm, oxytetracycline was administered, while the B farm did not use antibiotics during the geese productive cycle. One hundred geese of 1-day-old from the same batch were divided into the two farms. At hatching, the animals showed an average of E. coli loads was 6.83 ± 0.48 log CFU/g, and 0.28 ± 0.28, 0, 5.12 ± 0.54 log CFU/g for E. coli resistant to nalidixic acid (E. colinal), to cefotaxime (E. colicef) and to tetracyclines (E. colitet), respectively. The loads of E. coli, E. colinal, E. colicef and E. colitet on 224 environmental faecal pools were determined at 8 time points. Antimicrobial susceptibility and molecular characterization of E. colicef isolates were performed. The ANOVA was used to assess the difference in bacterial loads between the two farms. We described more than 50% of resistances for tetracyclines in both farms, and sulphonamides and cephazolin in the A farm. The loads of E. coli and E. colinal in faeces were estimated at approximately 6–7 log (CFU/g) and 5–6 log (CFU/g) in the two farms, respectively. The average load of extended-spectrum beta-lactamase Escherichia coli (ESBL EC) in goose faeces varied broadly along the production cycle: in the first weeks, a sharp increase was observed in both farms, while later on A farm, the burden of ESBL EC remained steady until the end of the production cycle and on B farm the load dramatically decreased from 6 wk of age onward. An increase in the proportion of E. colinal was observed on A farm shortly after the antibiotic administration. Our study shows that the dynamics of antibiotic-resistant E. coli in farmed geese are similar to the ones observed in broilers. However, the risk of the emergence of antibiotic-resistant commensal E. coli, might be mitigated by the adoption of good management practices, including prudent use of antibiotics.
The spread of extended-spectrum β-lactamase (ESBL)-producing
Escherichia coli
is a major public health issue. Bivalves are filter-feeder animals capable of bioaccumulating the microorganisms present ...in water. This physiological characteristic makes them both good indicators of environmental contamination and possible carriers of pathogenic bacteria, including those resistant to antimicrobials. The aim of this study was to investigate the occurrence of ESBL-producing
E. coli
in clams (
n
= 308) collected from harvesting areas of the Central Adriatic Sea between 2018 and 2019. ESBL- /class C β-lactamase (AmpC)- producing
E. coli
and
Escherichia
spp. were isolated by streaking over the surface of MacConkey agar plates supplemented with cefotaxime enriched broths of the initial shellfish suspension.
E. coli
and
Escherichia
spp. resistant to cefotaxime were screened for ESBL production by using the double disk synergy test. Susceptibility to different antimicrobials and confirmation of ESBL-production were determined by the minimum inhibitory concentration (MIC) test. Isolates were further characterized by whole genome sequencing (WGS) and bioinformatic analysis of genomes with different tools. Overall, ESBL-producing
E. coli
were isolated from 3% of the samples. Of 13 ESBL- and ESBL−/AmpC-producing
Escherichia
spp. (
n
= 11
E. coli
,
n
= 1
E. marmotae
,
n
= 1
E
.
ruysiae
) isolates, 13 were resistant to ampicillin and cefotaxime, 9 to sulfamethoxazole, 6 to tetracycline and nalidixic acid, 4 to trimethoprim, and 3 to ceftazidime, cefoxitin, ciprofloxacin, and chloramphenicol. Moreover, the majority (8/11) of the ESBL-producing
E. coli
isolates were multidrug-resistant. WGS showed that the isolates predominantly carried the
bla
CTX-M-15
gene (3/11) and
bla
CTX-M-14
and
bla
CTX-M-1
(2/11 each). The AmpC β-lactamase CMY-2 was found in two isolates. Phylogroup A was the most prevalent (5/11), followed by phylogroups D (4/11), F (1/11), and B2 (1/11). Ten different sequence types (STs) were identified. Occurrence at sampling sites ranged between 0 and 27%. To identify associations between the occurrence of ESBL-producing
E. coli
and
E. coli
levels, samples were divided into two groups, with
E. coli
at >230 MPN/100 g and
E. coli
at ≤230 MPN/100 g. ESBL-producing
E. coli
isolates were significantly more commonly recovered in samples with higher
E. coli
levels (14%) than in those with lower levels of
E. coli
(2%). Moreover, the majority (3/4) of the potentially pathogenic strains were isolated in samples with higher
E. coli
levels. These findings provided evidence for the bacterial indicator of fecal contamination,
E. coli
, as an index organism for ESBL-producing
E. coli
isolates in bivalves.
•Pasteurellosis by P.multocida is one of the predominant bacterial diseases in rabbit.•We detected three dominant ST in P. multocida from diseased rabbits in Italy.•These three ST were already ...described in other animal species.•Clonal complexes were associated with specific capsular, virulence and LPS genotypes.•The clonal relationships differed from previously reported ST from rabbit.
In rabbit, P. multocida is considered a predominant pathogenic agent; despite this, few data on the molecular epidemiology are available so far. The aim of this work was to characterize P. multocida isolates from rabbit affected by various diseases in Italy. Comparison was made to reference strains from other countries. Thirty-nine isolates were tested using PCRs to detect the genes coding capsular antigens, virulence factors and lipopolysaccharide structures (LPS). Multilocus sequence typing (MLST) was performed and 19 STs registered that belonged to 9 clonal complexes. Italian isolates were all related to P. multocida subsp. P. multocida. Three sequence types dominated (ST9, ST50 and ST74). The isolates were assigned to capsular types A (20/39), D (9/39) and F (10/39), to virulence genes pfhA (13/39), hgbB (21/39) and pfhA+hgbB (4/39) (one without virulence factors) and the isolates either belonged to the LPS genotypes 3 (22/39) or 6 (17/39). The clonal relationships of the Italian strains from rabbit had similarity to previously reported rabbit isolates that belonged to ST9, ST74, ST204 and ST206, however, they differed from other rabbit references strains that belonged to six other STs. In particular, ST9 with capsular type F has been previously reported from diseased rabbit in Czech Republic and ST74 has been observed for older rabbit isolates. ST50 has probably been reported from Spain. ST9 and ST50 have previously also been reported from birds and pig, respectively, whereas ST74 has exclusively been reported from pig. It remains to be investigated if the isolates obtained from diseased rabbit in Italy represent introductions from other host or they are primarily of rabbit origin.
Gastrointestinal disease is frequent in pigs, and among the different etiological agents involved, viruses are considered the leading cause of infection in this animal species. Furthermore, about ...half of the newly identified swine pathogens are viruses, many of which may be transmitted to humans by direct contact or by indirect transmission pathways. In this study, the prevalence of astrovirus (AstV), group A rotavirus (RVA), norovirus (NoV) and hepatitis E virus (HEV) infections in pigs was investigated. During 2012-2014, 242 fecal samples were collected from pigs at different production stages (5 to 220 days old) on eight swine farms located in northern, central and southern Italy. Seven out of eight farms analyzed were positive for AstV, which was detected in 163 out of 242 (67.4 %) samples and was the most prevalent virus; 61 of the 163 AstV-positive animals (37.4 %) had diarrhea. HEV was detected on six farms and in 45 (18.6 %) of the 242 samples analyzed. Twenty-three HEV-infected pigs had diarrhea (51.1 %). A lower prevalence was observed for RVA, which was found in 10 of the 242 samples (4.1 %) from three positive farms, and diarrhea was present only in six infected pigs (60.0 %). No swine samples were found to be positive for NoV. Genetic diversity and phylogenetic relationships of some strains representative of the different viruses detected were investigated, confirming a wide heterogeneity of viral strains circulating among pigs.
One hundred forty-five florfenicol-resistant enterococci, isolated from swine fecal samples collected from 76 pig farms, were investigated for the presence of
,
, and
genes by PCR. Thirty ...florfenicol-resistant
isolates had at least one linezolid resistance gene.
was found to be the most widespread linezolid resistance gene (23/30), while
and
were detected in 6/30 and 7/30 enterococcal isolates, respectively. WGS analysis also showed the presence of the
(D) gene in
(
= 2 isolates) and in
(
= 1 isolate). The linezolid resistance genes hybridized both on chromosome and plasmids ranging from ~25 to ~240 kb. Twelve isolates were able to transfer linezolid resistance genes to enterococci recipient. WGS analysis displayed a great variability of
genetic contexts identical or related to transposons (Tn
and Tn
), plasmids (pE035 and pWo27-9), and chromosomal regions.
environments showed identities with Tn
-like transposon and a region from p12-2300 plasmid;
(D) genetic contexts were related to the corresponding region of the plasmid 4 of
E8014;
was always found on Tn
. Circular forms were obtained only for
- and
-carrying genetic contexts. Clonality analysis revealed the presence of
(ST16, ST27, ST476, and ST585) and
(ST21) clones previously isolated from humans. These results demonstrate a dissemination of linezolid resistance genes in enterococci of swine origin in Central Italy and confirm the spread of linezolid resistance in animal settings.
The emergence of
as the main agent of antibiotic-associated diarrhoea has raised concerns about its potential zoonotic role in different animal species. The use of antimicrobials is a major risk ...factor for
infection. Here, we provide data on
infection in dairy and beef calves in Umbria, a region in central Italy. This cross-sectional study focuses on prevalence, risk factors, ribotypes, toxinotypes and antimicrobial resistance profiles of circulating ribotypes. A prevalence of 19.8% (CI95%, 12-27.6%) positive farms was estimated, and the prescription of penicillins on the farms was associated with
detection (OR = 5.58). Eleven different ribotypes were found, including the ST11 sublineages RT-126 and -078, which are also commonly reported in humans. Thirteen isolates out of 17 showed resistance to at least one of clindamycin, moxifloxacin, linezolid and vancomycin. Among them, multiple-drug resistance was observed in two isolates, belonging to RT-126. Furthermore, RT-126 isolates were positive for tetracycline resistance determinants, confirming that tetracycline resistance is widespread among ST11 isolates from cattle. The administration of penicillins increased the risk of
in calves: this, together with the recovery of multi-resistant strains, strongly suggests the need for minimising antibiotic misuse on cattle farms.
The overuse of antibiotics in livestock contributes to the antibiotic resistance pandemic. The assessment of the actual antibiotic consumption is crucial in limiting the expansion of the problem ...effectively. The aim of this study was to provide the first qualitative and quantitative analysis of antimicrobial usage using data from paper-based registers on dairy and beef farms located in the Umbria region, Italy. Antimicrobial therapies of a one-year period were collected from 101 farms with at least 50 cattle each. Defined daily doses (DDD
) and defined course doses (DCD
) were calculated per administration route and antimicrobial class. The total courses administered were fewer in beef (330.7 × 10
DCD
/year) than in dairy farms (1034.1 × 10
DCD
/year). The use of the highest priority critically important antimicrobials (HPCIAs) was higher (
= 0.0033) in dairy than in beef herds. In terms of DDD
, the parenteral fluoroquinolone administration ranked second and fourth on dairy and beef farms, respectively; the consumption of beta-lactams was ten times higher on dairy than on beef farms. Our results confirm that intensive dairy management practices are associated with increased antibiotic consumption and highlight the necessity to strengthen the existing stewardship programs by involving all stakeholders in effective antimicrobial resistance reduction plans.
Comamonas kerstersii is rarely associated with infections in humans and has never been reported in animals until now.
Herein, we describe a case of urinary tract infection caused by C. kerstersii in ...a young goat. A seven-month-old male goat showed lethargy, generalised weakness and anorexia and in the last hours before its death, severe depression, slight abdominal distention, ruminal stasis, and sternal recumbency. Grossly, multifocal haemorrhages in different organs and tissues, subcutaneous oedema and hydrocele, serous fluid with scattered fibrin deposition on the serosa of the abdominal organs and severe pyelonephritis with multifocal renal infarction were detected. Histopathological examination confirmed severe chronic active pyelonephritis with renal infarcts, multi-organ vasculitis and thrombosis suggestive of an infectious diseases of bacterial origin. The bacterium was identified using routine methods, matrix assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS), and sequencing of the gyrB gene.
To the best of our knowledge, this is the first report of C. kerstersii infection in animals (goat). Our findings support the possibility of C. kerstersii isolation from extraintestinal sites and suggest this organism as a possible cause of urinary tract infection.
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