Staphylococcus saprophyticus: Infectious substances pathogen safety data sheet

Section I – Infectious agent

Name

Staphylococcus saprophyticus

Agent type

Bacteria

Taxonomy

Family

Staphylococcaceae

Genus

Staphylococcus

Species

saprophyticus

Synonym or cross-reference

Formerly classified as Micrococcus subgroup 3^{Footnote 1Footnote 2}. S. saprophyticus is a member of the coagulase-negative Staphylococcus (CoNS) group^{Footnote 3}.

Characteristics

Brief description

S. saprophyticus are Gram-positive, non-motile cocci, measuring 0.6-1.4 μm in diameter^Footnote3. Cells may occur singly or in pairs, short chains, or clusters^Footnote3. S. saprophyticus are facultative anaerobes and can grow in the presence of 10% NaCl^Footnote3. S. saprophyticus are coagulase-negative, oxidase-negative, and catalase-positive^Footnote3. Cells can contain multiple plasmids that encode genes for biofilm formation, antibiotic resistance, and tolerance to specific disinfectants^{Footnote 4Footnote 5}. S. saprophyticus can exist as a biofilm or as planktonic cells (free cells). The biofilm formation in S. saprophyticus depends on Polysaccharide Intercellular Adhesion (PIA), whose biosynthesis is mediated by the ica operon^{Footnote 6}. Conjugation occurs at a higher proportion between bacterial cells in biofilms than between planktonic cells^{Footnote6Footnote 7}. Bacterial biofilm communities differ from the planktonic ones in their s growth rate, gene expression, transcription and translation^{Footnote 8}.

Properties

S. saprophyticus is a commensal bacterium of the gastrointestinal and genitourinary tract in 5 to 10% of healthy women^{Footnote1Footnote 9}. Colonization sites in women include the rectum as the most frequent site, followed by the urethra, urine, and cervix^Footnote9. S. saprophyticus can also be found in urine from healthy adolescents and men^{Footnote 10Footnote 11}.

S. saprophyticus produces adhesion proteins (e.g., Aas, UafA, UafB) that enable adherence to uroepithelial cells in the urinary tract allowing for colonization, and biofilm formation^{Footnote 12Footnote 13Footnote 14}. Several transport proteins enable S. saprophyticus to adapt to osmotic and pH changes^Footnote12. After colonization, S. saprophyticus secrete invasive factors such as lipase, urease, and elastase that promote growth in urine and cause damage to uroepithelial cells^{Footnote13Footnote 15}.

Section II – Hazard identification

Pathogenicity and toxicity

S. saprophyticus is an opportunistic pathogen that causes urinary tract infections (UTI), and inflammation of the bladder (acute cystitis). Approximately 90% of UTI patients are symptomatic^Footnote15. Symptoms include dysuria, increased urinary frequency/urgency, pyuria, proteinuria, and hematuria^Footnote15. Symptoms typically resolve 3 days after treatment^{Footnote 16}; however, recurrent S. saprophyticus-associated UTIs are not unusual^{Footnote 17}. Despite highly successful treatment rates, up to 60% of all patients will experience a recurrent UTI within one year^{Footnote 18}. UTI complications include acute pyelonephritis, and in men, urethritis, epididymitis, and prostatitis^{Footnote2Footnote11}. Additionally, in men S. saprophyticus was also shown to cause teratozoospermia, impair sperm deprotamination, and cause abnormalities in sperm chromatin condensation. Which was associated with a lower likelihood of clinical pregnancy in couples with various factors of male infertility^{Footnote 19}. S. saprophyticus has been implicated in ocular infections^{Footnote 20Footnote 21}, endocarditis^{Footnote 22}, skin lesions^{Footnote 23}, septicaemia^{Footnote 24Footnote 25}, post-neurosurgical meningitis^{Footnote 26}, and colonization of implant devices^{Footnote 27}.

S. saprophyticus has been isolated from the skin of dogs showing clinical signs of dermatitis^{Footnote 28} and from the urine of cats and dogs with clinical signs of a UTI^{Footnote 29Footnote 30}. S. saprophyticus is the etiological agent in approximately 3% of canine UTI cases^Footnote30. S. saprophyticus has also been isolated from healthy pigs^{Footnote 31}, horses^{Footnote 32}, goats^{Footnote 33}, sheep^{Footnote 34}, and poultry^{Footnote 35}.

Epidemiology

Globally, there have been over 400 million cases and over 235,000 reported deaths associated with UTIs between 1990 and 2019^{Footnote 36}, mostly young sexually active women^{Footnote2Footnote 37}. Urinary tract infections are the most common outpatient infections, with a lifetime incidence of 50-60% in adult women. Recurrence within 6 months is common^{Footnote 38}. S. saprophyticus causes 5-20% of non-hospital acquired UTIs^{Footnote 39Footnote 40Footnote 41Footnote 42Footnote 43}. UTIs caused by S. saprophyticus do not usually occur in hospitalized patients^Footnote11. The majority of S. saprophyticus–associated UTIs occur in premenopausal females^{Footnote39Footnote42}. In men, individuals over 50 years of age are more commonly affected^Footnote11. A seasonal trend has been observed in some studies, with most S. saprophyticus-associated UTIs occurring in late summer or early autumn^{Footnote1Footnote 44}.

Host range

Natural host(s)

Humans, non-human primates^{Footnote 45}, cows^{Footnote 46}, pigs^Footnote31, horses^Footnote32, goats^Footnote33, cats^Footnote29, dogs^{Footnote30Footnote 47}, rodents^{Footnote 48}, and birds^{Footnote 49}.

Other host(s)

None.

Infectious dose

Unknown.

Incubation period

Unknown.

Communicability

S. saprophyticus is part of flora on human and animal skin, and has been isolated from a wide variety of sources including foods of animal origin, recreational water^{Footnote 50}, airborne particles^{Footnote 51Footnote 52}, and fomites such as fabric and currency^{Footnote 53}. Given the prevalence of S. saprophyticus on ready-to-eat foods such as deli meats, fish products, sausages^{Footnote 54Footnote 55Footnote 56}, unpasteurized milk, and milk products^{Footnote50Footnote 57Footnote 58}, ingestion is a likely route of S. saprophyticus exposure in humans. Additionally, evidence found that the meat-production chain is a major source of S. saprophyticus causing human UTIs^{Footnote 59}. Airborne S. saprophyticus has been isolated from a variety of environments including hospitals^{Footnote51Footnote 60}, schools^Footnote50, and farms^{Footnote 61}, indicating that inhalation is also a likely route of S. saprophyticus exposure in humans. It has been demonstrated that S. saprophyticus can be transferred directly (hand-to-hand) and indirectly (fomite-hand-fomite)^{Footnote 62Footnote 63}. S. saprophyticus is prevalently found in women aged 13-40, but not males in that range, nor is it commonly found in women older than 40 years of age, indicating a potential reservoir of self-infection^Footnote39.

Section III – Dissemination

Reservoir

S. saprophyticus is ubiquitous in the environment. It has been isolated from a wide range of healthy mammals and birds; however, a primary reservoir has not been identified^{Footnote 64}.

Zoonosis

S. saprophyticus is frequently detected on skin lesions and hands of individuals who have close contact with animals, indicating potential zoonosis^Footnote11.

Vectors

None.

Section IV – Stability and viability

Drug susceptibility/resistance

Most S. saprophyticus isolates are sensitive to trimethoprim-sulfamethoxazole^{Footnote6Footnote37Footnote42}; fluroquinolones (e.g., ciprofloxacin^{Footnote37Footnote 65}, norfloxacin^Footnote6, levofloxacin^Footnote9, ofloxacin^Footnote9); cephalosporins (e.g., ceftriaxone^{Footnote37Footnote65}, cephalexin^Footnote37, ceftazidime^Footnote37, cefpodoxime^Footnote65); amoxicillin-clavulanate^Footnote63; carbapenems (e.g., imipenem); some aminoglycosides (e.g., gentamicin^{Footnote37Footnote42Footnote65Footnote 66}); fosfomycin^{Footnote 67}; oxazolidinones (e.g., linezolid^Footnote66); nitrofurantoin^{Footnote37Footnote42Footnote67} and vancomycin^{Footnote6Footnote66}.

All S. saprophyticus isolates are resistant to novobiocin^{Footnote 68}. Biofilm cells of S. saprophyticus are generally less sensitive to antibiotics than planktonic cells^{Footnote6Footnote66}. Resistance to antibiotics varies according to geographic location^{Footnote 69}. Most S. saprophyticus isolates are resistant to quinolones (e.g., nalidixic acid^{Footnote37Footnote65}); penicillin derivatives (e.g., methicillin, amoxicillin^{Footnote37Footnote65}, oxacillin^{Footnote66Footnote68}, cloxacillin^Footnote37); tetracycline^{Footnote35Footnote60Footnote65}; macrolides (e.g., erythromycin^Footnote66); some aminoglycosides (e.g., streptomycin^Footnote65); and chloramphenicol^{Footnote35Footnote65}.

Additionally, S. saprophyticus strain KM1053 exhibited resistance to penicillin G and tetracycline when isolated from a Korean high-salt-fermented seafood^{Footnote 70}.

Susceptibility to disinfectants

S. saprophyticus is susceptible to phenols and their derivatives, salicylanilides, carbanilides, ethanol (70%), glutaraldehyde (2%), and halogens (chlorine and iodine and their derivatives)^{Footnote1Footnote62}. Quaternary ammonium compounds such as benzalkonium chloride (200ppm) gave a 3-log reduction against S. saprophyticus biofilm^Footnote4.

Physical inactivation

Other coagulase-negative Staphylococcus species are inactivated by UV irradiation^{Footnote 71Footnote 72}, and moist heat treatment at 121°C for 15 minutes^{Footnote 73}.

Survival outside host

Other coagulase-negative staphylococci survived for 6 to 28 days on fabric and more than 90 days on plastic^{Footnote 74}.

Section V – First aid/medical

Surveillance

Diagnosis is accomplished through the monitoring of clinical symptoms. S. saprophyticus can be detected in clinical specimens using culture-based methods, followed by a biochemical or molecular test for species-specific identification (Becker, Bergys). Many commercial identification systems are available such as API Staph (bioMérieux, France), HiStaph™ Identification Kit (HiMedia Laboratories Ltd), Rapidec Staph (bioMérieux, France), Biolog (Biolog, Hayward, CA), and RapidBAC immunoassay^{Footnote3Footnote 75}. MALDI-TOF and PCR have also been used to identify Staphylococcus species^{Footnote3Footnote39Footnote 76}.

Note: The specific recommendations for surveillance in the laboratory should come from the medical surveillance program, which is based on a local risk assessment of the pathogens and activities being undertaken, as well as an overarching risk assessment of the biosafety program as a whole. More information on medical surveillance is available in the Canadian Biosafety Handbook.

First aid/treatment

S. saprophyticus infections can be treated with appropriate antibiotics; antibiotic choice depends on the susceptibility profile of the isolate. Nitrofurantoin, trimethoprim-sulfamethoxazole, fluoroquinolones, cephalosporins, and amoxicillin-clavulanate have been used to treat infections caused by S. saprophyticus^{Footnote 77}.

Note: The specific recommendations for first aid/treatment in the laboratory should come from the post-exposure response plan, which is developed as part of the medical surveillance program. More information on the post-exposure response plan can be found in the Canadian Biosafety Handbook.

Immunization

None.

Note: More information on the medical surveillance program can be found in the Canadian Biosafety Handbook, and by consulting the Canadian Immunization Guide.

Prophylaxis

None.

Note: More information on prophylaxis as part of the medical surveillance program can be found in the Canadian Biosafety Handbook.

Section VI – Laboratory hazard

Laboratory-acquired infections

None reported to date.

Note: Please consult the Canadian Biosafety Standard and Canadian Biosafety Handbook for additional details on requirements for reporting exposure incidents.

Sources/specimens

Urine, blood.

Primary hazards

Exposure to infections material on fomites, transfer to mucous membranes or damaged skin, and autoinoculation with infectious material.

Special hazards

None.

Section VII – Exposure controls/personal protection

Risk group classification

S. saprophyticus is a Risk Group 2 Human Pathogen and a Risk Group 1 Animal Pathogen^{Footnote 78Footnote 79}.

Containment requirements

Containment Level 2 facilities, equipment, and operational practices outlined in the Canadian Biosafety Standard for work involving infectious or potentially infectious materials, animals, or cultures.

Protective clothing

The applicable Containment Level 2 requirements for personal protective equipment and clothing outlined in the Canadian Biosafety Standard are to be followed. The personal protective equipment could include the use of a lab coat and dedicated footwear (e.g., boots, shoes) or additional protective footwear (e.g., boot or shoe covers) where floors may be contaminated (e.g., animal cubicles, post mortem rooms), gloves when direct skin contact with infected materials or animals is unavoidable, and eye protection where there is a known or potential risk of exposure to splashes.

Note: A local risk assessment will identify the appropriate hand, foot, head, body, eye/face, and respiratory protection, and the personal protective equipment requirements for the containment zone and work activities must be documented.

Other precautions

A biological safety cabinet (BSC) or other primary containment device to be used for activities with open vessels, based on the risks associated with the inherent characteristics of the regulated material, the potential to produce infectious aerosols or aerosolized toxins, the handling of high concentrations of regulated materials, or the handling of large volumes of regulated materials.

Use of needles and syringes are to be strictly limited. Bending, shearing, re-capping, or removing needles from syringes to be avoided, and if necessary, performed only as specified in standard operating procedures (SOPs). Additional precautions are required for work involving animals or large-scale activities.

For diagnostic laboratories handling primary specimens that may contain S. saprophyticus the following resources may be consulted:

• Human Diagnostic Activities Biosafety Guideline
• Local Risk Assessment Biosafety Guideline

Section VIII – Handling and storage

Spills

Allow aerosols to settle. While wearing personal protective equipment, gently cover the spill with absorbent paper towel and apply suitable disinfectant, starting at the perimeter and working towards the centre. Allow sufficient contact time with disinfectant before clean up (Canadian Biosafety Handbook).

Disposal

All materials/substances that have come in contact with the regulated materials to be completely decontaminated before they are removed from the containment zone or standard operating procedures (SOPs) to be in place to safely and securely move or transport waste out of the containment zone to a designated decontamination area or third party. This can be achieved by using decontamination technologies and processes that have been demonstrated to be effective against the regulated material, such as chemical disinfectants, autoclaving, irradiation, incineration, an effluent treatment system, or gaseous decontamination (Canadian Biosafety Handbook).

Storage

The applicable Containment Level 2 requirements for storage outlined in the Canadian Biosafety Standard are to be followed. Primary containers of regulated materials removed from the containment zone to be labelled, leakproof, impact resistant, and kept either in locked storage equipment or within an area with limited access.

Section IX – Regulatory and other information

Canadian regulatory information

Controlled activities with Staphylococcus saprophyticus require a Pathogen and Toxin licence issued by the Public Health Agency of Canada.

The following is a non-exhaustive list of applicable designations, regulations, or legislations:

• Human Pathogens and Toxins Act and Human Pathogens and Toxins Regulations

Last file update

February, 2024

Prepared by

Centre for Biosecurity, Public Health Agency of Canada.

Disclaimer

The scientific information, opinions, and recommendations contained in this Pathogen Safety Data Sheet have been developed based on or compiled from trusted sources available at the time of publication. Newly discovered hazards are frequent and this information may not be completely up to date. The Government of Canada accepts no responsibility for the accuracy, sufficiency, or reliability or for any loss or injury resulting from the use of the information.

Persons in Canada are responsible for complying with the relevant laws, including regulations, guidelines and standards applicable to the import, transport, and use of pathogens in Canada set by relevant regulatory authorities, including the Public Health Agency of Canada, Health Canada, Canadian Food Inspection Agency, Environment and Climate Change Canada, and Transport Canada. The risk classification and related regulatory requirements referenced in this Pathogen Safety Data Sheet, such as those found in the Canadian Biosafety Standard, may be incomplete and are specific to the Canadian context. Other jurisdictions will have their own requirements.

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