Genomic analyses of Streptococcus uberis reveal high diversity but few antibiotic resistance genes

This study aimed to investigate the diversity of milk isolates of Streptococcus uberis from Swedish dairy cows with mastitis, focusing on antibiotic resistance and virulence genes. We analyzed 115 S. uberis isolates using whole genome sequencing revealing a high level of diversity. Within the same farms, we identified both indistinguishable strains with identical sequence types (ST), and distinct isolates belonging to different ST types. This suggests both clonal and non-clonal spread of the bacterium, although primarily non-clonal. We found small clusters of two to eight closely related isolates both within and between farms. Differences in penicillin susceptibility were observed, probably linked to specific variants of penicillin-binding proteins. Few isolates were resistant to antibiotics, and few resistance genes were detected. In most cases, only one or two resistance genes were present, and only one isolate was multi-drug resistant. Two isolates had resistance genes against tetracyclines, a tet(M) and a tet(O) gene, two had a resistance gene against lincosamides, an lnu(C) and an lnu(D) gene, while a single isolate had an erm(B) gene conferring resistance to both macrolides and lincosamides. A single isolate carried a mef(A) gene, which confers resistance to macrolides via an efflux pump mechanism. However, we found aminoglycoside genes in 10 isolates, all 10 had the ant(6)-Ia gene, and one in addition aph(3')-IIIa, and a spectinomycin resistance gene, spw, in eight isolates. Finally, one isolate carried a streptothricin resistance gene, sat4. The genes sat4 and spw have apparently not previously been reported in S. uberis. Interestingly, isolates with elevated MIC to penicillin also significantly more often carried other resistance factors. Most isolates carried several virulence genes, including genes for capsule formation, adhesion to host cells or extracellular matrix proteins, and acquisition of essential nutritional factors, such as amino acids, iron and manganese.

EFSA Panel on Animal Health and Welfare (AHAW), Nielsen SS, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortazar Schmidt C, Herskin M, Michel V, Miranda Chueca MA, Padalino B, Pasquali P, Roberts HC, Spoolder H, Stahl K, Velarde A, Viltrop A, Winckler C, Dewulf J, Guardabassi L, Hilbert F, Mader R, Baldinelli F, Alvarez J. Assessment of animal diseases caused by bacteria resistant to antimicrobials: cattle

In this opinion, the antimicrobial resistant bacteria responsible for transmissible diseases that constitute a threat to the health of cattle have been assessed. The assessment has been performed following a methodology based on information collected by an extensive literature review and expert judgement. Details of the methodology used for this assessment are explained in a separate opinion. A global state of play on antimicrobial resistance in clinical isolates of Escherichia coli (non-VTEC), Klebsiella pneumoniae, Staphylococcus aureus, Streptococcus uberis, Streptococcus dysgalactiae, Pasteurella multocida, Mannheimia haemolytica, Histophilus somni, Mycoplasma bovis, Moraxella bovis, Fusobacterium necrophorum and Trueperella pyogenes is provided. Among those bacteria, EFSA identified E. coli and S. aureus with ≥ 66% certainty as being the most relevant antimicrobial resistant bacteria in cattle in the EU based on the available evidence. The animal health impact of these most relevant bacteria, as well as their eligibility for being listed and categorised within the animal health law framework will be assessed in separate scientific opinions.

Antimicrobial susceptibility of nine udder pathogens recovered from bovine clinical mastitis milk in Europe 2015-2016: VetPath results

VetPath is an ongoing pan-European antimicrobial susceptibility monitoring programme collecting pathogens from diseased cattle, pigs and poultry not recently treated with antibiotics. Non-duplicate isolates (n = 1244) were obtained from cows with acute clinical mastitis in eight countries during 2015-2016 for centrally antimicrobial susceptibility testing according CLSI standards. Among Escherichia coli (n = 225), resistance was high to ampicillin and tetracycline, moderate to kanamycin and low to amoxicillin/clavulanic acid and cefazolin. The MIC_50/90 of danofloxacin, enrofloxacin and marbofloxacin were 0.03 and 0.06 μg/mL. For Klebsiella spp. (n = 70), similar results were noted, except for ampicillin and kanamycin. We detected 3.7 % (11/295) Enterobacteriaceae isolates carrying an ESBL/AmpC gene. Staphylococcus aureus (n = 247) and coagulase-negative staphylococci (CoNS; n = 189) isolates were susceptible to most antimicrobials tested except to penicillin (25.1 and 29.1 % resistance). Two S. aureus and thirteen CoNS isolates harboured mecA gene. Streptococcus uberis isolates (n = 208) were susceptible to β-lactam antibiotics (87.1-94.7 % susceptibility), 23.9 % were resistant to erythromycin and 37.5 % to tetracycline. Resistance to pirlimycin was moderate. For Streptococcus dysgalactiae (n = 132) the latter figures were 10.6 and 43.2 %; pirlimycin resistance was low. MIC values for Streptococcus agalactiae, Trueperella pyogenes and Corynebacterium spp. were generally low. This current VetPath study shows that mastitis pathogens were susceptible to most antimicrobials with exceptions of staphylococci against penicillin and streptococci against erythromycin or tetracycline. For most antimicrobials, the percentage resistance and MIC_50/90 values among the major pathogens were comparable to that of the preceeding VetPath surveys. This work highlights the high need to set additional clinical breakpoints for antimicrobials frequently used to treat mastitis.

Effects of Dietary Vibroactivated Clinoptilolite Supplementation on the Intramammary Microbiological Findings in Dairy Cows

Simple Summary

This study aimed to determine the effects of dietary vibroactivated clinoptilolite supplementation on the intramammary microbiological findings in dairy cows, causative agents of intramammary infection, and their sensitivity to antibiotics. The cows (n = 78) were randomly divided into two groups: the clinoptilolite (CPL)-treated group that received 100 g of clinoptilolite (CPL) in-feed (n = 38) from the seventh month of pregnancy to 75 days after calving and the control group (CON) of untreated cows (n = 40). Milk samples were taken from each cow on days 7, 25, 45, and 75 postpartum. Different causative pathogens were isolated in 86 udder quarters (7.07%), in 3.87% environmental microflora, and 89.06% were bacteriologically negative. The most effective antibiotics were cefoperazone and amoxicillin-clavulanic acid, while cloxacillin and tetracycline were the least effective. In the CPL group (14 cows), nine pathogens were isolated in 27 quarters, while in the control (CON) group (24 cows), 13 pathogens in 59 quarters. Cows from the CON group had a 1.96 times higher risk of intramammary infection than cows from the CPL group.

Abstract

The aim of this study was to determine the effects of dietary vibroactivated clinoptilolite supplementation on the intramammary microbiological findings in dairy cows, causative agents of potential intramammary infection, and their sensitivity to antibiotics. Cows (n = 78) were randomly divided into two groups: CPL-treated group that received clinoptilolite (CPL) in-feed (n = 38), i.e., 50 g natural powdered zeolite CPL, twice daily from the seventh month of pregnancy to 75 days after calving, and the control group (CON) of untreated cows (n = 40). Milk samples were taken from each cow on days 7, 25, 45, and 75 postpartum. The following causative pathogens were isolated in 86 udder quarters: Staphylococcus aureus in 5.81% of positive samples, Staphylococcus spp. 9.32%, coagulase-negative Staphylococcus (CNS) 22.09%, Streptococcus uberis 13.95%, Streptococcus agalactiae 1.16%, Streptococcus sp. 3.49%, Escherichia coli 8.13%, Enterococcus spp. 6.98%, Corynebacterium spp. 11.63%, Pasteurella sp. 10.47%, Serratia spp. 2.33%, and Arcanobacterium pyogenes, Citrobacter sp., Prototheca sp., and yeasts each in 1.16% of samples. Additionally, 3.87% of environmental microflora samples (n = 47) and 89.06% of udder samples (n = 1083) were bacteriologically negative. The most effective antibiotics were cefoperazone and amoxicillin-clavulanic acid, while cloxacillin and tetracycline were the least effective antibiotics in both groups. In the clinoptilolite supplemented (CPL) group (n = 38) of 14 cows, nine causative agents of mastitis were isolated in 27 quarters, while in the control (CON) group (n = 40) of 24 cows, 13 causative agents of mastitis were isolated in 59 quarters. Cows from the CON group had a 1.96 times higher risk of intramammary infection than cows from the CPL group during the observation period (odds ratio = 1.96, p = 0.0031; 95% CI = 1.2570–3.0770).

Antimicrobial Susceptibility of Streptococci Most Frequently Isolated from Czech Dairy Cows with Mastitis

The aim was to investigate the antimicrobial susceptibility of most frequently isolated streptococci from Czech dairy herds. A total of 3,719 quarter milk samples were collected and cultivated between January 2017 and June 2018 from cows with clinical or subclinical mastitis from 112 farms. Only one isolate of each species, collected from the same farm per six-month period, was included in the susceptibility testing. The susceptibilities of Streptococcus uberis (163 isolates) and S. dysgalactiae (25 isolates) to 10 antimicrobials (penicillin – PEN, amoxicillin/clavulanic acid – AMC, ceftiofur – EFT, clindamycin – CLI, gentamicin – GEN, streptomycin – STR, trimethoprim/sulfamethoxazole – SXT, enrofloxacin – ENR, tetracycline – TET, rifampicin – RIF) from 9 groups were determined by measuring their minimum inhibitory concentrations. The percentages of resistant S. uberis isolates to the antimicrobials were as follows: TET (63.2%), STR (52.1%), CLI (30.1%), and RIF (2.5%). Intermediate susceptibility was found to RIF (63.2%), PEN (35%), ENR (2.5%), EFT (1.8%), and AMC (1.2%). All the S. uberis isolates were susceptible to GEN and SXT (100%). However, only 6.7% of S. uberis isolates were susceptible to all tested antimicrobials, and 38.7% of isolates were multidrug resistant (≥ 3 groups of antimicrobials). All the S. dysgalactiae isolates were susceptible to PEN, AMC, EFT, GEN, SXT, and ENR (100%). Resistant S. dysgalactiae isolates were found to TET (60%), STR (28%), CLI (12%), and intermediate to TET (24%) and RIF (20%). Sixteen percent of S. dysgalactiae isolates were multidrug resistant. The relatively high occurrence of (multiple) resistance, relative to mastitis pathogens, highlights the importance of monitoring this condition in dairy herds.

Antimicrobial Resistance in Streptococcus spp

The genus Streptococcus includes Gram-positive organisms shaped in cocci and organized in chains. They are commensals, pathogens, and opportunistic pathogens for humans and animals. Most Streptococcus species of veterinary relevance have a specific ecological niche, such as S. uberis, which is almost exclusively an environmental pathogen causing bovine mastitis. In contrast, S. suis can be considered as a true zoonotic pathogen, causing specific diseases in humans after contact with infected animals or derived food products. Finally, Streptococcus species such as S. agalactiae can be sporadically zoonotic, even though they are pathogens of both humans and animals independently. For clarification, a short taxonomical overview will be given here to highlight the diversity of streptococci that infect animals. Several families of antibiotics are used to treat animals for streptococcal infections. First-line treatments are penicillins (alone or in combination with aminoglycosides), macrolides and lincosamides, fluoroquinolones, and tetracyclines. Because of the selecting role of antibiotics, resistance phenotypes have been reported in streptococci isolated from animals worldwide. Globally, the dynamic of resistance acquisition in streptococci is slower than what is experienced in Enterobacteriaceae, probably due to the much more limited horizontal spread of resistance genes. Nonetheless, transposons or integrative and conjugative elements can disseminate resistance determinants among streptococci. Besides providing key elements on the prevalence of resistance in streptococci from animals, this article will also largely consider the mechanisms and molecular epidemiology of the major types of resistance to antimicrobials encountered in the most important streptococcal species in veterinary medicine.

Monitoring of antimicrobial susceptibility of udder pathogens recovered from cases of clinical mastitis in dairy cows across Europe: VetPath results

VetPath is an ongoing pan-European antimicrobial susceptibility monitoring programme collecting pathogens from diseased cattle, pigs and poultry not recently treated with antibiotics. Non-duplicate milk samples were collected from cows with acute clinical mastitis in nine countries and 934 isolates were obtained during 2009-2012 for subsequent antimicrobial susceptibility testing in a central laboratory. CLSI broth microdilution methodology was used, and where available, MICs were interpreted using CLSI approved veterinary-specific (ceftiofur) otherwise human clinical breakpoints. Among Escherichia coli (n=207) and Klebsiella spp., (n=87), resistance was moderate to tetracycline and high to cephapirin (E. coli only) whereas resistance to other β-lactam antibiotics was very low (ceftiofur) to low (amoxicillin/clavulanic acid, cephalexin, cephalonium). The MIC₉₀ of enrofloxacin and marbofloxacin was 0.03 and 0.06μg/mL respectively (E. coli) with 0.5% strains displaying higher MICs. Staphylococcus aureus (n=192) and coagulase-negative staphylococci (CNS; n=165) strains were susceptible to most antibiotics tested except to penicillin (25.0 and 29.1% resistance), respectively. Three S. aureus and seven CNS strains were oxacillin-resistant and harboured mecA. Streptococcus uberis strains (n=188) were susceptible to the β-lactam antibiotics although 35.6% were penicillin intermediately susceptible, and 20.2% were resistant to erythromycin, 36.7% to tetracycline. For Streptococcus dysgalactiae (n=95) the latter figures were 13.7 and 56.8%, respectively. For most antibiotics, the percentage resistance among E. coli, S. aureus and S. uberis was comparable to that of the VetPath 2002-2006 survey. This current, expanded VetPath study shows that mastitis pathogens were susceptible to most antibiotics with exceptions of staphylococci tested against penicillin and streptococci against erythromycin or tetracycline. This work highlights the high need to set additional clinical breakpoints for antibiotics frequently used to treat mastitis.

Proposal for agar disk diffusion interpretive criteria for susceptibility testing of bovine mastitis pathogens using cefoperazone 30μg disks

Cefoperazone is a third generation cephalosporin which is commonly used for bovine mastitis therapy. Bacterial pathogens involved in bovine mastitis are frequently tested for their susceptibility to cefoperazone. So far, the cefoperazone susceptibility testing using 30μg disks has been hampered by the lack of quality control (QC) ranges as well as the lack of interpretive criteria. In 2014, QC ranges for 30 μg cefoperazone disks have been established for Staphylococcus aureus ATCC^® 25923 and Escherichia coli ATCC^® 25922. As a next step, interpretive criteria for the susceptibility testing of bovine mastitis pathogens should be developed. For this, 637 bovine mastitis pathogens (including 112 S. aureus, 121 coagulase-negative staphylococci (CoNS), 103 E. coli, 101 Streptococcus agalactiae, 100 Streptococcus dysgalactiae and 100 Streptococcus uberis) were investigated by agar disk diffusion according to the document Vet01-A4 of the Clinical and Laboratory Standards Institute (CLSI) using 30μg cefoperazone disks and the results were compared to the corresponding MIC values as determined by broth microdilution also according to the aforementioned CLSI document. Based on the results obtained and taking into account the achievable milk concentration of cefoperazone after regular dosing, the following interpretive criteria were proposed as a guidance for mastitis diagnostic laboratories: for staphylococci and E. coli ≥23mm (susceptible), 18-22mm (intermediate) and ≤17mm (resistant) and for streptococci ≥18mm (susceptible), and ≤17mm (non-susceptible). These proposed interpretive criteria shall contribute to a harmonization of cefoperazone susceptibility testing of bovine mastitis pathogens.

Misidentification of Streptococcus uberis as a human pathogen: a case report and literature review

Streptococcus uberis is an environmental bacterium responsible for bovine mastitis. It is occasionally described as a human pathogen, though in most cases the identification was based on biochemical phenotyping techniques. This report shows that the biochemical phenotyping may incorrectly identify Enterococcus faecium as S. uberis.

Antimicrobial resistance in Staphylococcus aureus, Streptococcus uberis and Streptococcus dysgalactiae from dairy cows with mastitis

AIMS

To determine the minimal inhibitory concentrations (MIC) of antimicrobials for common mastitis pathogens from dairy cows in New Zealand; and to assess the effect of source of the isolates, i.e. commercial veterinary laboratories or collected as part of research studies; the clinical status of the cow, i.e. subclinical or clinical mastitis; cow age and herd on the distribution of the MIC.

METHODS

Minimal inhibitory concentrations for Staphylococcus aureus (n=364), Streptococcus dysgalactiae (n=65) and Streptococcus uberis (n=102) isolated from milk samples from dairy cows were determined for a variety of antimicrobials using broth microdilution. Isolates of S. aureus were sourced from research studies from both subclinically (n=161) and clinically (n=104) affected cows, as well as from commercial veterinary laboratories (n=101); while all the streptococcal isolates were from commercial laboratories. Resistance was defined using the cut-points provided by the Clinical and Laboratory Standards Institute (CLSI).

RESULTS

The distribution of MIC varied among the bacterial species for every antimicrobial tested (p<0.001). Of the S. aureus isolates, 28, 2 and 0.5% were resistant to penicillin, ampicillin and trimethoprim/sulfamethoxazole, respectively. For S. dysgalactiae and S. uberis isolates, 17 and 13% were resistant to trimethoprim/sulfamethoxazole, respectively. One isolate (1%) of S. uberis was resistant to penicillin. The distribution of MIC of S. aureus varied with clinical status, between herds, and with age of cow (p<0.05). The distribution of MIC for S. aureus for penicillin, amoxicillin/clavulanic acid, cloxacillin and ampicillin were lower from clinical than subclinical cases, and those for amoxicillin/clavulanic acid and oxytetracycline from isolates from veterinary laboratories were lower than for those from research studies.

CONCLUSIONS

Resistance to some beta-lactam antimicrobials and trimethoprim/sulfamethoxazole were found in isolates from cases of bovine mastitis. The distribution of MIC for isolates of S. aureus varied with clinical status of the cow, the age of the cow, the herd and with the source of isolate.

CLINICAL SIGNIFICANCE

Resistance to penicillin was found in a quarter of S. aureus isolates, but in virtually no Streptococcus isolates; therefore microbial identification and sensitivity testing would be beneficial when assessing treatment options. The source of the isolates affected the estimated MIC, suggesting that selection of isolates for monitoring of resistance requires care and that use of routine submissions to commercial laboratories to assess antimicrobial resistance patterns may result in biased estimates of prevalence of resistance.

Short communication: Streptococcus species isolated from mastitis milk samples in Germany and their resistance to antimicrobial agents

Mastitis is one of the most frequent infectious diseases in dairy cattle and is a reason for antimicrobial drug usage in dairy cows. The bacteria involved in bovine mastitis are mainly Streptococcus spp., Staphylococcus spp., and coliforms. The aim of this study was to determine antimicrobial resistance among Streptococcus spp. isolated from bovine mastitis milk. Antimicrobial resistance in Strep. uberis (n=227), Strep. dysgalactiae (n=49), and Strep. agalactiae (n=3) was determined for 9 antimicrobial agents using the broth microdilution method in accordance with Clinical and Laboratory Standards Institute recommendations. Of all Streptococcus spp., 13% were multidrug resistant. The rate of multidrug resistance was higher among Strep. uberis (15%) than among Strep. dysgalactiae (6%) and Strep. agalactiae (0%). Resistance to tetracycline was the most common, followed by resistance to erythromycin, pirlimycin, and gentamicin. Resistance rates were higher on farms with more than 80 cows compared with those with fewer than 20 cows. β-Lactams should remain the drugs of choice in the treatment of streptococcal mastitis. The slightly elevated minimum inhibitory concentrations determined for these antibiotics may indicate, however, the emergence of resistant streptococci. To identify such changes in susceptibility as early as possible, antimicrobial resistance in streptococci should be surveyed regularly.