Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of Staphylococcus saprophyticus

Abstract

Staphylococcus saprophyticus is the leading Gram-positive cause of uncomplicated urinary tract infections. Recent reports of increasing antimicrobial resistance (AMR) in S. saprophyticus warrant investigation of its understudied resistance patterns. Here, we characterized a diverse collection of S. saprophyticus ( n = 275) using comparative whole genome sequencing. We performed a phylogenetic analysis of core genes (1,646) to group our S. saprophyticus and investigated the distributions of antibiotic resistance genes (ARGs). S. saprophyticus isolates belonged to two previously characterized lineages, and 14.91% (41/275) demonstrated multidrug resistance. We compared antimicrobial susceptibility phenotypes of our S. saprophyticus with the presence of different ARGs and gene alleles. 29.8% (82/275) carried staphylococcal cassette chromosome mobile elements, among which 25.6% (21/82) were mecA + . Penicillin resistance was associated with the presence of mecA or blaZ . The mecA gene could serve as a marker to infer cefoxitin and oxacillin resistance of S. saprophyticus , but the absence of this gene is not predictive of susceptibility. Utilizing computational modeling, we found several genes were associated with cefoxitin and oxacillin resistance in mecA − isolates, some of which have predicted functions in stress response and cell wall synthesis. Furthermore, phenotype association analysis indicates ARGs against non-β-lactams reported in other staphylococci may serve as resistance determinants of S. saprophyticus . Lastly, we observed that two ARGs [ erm and erm (44)v ], carried by bacteriophages, were correlated with high phenotypic non-susceptibility against erythromycin (11/11 and 10/10) and clindamycin (11/11 and 10/10). The AMR-correlated genetic elements identified in this work can help to refine resistance prediction of S. saprophyticus during antibiotic treatment. IMPORTANCE Staphylococcus saprophyticus is the second most common bacteria associated with urinary tract infections (UTIs) in women. The antimicrobial treatment regimen for uncomplicated UTI is normally nitrofurantoin, trimethoprim-sulfamethoxazole (TMP-SMX), or a fluoroquinolone without routine susceptibility testing of S. saprophyticus recovered from urine specimens. However, TMP-SMX-resistant S. saprophyticus has been detected recently in UTI patients, as well as in our cohort. Herein, we investigated the understudied resistance patterns of this pathogenic species by linking genomic antibiotic resistance gene (ARG) content to susceptibility phenotypes. We describe ARG associations with known and novel SCC mec configurations as well as phage elements in S. saprophyticus , which may serve as intervention or diagnostic targets to limit resistance transmission. Our analyses yielded a comprehensive database of phenotypic data associated with the ARG sequence in clinical S. saprophyticus isolates, which will be crucial for resistance surveillance and prediction to enable precise diagnosis and effective treatment of S. saprophyticus UTIs.

SWOT and Root Cause Analyses of Antimicrobial Resistance to Oral Antimicrobial Treatment of Cystitis

“…(1) Cystitis treatment failures and AMR result from a bladder milieu that allows adaptable microbes [8] to shelter under a biofilm [91] to evade antimicrobials [38], and membrane pumps [121] allow them to expel OAT; (2) Interchangeable use of the term UTI and cystitis. While absorbed OAT can reach pathogens in upper urinary tracts via perfused blood, the uropathogens causing cystitis can only be eliminated by the urinary fraction of absorbed OAT (Figure 2), because the circulating levels [126,127,130] of the drug are less likely to reach the planktonic microbes and those attaching to the apical side of umbrella cells (Figure 1); (3) The battle between OAT and the uropathogens provoking cystitis is heavily influenced by the physiology of urine flow [20,25,113] and drug physiochemistry [107,132]; (4) The principle of the five Ds-drug, dose, duration, drug route, and de-escalation-for AMS [44] advocates for obtaining the right drug concentration in urine above the MIC (Figures 2-5) [124,154].…”

“…If one looks at the menace of AMR through the lens of a geological time scale [4], it is easy to surmise that it is just an expression of the 3.8 billion-year-old evolutionary conserved hereditary trait [5][6][7][8]16] to adapt and survive environmental stresses such as natural or synthetic antimicrobial substances. Our inference is supported by the first published report on AMR arriving just a few years after the marketing of Penicillin [45].…”

“…A study on healthy humans [23] indicated the role of the factors listed above in the inter-individual variability in the mean value of urine T max, which is delayed by 2.5 h relative to the plasma T max . The variability in the urine T max can potentially contribute to the variability in the emergence of AMR [8]. While the MIC of OAT is sensitive to the pH [107], the extrapolation of in vitro MIC to the bladder is rendered untenable by a wide range of potential intravesical acidity/alkalinity.…”

“…As the estimated age of our planet is only 4.54 billion years, those earliest imprints of life preserved on rocks are a testament to the adaptability of microbes [3] to survive the catastrophes [4] that made many larger life forms extinct. While their size is microscopic, an unparalleled proliferation pace with genetic drift [5][6][7] equips microbes to be the most prevalent life forms on the planet, capable of thriving amidst all other forms of life, including in the highly acidic pH of the stomach [3] and in hyperosmotic urine [8] of mammals. The variable pH and the osmolality of stored urine [9] nearly mimic the threats to survival faced by the ancestors of uropathogens surviving in hot springs, billions of years ago [1,2].…”

“…Accordingly, this broad-based review focusses on the relevant published literature of the last two-to-three decades for describing the nuances of renal physiology [26,34,35] and pharmacokinetics relevant to understanding the strengths, weaknesses, opportunity, and threats (SWOT) of OAT in treatment successes and failures and recurrent infections [36]. The SWOT analysis of OAT is brought into sharper focus by the root cause analysis of the efficacy determinants-urine levels above the MIC at the first contact with uropathogens [37]to benchmark AMR associated with OAT [8,38,39] to AMR associated with intravesical antimicrobial therapy (IAT). Accordingly, the selection process of articles was determined by the relevancy and the recency of urine pharmacokinetic information relevant for the SWOT and root cause analyses of AMR with or without antimicrobial stewardship (AMS) [40,41] practices in OAT for cystitis.…”